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Bump actions/setup-python from 4.7.1 to 5.0.0 - #1605

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Bump actions/setup-python from 4.7.1 to 5.0.0#1605
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Bumps actions/setup-python from 4.7.1 to 5.0.0.

Release notes

Sourced from actions/setup-python's releases.

v5.0.0

What's Changed

In scope of this release, we update node version runtime from node16 to node20 (actions/setup-python#772). Besides, we update dependencies to the latest versions.

Full Changelog: actions/setup-python@v4.8.0...v5.0.0

v4.8.0

What's Changed

In scope of this release we added support for GraalPy (actions/setup-python#694). You can use this snippet to set up GraalPy:

steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v4 with:
python-version: 'graalpy-22.3' - run: python my_script.py

Besides, the release contains such changes as:

New Contributors

Full Changelog: actions/setup-python@v4...v4.8.0

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Bump actions/setup-python from 4.7.1 to 5.0.0
cf76095
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
@dependabotdependabotBot added dependencies Pull requests that update a dependency file github_actions Pull requests that update GitHub Actions code labels Dec 11, 2023
@jhamman

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@dependabot squash and merge

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Dependabot tried to merge this PR, but received the following error from GitHub:

At least 1 approving review is required by reviewers with write access.

@jhamman
jhamman merged commit c2f5f00 into mainDec 20, 2023
@dependabot
dependabotBot deleted the dependabot/github_actions/actions/setup-python-5.0.0 branch December 20, 2023 03:47
jhamman added a commit to jhamman/zarr-python that referenced this pull request Jan 24, 2024
@dependabot@jhamman
Bump actions/setup-python from 4.7.1 to 5.0.0 (zarr-developers#1605)
a5b4b90
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
jhamman added a commit that referenced this pull request Oct 11, 2024
@jhamman@dependabot
@janickm@dstansby@DimitriPapadopoulos@d-v-b@joshmoore@pre-commit-ci@jakirkham@jeffpeck10x@normanrz@sanketverma1704@hoodmane@oeway@DahnJ@dcherian@itcarroll@martindurant@rabernat@sneakers-the-rat
V3 main sync w/ merge (#2335)
ce5f53e
* Bump pypa/gh-action-pypi-publish from 1.8.10 to 1.8.11 (#1586)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.10 to 1.8.11.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.10...v1.8.11)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump conda-incubator/setup-miniconda from 2.3.0 to 3.0.1 (#1587)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 2.3.0 to 3.0.1.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v2.3.0...v3.0.1)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* * Cache result of FSStore._fsspec_installed (#1581)
Prevent runtime-overhead in doing this check multiple times
* Bump version of black in pre-commit (#1559)
* Use list comprehension where applicable (#1555)
Even if this is only a test, list comprehensions are faster than
repeatedly call append().
Also use tuple instead of list when possible.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Bump numcodecs from 0.11.0 to 0.12.1 (#1580)
Bumps [numcodecs](https://github.com/zarr-developers/numcodecs) from 0.11.0 to 0.12.1.
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.rst)
- [Commits](https://github.com/zarr-developers/numcodecs/compare/v0.11.0...v0.12.1)
---
updated-dependencies:
- dependency-name: numcodecs
dependency-type: direct:development
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Use format specification mini-language to format string (#1558)
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Single startswith() call instead of multiple ones (#1556)
It's faster and probably more readable.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump pymongo from 4.5.0 to 4.6.1 (#1585)
Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.5.0 to 4.6.1.
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.5.0...4.6.1)
---
updated-dependencies:
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Move codespell options around (#1196)
Starting with codespell 2.2.2, options can be specified in
`pyrpoject.toml` in addition to `setup.cfg`:
https://github.com/codespell-project/codespell#using-a-config-file
Specifying options in a config file instead of command line options in
`.pre-commit-config.yaml` ensures codespell uses the same options when
run as pre-commit hook or from the command line in the repository root
directory.
* Bump fsspec from 2023.10.0 to 2023.12.1 (#1600)
* Bump fsspec from 2023.10.0 to 2023.12.1
Bumps [fsspec](https://github.com/fsspec/filesystem_spec) from 2023.10.0 to 2023.12.1.
- [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.10.0...2023.12.1)
---
updated-dependencies:
- dependency-name: fsspec
dependency-type: direct:development
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
* Update s3fs as well
* Fix s3fs
---------
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Add type hints to zarr.create (#1536)
* Add type hints to zarr.create
* Use protocol for MetaArray
* Use protocol for Synchronizer
* Fix Path typing
* Add release note
* Fix dim separator typing
* Ignore ... in coverage reporting
* Fix chunk typing
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Remove unused mypy ignore comments (#1602)
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Bump actions/setup-python from 4.7.1 to 5.0.0 (#1605)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump github/codeql-action from 2 to 3 (#1609)
Bumps [github/codeql-action](https://github.com/github/codeql-action) from 2 to 3.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/github/codeql-action/compare/v2...v3)
---
updated-dependencies:
- dependency-name: github/codeql-action
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore: update pre-commit hooks (#1448)
* chore: update pre-commit hooks
updates:
- https://github.com/charliermarsh/ruff-pre-commit → https://github.com/astral-sh/ruff-pre-commit
- [github.com/astral-sh/ruff-pre-commit: v0.0.224 → v0.1.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.224...v0.1.8)
- [github.com/psf/black: 23.10.1 → 23.12.0](https://github.com/psf/black/compare/23.10.1...23.12.0)
- [github.com/codespell-project/codespell: v2.2.5 → v2.2.6](https://github.com/codespell-project/codespell/compare/v2.2.5...v2.2.6)
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.4.0...v4.5.0)
- [github.com/pre-commit/mirrors-mypy: v1.3.0 → v1.7.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.3.0...v1.7.1)
* Attempt to fix ruff
* Use isinstance
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* chore: update pre-commit hooks (#1618)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.8 → v0.1.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.8...v0.1.9)
- [github.com/psf/black: 23.12.0 → 23.12.1](https://github.com/psf/black/compare/23.12.0...23.12.1)
- [github.com/pre-commit/mirrors-mypy: v1.7.1 → v1.8.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.7.1...v1.8.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Bump fsspec from 2023.12.1 to 2023.12.2 (#1606)
* Bump fsspec from 2023.12.1 to 2023.12.2
Bumps [fsspec](https://github.com/fsspec/filesystem_spec) from 2023.12.1 to 2023.12.2.
- [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.12.1...2023.12.2)
---
updated-dependencies:
- dependency-name: fsspec
dependency-type: direct:development
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
* Update requirements_dev_optional.txt
---------
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump pytest-doctestplus from 1.0.0 to 1.1.0 (#1619)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.0.0 to 1.1.0.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.0.0...v1.1.0)
---
updated-dependencies:
- dependency-name: pytest-doctestplus
dependency-type: direct:development
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump pytest from 7.4.3 to 7.4.4 (#1622)
* chore: update pre-commit hooks (#1626)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.1.11](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.9...v0.1.11)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Create TEAM.md (#1628)
* Drop python 3.8 and numpy 1.20 (#1557)
* Drop 3.8 and add 3.12
* Try removing line_profiler
* Also bump the minimal numpy to 1.21
* Drop 3.12 again
* Revert "Try removing line_profiler"
This reverts commit 837854bec99a9d25aece2ead9666f01690d228cc.
* Update release.rst
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: jakirkham <jakirkham@gmail.com>
* Add Norman Rzepka to core-dev team (#1630)
* chore: update pre-commit hooks (#1633)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.11 → v0.1.13](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.11...v0.1.13)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Bump actions/download-artifact from 3 to 4 (#1611)
* Bump actions/download-artifact from 3 to 4
Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4.
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](https://github.com/actions/download-artifact/compare/v3...v4)
---
updated-dependencies:
- dependency-name: actions/download-artifact
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
* Also bump upload-artifact
see https://github.com/actions/download-artifact?tab=readme-ov-file#breaking-changes
> Downloading artifacts that were created from action/upload-artifact@v3 and below are not supported.
---------
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Update tutorial.rst to include section about accessing Zip Files on S3 (#1615)
* Update tutorial.rst to include section about accessing Zip Files on S3
Per discussion here, add information about about accessing zip files on s3:
https://github.com/zarr-developers/zarr-python/discussions/1613
* Update release.rst
* Implement d-v-b's suggestions
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* doc(v3): add v3 roadmap and design document (#1583)
* doc(v3): add v3 roadmap and design document
* Update v3-roadmap-and-design.md
* updates after latest round of reviews
* Update v3-roadmap-and-design.md
Co-authored-by: Norman Rzepka <code@normanrz.com>
* Update v3-roadmap-and-design.md
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
---------
Co-authored-by: Norman Rzepka <code@normanrz.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore: update pre-commit hooks (#1636)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.13 → v0.1.14](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.13...v0.1.14)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix zarr sync (#1663)
This patch removes fasteners and disables zarr.sync which uses process and thread
Co-authored-by: Wei Ouyang <oeway007@gmail.com>
* Update release.rst (#1621)
* Update release.rst
* Update release.rst
* Change 2.16.2 → 2.17.0
* Update moto for test_s3
* Skip bsddb3 tests to prevent warning failure
* Fix more user warning tests
* Fix even more user warning tests
* Skip coverage for importorskips
* Move to have_X skip method for deps
* Update release.rst (PR#1663)
* Fix test_core.py 'compile' issues
* Add black formatting
* Drop Windows/3.9 build due to unrelated failures
* fix typo
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Bump numpy from 1.24.3 to 1.26.1 (#1543)
Bumps [numpy](https://github.com/numpy/numpy) from 1.24.3 to 1.26.1.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.24.3...v1.26.1)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* chore: update pre-commit hooks (#1642)
* chore: update pre-commit hooks
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.14 → v0.2.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.14...v0.2.1)
- [github.com/psf/black: 23.12.1 → 24.2.0](https://github.com/psf/black/compare/23.12.1...24.2.0)
* run black incl. comments for '...'
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Bump ipywidgets from 8.1.0 to 8.1.1 (#1538)
Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.1.0 to 8.1.1.
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.0...8.1.1)
---
updated-dependencies:
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Proper argument for numpy.reshape (#1425)
`numpy.reshape` not only accepts a tuple of ints, but also a simple int.
Besides `(10)` is not a tuple and is identical to `10`, unlike `(10,)`.
* Bump ipywidgets from 8.1.1 to 8.1.2 (#1666)
Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.1.1 to 8.1.2.
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.1...8.1.2)
---
updated-dependencies:
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* docs: ZIP-related tweaks (#1641)
* docs: use 'ZIP archive' instead of 'zip file'; clarify utility of caching in s3 + ZIP example; style
* docs: update release notes, correct spelling of greg lee's name in past release notes, and fix markup in past release notes
* docs: use 'ZIP archive' instead of 'zip file'; clarify utility of caching in s3 + ZIP example; style
* docs: update release notes, correct spelling of greg lee's name in past release notes, and fix markup in past release notes
* Bump numpy from 1.26.1 to 1.26.4 (#1669)
Bumps [numpy](https://github.com/numpy/numpy) from 1.26.1 to 1.26.4.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.1...v1.26.4)
---
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- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
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* Change occurrences of % and format() to f-strings (#1423)
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* chore: update pre-commit hooks (#1672)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.1 → v0.2.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.1...v0.2.2)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Bump pymongo from 4.6.1 to 4.6.2 (#1674)
Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.6.1 to 4.6.2.
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/4.6.2/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.6.1...4.6.2)
---
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* Bump conda-incubator/setup-miniconda from 3.0.1 to 3.0.2 (#1677)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.1 to 3.0.2.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.1...v3.0.2)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
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* Update config.yml with Zulip
* Type dimension separator (#1620)
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Replace Gitter with new Zulip Chat link (#1685)
* Replace Gitter with Zulip
* Replace Gitter with Zulip in remaining places
* Bump redis from 5.0.1 to 5.0.2 (#1688)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.1 to 5.0.2.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.1...v5.0.2)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* Bump pypa/gh-action-pypi-publish from 1.8.11 to 1.8.12 (#1691)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.11 to 1.8.12.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.11...v1.8.12)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
...
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* Bump pytest-doctestplus from 1.1.0 to 1.2.0 (#1693)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.1.0 to 1.2.0.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.1.0...v1.2.0)
---
updated-dependencies:
- dependency-name: pytest-doctestplus
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* Fix RTD build (#1694)
* Update release.rst for v2.17.1 (#1673)
* Update release.rst for v2.17.1
* Change the copyright year from 2023 → 2024.
* Update release.rst for v2.17.1
* Bump pytest-timeout from 2.2.0 to 2.3.1 (#1697)
Bumps [pytest-timeout](https://github.com/pytest-dev/pytest-timeout) from 2.2.0 to 2.3.1.
- [Commits](https://github.com/pytest-dev/pytest-timeout/compare/2.2.0...2.3.1)
---
updated-dependencies:
- dependency-name: pytest-timeout
dependency-type: direct:development
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...
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* Bump conda-incubator/setup-miniconda from 3.0.2 to 3.0.3 (#1690)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.2 to 3.0.3.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.2...v3.0.3)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
...
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Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* docs(tutorial.rst): fix link to GCSMap (#1689)
* Update installation.rst stating version support policy (#1665)
* Update installation.rst stating version support policy
* Update docs/installation.rst
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Update docs/installation.rst
---------
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Bump pypa/gh-action-pypi-publish from 1.8.12 to 1.8.14 (#1700)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.12 to 1.8.14.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.12...v1.8.14)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
...
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* Bump pytest-doctestplus from 1.2.0 to 1.2.1 (#1699)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.2.0 to 1.2.1.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.2.0...v1.2.1)
---
updated-dependencies:
- dependency-name: pytest-doctestplus
dependency-type: direct:development
update-type: version-update:semver-patch
...
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Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Bump redis from 5.0.2 to 5.0.3 (#1698)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.2 to 5.0.3.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.2...v5.0.3)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* Add Python 3.12 to CI (#1719)
* Update python-package.yml
* bump numpy versions
* bump min python version
* Update release.rst
* Bump pytest-cov from 4.1.0 to 5.0.0 (#1722)
Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 4.1.0 to 5.0.0.
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest-cov/compare/v4.1.0...v5.0.0)
---
updated-dependencies:
- dependency-name: pytest-cov
dependency-type: direct:development
update-type: version-update:semver-major
...
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* chore: update pre-commit hooks (#1708)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.2 → v0.3.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.2...v0.3.3)
- [github.com/psf/black: 24.2.0 → 24.3.0](https://github.com/psf/black/compare/24.2.0...24.3.0)
- [github.com/pre-commit/mirrors-mypy: v1.8.0 → v1.9.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.8.0...v1.9.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore: update pre-commit hooks (#1723)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.3 → v0.3.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.3...v0.3.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix release notes (following #1719) (#1725)
* Override ipython repr methods. (#1724)
Closes #1716
This avoids expensive lookups against object stores.
* Bump pymongo from 4.6.2 to 4.6.3 (#1729)
* Remove v1 and v2 specification (#1582)
* Remove v1 and v2 specification
* fix warning
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* chore: update pre-commit hooks (#1738)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.4 → v0.3.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.4...v0.3.5)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Optimize Array.info and Group.info (#1733)
* Optimize Array.info.
Avoid repeated computes of the same value (getsize)
* Don't have InfoReporter query items twice.
Apparently IPython will run both __repr__ and _repr_html_
so we were calling `getsize` twice.
* Group too
* Apply suggestions from code review
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
---------
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Bump actions/setup-python from 5.0.0 to 5.1.0 (#1736)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.0.0 to 5.1.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.0.0...v5.1.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-minor
...
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* Couple fixes (#1737)
* Use `is` when comparing `type` of two objects
* Unnecessary `None` provided as default
* Fix tests with Pytest 8 (#1714)
* Bump pytest version
* Use editable install when testing
---------
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Avoid redundant __contains__ (#1739)
Let's try grabbing the array.json and group.json files,
and check for `*NotFoundError`, instead of using contains first.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Array & Group: Use already loaded attributes to populate cache. (#1734)
* Array: Use already loaded attributes to populate cache.
* Group: Use already loaded attributes to populate cache.
* Fix
* Add release note
* Optimize attribute setting (#1741)
* Optimize attribute setting
* Add release note
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Make sure fs exceptions are raised if not MissingFs exceptions (clone) (#1604)
* Make sure fs exceptions are raised if not Missing
* lint
* add missing argument in tests, lint
* clear memory filesystem during test
* improve commenting
* add memory_store fixture, getitems performance
* Update release.rst
* improve FSStore.test_exception coverage
---------
Co-authored-by: Martin Durant <martin.durant@alumni.utoronto.ca>
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore(release): update changelog for 2.17.2 (#1775)
* chore(docs): reset release notes as unreleased (#1776)
* Bump codecov/codecov-action from 3 to 4 (#1647)
* Bump codecov/codecov-action from 3 to 4
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v3...v4)
---
updated-dependencies:
- dependency-name: codecov/codecov-action
dependency-type: direct:production
update-type: version-update:semver-major
...
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* Set codecov env
---------
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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Update release.rst for v2.17.2 (#1778)
* Update release.rst for v2.17.2
* Minor edits
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Deprecate the experimental v3 implementation (#1802)
* deprecate(exp-v3): Add a future warning about the pending removal of the experimental v3 implementation
* ignore warning
* add test
* chore: update pre-commit hooks (#1779)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.3.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.5...v0.3.7)
- [github.com/psf/black: 24.3.0 → 24.4.0](https://github.com/psf/black/compare/24.3.0...24.4.0)
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v4.6.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix `is_total_slice` for size-1 dimensions (#1800)
Closes #1730
Co-authored-by: Ryan Abernathey <ryan.abernathey@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* add note to the top of the release page noting the plan for 2.18.* and 3.0 (#1816)
* Bump conda-incubator/setup-miniconda from 3.0.3 to 3.0.4 (#1824)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.3 to 3.0.4.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.3...v3.0.4)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
...
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* dep(docs): deprecate experimental v3 support in docs (#1807)
* dep(docs): deprecate experimental v3 support in docs
* Apply suggestions from code review
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
---------
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Bump h5py from 3.10.0 to 3.11.0 (#1786)
Bumps [h5py](https://github.com/h5py/h5py) from 3.10.0 to 3.11.0.
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](https://github.com/h5py/h5py/compare/3.10.0...3.11.0)
---
updated-dependencies:
- dependency-name: h5py
dependency-type: direct:development
update-type: version-update:semver-minor
...
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Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump redis from 5.0.3 to 5.0.4 (#1810)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.3 to 5.0.4.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.3...v5.0.4)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* deprecate(stores): add deprecation warnings to stores that we plan to remove in v3 (#1801)
* deprecate(stores): add deprecation warnings to DBMStore, LMDBStore, SQLiteStore, MongoDBStore, RedisStore, and ABSStore
* filter warnings in pytest config
* more deprecation warnings in docstrings
* add release note
* use np.inf instead of PINF/NINF (#1842)
* use np.inf instead of PINF/NINF
* update release notes
* chore: update pre-commit hooks (#1825)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.1 → v0.4.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.1...v0.4.3)
- [github.com/psf/black: 24.4.0 → 24.4.2](https://github.com/psf/black/compare/24.4.0...24.4.2)
- [github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.9.0...v1.10.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Enable ruff/bugbear rules (B) and fix issues (#1702)
* Enable ruff/bugbear rules (B)
As suggested by Repo-Review.
* Fix ruff/bugbear issue (B007)
B007 Loop control variable `key` not used within loop body
https://docs.astral.sh/ruff/rules/unused-loop-control-variable/
* Fix ruff/bugbear issue (B015)
B015 Pointless comparison. Did you mean to assign a value?
Otherwise, prepend `assert` or remove it.
https://docs.astral.sh/ruff/rules/useless-comparison/
* Fix ruff/bugbear issues (B028)
B028 No explicit `stacklevel` keyword argument found
https://docs.astral.sh/ruff/rules/no-explicit-stacklevel/
* Fix ruff/bugbear issues (B904)
B904 Within an `except` clause, raise exceptions with `raise ... from err` or
`raise ... from None` to distinguish them from errors in exception handling
https://docs.astral.sh/ruff/rules/raise-without-from-inside-except/
* Document changes in docs/release.rst
* Disable ruff/bugbear rule (B017)
B017 `pytest.raises(Exception)` should be considered evil
https://docs.astral.sh/ruff/rules/assert-raises-exception/
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Release notes for 2.18.0 (#1843)
* doc: cleanup release notes for 2.18.0
* Update release.rst (#1850)
* Group dependabot updates (#1854)
* chore: update pre-commit hooks (#1876)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.3 → v0.4.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.3...v0.4.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix a regression with scalar indexing due to #1800 (#1875)
* release notes for 2.18.1 (#1885)
* reset release notes (#1886)
* Add zstd to old V3 supported codecs (#1914)
* add zstd to old V3 supported codecs
* get to full test coverage and add release note
* fix pre-commit
* doc: update release notes for 2.18.2 (#1915)
* Drop support for Python 3.9
* Revert "Drop support for Python 3.9"
This reverts commit a054afbbdaf7c8560d0ce5df77af969bc863e335.
* Update TEAM.md (#2071)
* [v2] Fix doctests with numpy 2.0 (#2073)
* Fix version number in built docs (#2044)
* Fix orthogonal indexing with scalar. (#1947)
Co-authored-by: David Stansby <dstansby@gmail.com>
* Bump the requirements group across 1 directory with 7 updates (#2092)
Bumps the requirements group with 7 updates in the / directory:
| Package | From | To |
| --- | --- | --- |
| [numpy](https://github.com/numpy/numpy) | `1.26.4` | `2.0.1` |
| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) | `8.1.2` | `8.1.3` |
| [setuptools-scm](https://github.com/pypa/setuptools_scm) | `8.0.4` | `8.1.0` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.1.1` | `8.3.2` |
| [lmdb](https://github.com/jnwatson/py-lmdb) | `1.4.1` | `1.5.1` |
| [redis](https://github.com/redis/redis-py) | `5.0.4` | `5.0.8` |
| [pymongo](https://github.com/mongodb/mongo-python-driver) | `4.6.3` | `4.8.0` |
Updates `numpy` from 1.26.4 to 2.0.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.4...v2.0.1)
Updates `ipywidgets` from 8.1.2 to 8.1.3
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.2...8.1.3)
Updates `setuptools-scm` from 8.0.4 to 8.1.0
- [Release notes](https://github.com/pypa/setuptools_scm/releases)
- [Changelog](https://github.com/pypa/setuptools_scm/blob/main/CHANGELOG.md)
- [Commits](https://github.com/pypa/setuptools_scm/compare/v8.0.4...v8.1.0)
Updates `pytest` from 8.1.1 to 8.3.2
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.1.1...8.3.2)
Updates `lmdb` from 1.4.1 to 1.5.1
- [Changelog](https://github.com/jnwatson/py-lmdb/blob/master/ChangeLog)
- [Commits](https://github.com/jnwatson/py-lmdb/compare/py-lmdb_1.4.1...py-lmdb_1.5.1)
Updates `redis` from 5.0.4 to 5.0.8
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.4...v5.0.8)
Updates `pymongo` from 4.6.3 to 4.8.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.6.3...4.8.0)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-major
dependency-group: requirements
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: setuptools-scm
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: pytest
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: lmdb
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump the actions group with 2 updates (#2087)
Bumps the actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `actions/setup-python` from 5.1.0 to 5.1.1
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.1.0...v5.1.1)
Updates `pypa/gh-action-pypi-publish` from 1.8.14 to 1.9.0
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.14...v1.9.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* [v2] Drop support for Python 3.9 (#2074)
* Drop support for Python 3.9
* Ignore B905 ruff rule
* Fix release notes
* Fix Array.__array__ for numpy 2.1 (#2106)
* Fix Array.__array__ for numpy 2.1
* Add changelog
* Depend on np.array for array coercions
* Bump test version of numcodecs (#2114)
* Bump test version of numcodecs
* Fix test for numcodecs 0.13
* fix: numpy 1.24 compat for Array.__array__ (#2123)
* Deprecate N5Store (#2103)
* deprecate(n5): add deprecation warning to N5Store
* also deprecate N5FSStore
* docs
* fix doc
* Run tests on numpy 1.23 (#2124)
* Bump the requirements group across 1 directory with 3 updates (#2129)
Bumps the requirements group with 3 updates in the / directory: [numpy](https://github.com/numpy/numpy), [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) and [azure-storage-blob](https://github.com/Azure/azure-sdk-for-python).
Updates `numpy` from 2.0.1 to 2.1.0
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.0.1...v2.1.0)
Updates `ipywidgets` from 8.1.3 to 8.1.5
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.3...8.1.5)
Updates `azure-storage-blob` from 12.16.0 to 12.21.0
- [Release notes](https://github.com/Azure/azure-sdk-for-python/releases)
- [Changelog](https://github.com/Azure/azure-sdk-for-python/blob/main/doc/esrp_release.md)
- [Commits](https://github.com/Azure/azure-sdk-for-python/compare/azure-storage-blob_12.16.0...azure-storage-blob_12.21.0)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: azure-storage-blob
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore: bump minimum numpy version to 1.24 (#2127)
* chore: bump minimum version to 1.24
* Update .github/workflows/python-package.yml
* Remove un-needed package installs in CI (#2095)
* Bump the actions group with 2 updates (#2146)
Bumps the actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `actions/setup-python` from 5.1.1 to 5.2.0
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.1.1...v5.2.0)
Updates `pypa/gh-action-pypi-publish` from 1.9.0 to 1.10.0
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.9.0...v1.10.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump numpy from 2.1.0 to 2.1.1 in the requirements group (#2151)
Bumps the requirements group with 1 update: [numpy](https://github.com/numpy/numpy).
Updates `numpy` from 2.1.0 to 2.1.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.0...v2.1.1)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore(docs): update release notes ahead of 2.18.4 (#2152)
* Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1 in the actions group (#2161)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.0 to 1.10.1
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.0...v1.10.1)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* [docs] remove primary sidebar from tutorial (#2142)
* remove primary sidebar from tutorial
* lint
* Bump pytest from 8.3.2 to 8.3.3 in the requirements group (#2172)
Bumps the requirements group with 1 update: [pytest](https://github.com/pytest-dev/pytest).
Updates `pytest` from 8.3.2 to 8.3.3
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.3.2...8.3.3)
---
updated-dependencies:
- dependency-name: pytest
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump pypa/gh-action-pypi-publish in the actions group (#2220)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.1 to 1.10.2
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.1...v1.10.2)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Update TEAM.md (#2227)
* Bump the requirements group across 1 directory with 3 updates (#2284)
Bumps the requirements group with 3 updates in the / directory: [redis](https://github.com/redis/redis-py), [pymongo](https://github.com/mongodb/mongo-python-driver) and [h5py](https://github.com/h5py/h5py).
Updates `redis` from 5.0.8 to 5.1.0
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.8...v5.1.0)
Updates `pymongo` from 4.8.0 to 4.10.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.8.0...4.10.0)
Updates `h5py` from 3.11.0 to 3.12.1
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](https://github.com/h5py/h5py/compare/3.11.0...3.12.1)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: h5py
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump pymongo from 4.10.0 to 4.10.1 in the requirements group (#2288)
Bumps the requirements group with 1 update: [pymongo](https://github.com/mongodb/mongo-python-driver).
Updates `pymongo` from 4.10.0 to 4.10.1
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.10.0...4.10.1)
---
updated-dependencies:
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Fix low contrast box titles (#2287) (#2292)
* Bump pypa/gh-action-pypi-publish in the actions group (#2304)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.2 to 1.10.3
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.2...v1.10.3)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump the requirements group with 2 updates (#2303)
Bumps the requirements group with 2 updates: [numpy](https://github.com/numpy/numpy) and [redis](https://github.com/redis/redis-py).
Updates `numpy` from 2.1.1 to 2.1.2
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.1...v2.1.2)
Updates `redis` from 5.1.0 to 5.1.1
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.1.0...v5.1.1)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump numcodecs from 0.13.0 to 0.13.1 in the requirements group (#2326)
Bumps the requirements group with 1 update: [numcodecs](https://github.com/zarr-developers/numcodecs).
Updates `numcodecs` from 0.13.0 to 0.13.1
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.rst)
- [Commits](https://github.com/zarr-developers/numcodecs/compare/v0.13.0...v0.13.1)
---
updated-dependencies:
- dependency-name: numcodecs
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* remove zarr.types from v2
---------
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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Janick Martinez Esturo <janick@jme.pub>
Co-authored-by: David Stansby <dstansby@gmail.com>
Co-authored-by: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com>
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: jakirkham <jakirkham@gmail.com>
Co-authored-by: Jeff Peck <jeffrey.peck@10xgenomics.com>
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Bump actions/setup-python from 4.7.1 to 5.0.0 by dependabot[bot] · Pull Request #1605 · zarr-developers/zarr-python · GitHub
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Bump actions/setup-python from 4.7.1 to 5.0.0 - #1605
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Dec 20, 2023
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Bump actions/setup-python from 4.7.1 to 5.0.0#1605
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Bumps actions/setup-python from 4.7.1 to 5.0.0.
Release notes
Sourced from actions/setup-python's releases.
v5.0.0
What's Changed
In scope of this release, we update node version runtime from node16 to node20 (actions/setup-python#772). Besides, we update dependencies to the latest versions.
Full Changelog: actions/setup-python@v4.8.0...v5.0.0
v4.8.0
What's Changed
In scope of this release we added support for GraalPy (actions/setup-python#694). You can use this snippet to set up GraalPy:
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v4 with:
python-version: 'graalpy-22.3' - run: python my_script.py
Besides, the release contains such changes as:
New Contributors
Full Changelog: actions/setup-python@v4...v4.8.0
Commits

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Bump actions/setup-python from 4.7.1 to 5.0.0
cf76095
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4.7.1...v5.0.0)
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Bump actions/setup-python from 4.7.1 to 5.0.0 (zarr-developers#1605)
a5b4b90
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-major
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jhamman added a commit
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@janickm@dstansby@DimitriPapadopoulos@d-v-b@joshmoore@pre-commit-ci@jakirkham@jeffpeck10x@normanrz@sanketverma1704@hoodmane@oeway@DahnJ@dcherian@itcarroll@martindurant@rabernat@sneakers-the-rat
V3 main sync w/ merge (#2335)
ce5f53e
* Bump pypa/gh-action-pypi-publish from 1.8.10 to 1.8.11 (#1586)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.10 to 1.8.11.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.10...v1.8.11)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
...
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* Bump conda-incubator/setup-miniconda from 2.3.0 to 3.0.1 (#1587)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 2.3.0 to 3.0.1.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v2.3.0...v3.0.1)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-major
...
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* * Cache result of FSStore._fsspec_installed (#1581)
Prevent runtime-overhead in doing this check multiple times
* Bump version of black in pre-commit (#1559)
* Use list comprehension where applicable (#1555)
Even if this is only a test, list comprehensions are faster than
repeatedly call append().
Also use tuple instead of list when possible.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Bump numcodecs from 0.11.0 to 0.12.1 (#1580)
Bumps [numcodecs](https://github.com/zarr-developers/numcodecs) from 0.11.0 to 0.12.1.
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.rst)
- [Commits](https://github.com/zarr-developers/numcodecs/compare/v0.11.0...v0.12.1)
---
updated-dependencies:
- dependency-name: numcodecs
dependency-type: direct:development
update-type: version-update:semver-minor
...
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Co-authored-by: Joe Hamman <joe@earthmover.io>
* Use format specification mini-language to format string (#1558)
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Single startswith() call instead of multiple ones (#1556)
It's faster and probably more readable.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump pymongo from 4.5.0 to 4.6.1 (#1585)
Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.5.0 to 4.6.1.
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.5.0...4.6.1)
---
updated-dependencies:
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
...
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Co-authored-by: Joe Hamman <joe@earthmover.io>
* Move codespell options around (#1196)
Starting with codespell 2.2.2, options can be specified in
`pyrpoject.toml` in addition to `setup.cfg`:
https://github.com/codespell-project/codespell#using-a-config-file
Specifying options in a config file instead of command line options in
`.pre-commit-config.yaml` ensures codespell uses the same options when
run as pre-commit hook or from the command line in the repository root
directory.
* Bump fsspec from 2023.10.0 to 2023.12.1 (#1600)
* Bump fsspec from 2023.10.0 to 2023.12.1
Bumps [fsspec](https://github.com/fsspec/filesystem_spec) from 2023.10.0 to 2023.12.1.
- [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.10.0...2023.12.1)
---
updated-dependencies:
- dependency-name: fsspec
dependency-type: direct:development
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
* Update s3fs as well
* Fix s3fs
---------
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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Add type hints to zarr.create (#1536)
* Add type hints to zarr.create
* Use protocol for MetaArray
* Use protocol for Synchronizer
* Fix Path typing
* Add release note
* Fix dim separator typing
* Ignore ... in coverage reporting
* Fix chunk typing
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Remove unused mypy ignore comments (#1602)
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Bump actions/setup-python from 4.7.1 to 5.0.0 (#1605)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump github/codeql-action from 2 to 3 (#1609)
Bumps [github/codeql-action](https://github.com/github/codeql-action) from 2 to 3.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/github/codeql-action/compare/v2...v3)
---
updated-dependencies:
- dependency-name: github/codeql-action
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore: update pre-commit hooks (#1448)
* chore: update pre-commit hooks
updates:
- https://github.com/charliermarsh/ruff-pre-commit → https://github.com/astral-sh/ruff-pre-commit
- [github.com/astral-sh/ruff-pre-commit: v0.0.224 → v0.1.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.224...v0.1.8)
- [github.com/psf/black: 23.10.1 → 23.12.0](https://github.com/psf/black/compare/23.10.1...23.12.0)
- [github.com/codespell-project/codespell: v2.2.5 → v2.2.6](https://github.com/codespell-project/codespell/compare/v2.2.5...v2.2.6)
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.4.0...v4.5.0)
- [github.com/pre-commit/mirrors-mypy: v1.3.0 → v1.7.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.3.0...v1.7.1)
* Attempt to fix ruff
* Use isinstance
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* chore: update pre-commit hooks (#1618)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.8 → v0.1.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.8...v0.1.9)
- [github.com/psf/black: 23.12.0 → 23.12.1](https://github.com/psf/black/compare/23.12.0...23.12.1)
- [github.com/pre-commit/mirrors-mypy: v1.7.1 → v1.8.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.7.1...v1.8.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Bump fsspec from 2023.12.1 to 2023.12.2 (#1606)
* Bump fsspec from 2023.12.1 to 2023.12.2
Bumps [fsspec](https://github.com/fsspec/filesystem_spec) from 2023.12.1 to 2023.12.2.
- [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.12.1...2023.12.2)
---
updated-dependencies:
- dependency-name: fsspec
dependency-type: direct:development
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
* Update requirements_dev_optional.txt
---------
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump pytest-doctestplus from 1.0.0 to 1.1.0 (#1619)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.0.0 to 1.1.0.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.0.0...v1.1.0)
---
updated-dependencies:
- dependency-name: pytest-doctestplus
dependency-type: direct:development
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump pytest from 7.4.3 to 7.4.4 (#1622)
* chore: update pre-commit hooks (#1626)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.1.11](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.9...v0.1.11)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Create TEAM.md (#1628)
* Drop python 3.8 and numpy 1.20 (#1557)
* Drop 3.8 and add 3.12
* Try removing line_profiler
* Also bump the minimal numpy to 1.21
* Drop 3.12 again
* Revert "Try removing line_profiler"
This reverts commit 837854bec99a9d25aece2ead9666f01690d228cc.
* Update release.rst
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: jakirkham <jakirkham@gmail.com>
* Add Norman Rzepka to core-dev team (#1630)
* chore: update pre-commit hooks (#1633)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.11 → v0.1.13](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.11...v0.1.13)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Bump actions/download-artifact from 3 to 4 (#1611)
* Bump actions/download-artifact from 3 to 4
Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4.
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](https://github.com/actions/download-artifact/compare/v3...v4)
---
updated-dependencies:
- dependency-name: actions/download-artifact
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
* Also bump upload-artifact
see https://github.com/actions/download-artifact?tab=readme-ov-file#breaking-changes
> Downloading artifacts that were created from action/upload-artifact@v3 and below are not supported.
---------
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Update tutorial.rst to include section about accessing Zip Files on S3 (#1615)
* Update tutorial.rst to include section about accessing Zip Files on S3
Per discussion here, add information about about accessing zip files on s3:
https://github.com/zarr-developers/zarr-python/discussions/1613
* Update release.rst
* Implement d-v-b's suggestions
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* doc(v3): add v3 roadmap and design document (#1583)
* doc(v3): add v3 roadmap and design document
* Update v3-roadmap-and-design.md
* updates after latest round of reviews
* Update v3-roadmap-and-design.md
Co-authored-by: Norman Rzepka <code@normanrz.com>
* Update v3-roadmap-and-design.md
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
---------
Co-authored-by: Norman Rzepka <code@normanrz.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore: update pre-commit hooks (#1636)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.13 → v0.1.14](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.13...v0.1.14)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix zarr sync (#1663)
This patch removes fasteners and disables zarr.sync which uses process and thread
Co-authored-by: Wei Ouyang <oeway007@gmail.com>
* Update release.rst (#1621)
* Update release.rst
* Update release.rst
* Change 2.16.2 → 2.17.0
* Update moto for test_s3
* Skip bsddb3 tests to prevent warning failure
* Fix more user warning tests
* Fix even more user warning tests
* Skip coverage for importorskips
* Move to have_X skip method for deps
* Update release.rst (PR#1663)
* Fix test_core.py 'compile' issues
* Add black formatting
* Drop Windows/3.9 build due to unrelated failures
* fix typo
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Bump numpy from 1.24.3 to 1.26.1 (#1543)
Bumps [numpy](https://github.com/numpy/numpy) from 1.24.3 to 1.26.1.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.24.3...v1.26.1)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* chore: update pre-commit hooks (#1642)
* chore: update pre-commit hooks
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.14 → v0.2.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.14...v0.2.1)
- [github.com/psf/black: 23.12.1 → 24.2.0](https://github.com/psf/black/compare/23.12.1...24.2.0)
* run black incl. comments for '...'
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Bump ipywidgets from 8.1.0 to 8.1.1 (#1538)
Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.1.0 to 8.1.1.
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.0...8.1.1)
---
updated-dependencies:
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Proper argument for numpy.reshape (#1425)
`numpy.reshape` not only accepts a tuple of ints, but also a simple int.
Besides `(10)` is not a tuple and is identical to `10`, unlike `(10,)`.
* Bump ipywidgets from 8.1.1 to 8.1.2 (#1666)
Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.1.1 to 8.1.2.
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.1...8.1.2)
---
updated-dependencies:
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* docs: ZIP-related tweaks (#1641)
* docs: use 'ZIP archive' instead of 'zip file'; clarify utility of caching in s3 + ZIP example; style
* docs: update release notes, correct spelling of greg lee's name in past release notes, and fix markup in past release notes
* docs: use 'ZIP archive' instead of 'zip file'; clarify utility of caching in s3 + ZIP example; style
* docs: update release notes, correct spelling of greg lee's name in past release notes, and fix markup in past release notes
* Bump numpy from 1.26.1 to 1.26.4 (#1669)
Bumps [numpy](https://github.com/numpy/numpy) from 1.26.1 to 1.26.4.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.1...v1.26.4)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Change occurrences of % and format() to f-strings (#1423)
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* chore: update pre-commit hooks (#1672)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.1 → v0.2.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.1...v0.2.2)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Bump pymongo from 4.6.1 to 4.6.2 (#1674)
Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.6.1 to 4.6.2.
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/4.6.2/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.6.1...4.6.2)
---
updated-dependencies:
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* Bump conda-incubator/setup-miniconda from 3.0.1 to 3.0.2 (#1677)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.1 to 3.0.2.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.1...v3.0.2)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
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* Update config.yml with Zulip
* Type dimension separator (#1620)
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Replace Gitter with new Zulip Chat link (#1685)
* Replace Gitter with Zulip
* Replace Gitter with Zulip in remaining places
* Bump redis from 5.0.1 to 5.0.2 (#1688)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.1 to 5.0.2.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.1...v5.0.2)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
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* Bump pypa/gh-action-pypi-publish from 1.8.11 to 1.8.12 (#1691)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.11 to 1.8.12.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.11...v1.8.12)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
...
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* Bump pytest-doctestplus from 1.1.0 to 1.2.0 (#1693)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.1.0 to 1.2.0.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.1.0...v1.2.0)
---
updated-dependencies:
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dependency-type: direct:development
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* Fix RTD build (#1694)
* Update release.rst for v2.17.1 (#1673)
* Update release.rst for v2.17.1
* Change the copyright year from 2023 → 2024.
* Update release.rst for v2.17.1
* Bump pytest-timeout from 2.2.0 to 2.3.1 (#1697)
Bumps [pytest-timeout](https://github.com/pytest-dev/pytest-timeout) from 2.2.0 to 2.3.1.
- [Commits](https://github.com/pytest-dev/pytest-timeout/compare/2.2.0...2.3.1)
---
updated-dependencies:
- dependency-name: pytest-timeout
dependency-type: direct:development
update-type: version-update:semver-minor
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* Bump conda-incubator/setup-miniconda from 3.0.2 to 3.0.3 (#1690)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.2 to 3.0.3.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.2...v3.0.3)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
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* docs(tutorial.rst): fix link to GCSMap (#1689)
* Update installation.rst stating version support policy (#1665)
* Update installation.rst stating version support policy
* Update docs/installation.rst
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Update docs/installation.rst
---------
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Bump pypa/gh-action-pypi-publish from 1.8.12 to 1.8.14 (#1700)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.12 to 1.8.14.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.12...v1.8.14)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
...
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* Bump pytest-doctestplus from 1.2.0 to 1.2.1 (#1699)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.2.0 to 1.2.1.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.2.0...v1.2.1)
---
updated-dependencies:
- dependency-name: pytest-doctestplus
dependency-type: direct:development
update-type: version-update:semver-patch
...
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Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Bump redis from 5.0.2 to 5.0.3 (#1698)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.2 to 5.0.3.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.2...v5.0.3)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
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* Add Python 3.12 to CI (#1719)
* Update python-package.yml
* bump numpy versions
* bump min python version
* Update release.rst
* Bump pytest-cov from 4.1.0 to 5.0.0 (#1722)
Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 4.1.0 to 5.0.0.
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest-cov/compare/v4.1.0...v5.0.0)
---
updated-dependencies:
- dependency-name: pytest-cov
dependency-type: direct:development
update-type: version-update:semver-major
...
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* chore: update pre-commit hooks (#1708)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.2 → v0.3.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.2...v0.3.3)
- [github.com/psf/black: 24.2.0 → 24.3.0](https://github.com/psf/black/compare/24.2.0...24.3.0)
- [github.com/pre-commit/mirrors-mypy: v1.8.0 → v1.9.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.8.0...v1.9.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore: update pre-commit hooks (#1723)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.3 → v0.3.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.3...v0.3.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix release notes (following #1719) (#1725)
* Override ipython repr methods. (#1724)
Closes #1716
This avoids expensive lookups against object stores.
* Bump pymongo from 4.6.2 to 4.6.3 (#1729)
* Remove v1 and v2 specification (#1582)
* Remove v1 and v2 specification
* fix warning
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* chore: update pre-commit hooks (#1738)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.4 → v0.3.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.4...v0.3.5)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Optimize Array.info and Group.info (#1733)
* Optimize Array.info.
Avoid repeated computes of the same value (getsize)
* Don't have InfoReporter query items twice.
Apparently IPython will run both __repr__ and _repr_html_
so we were calling `getsize` twice.
* Group too
* Apply suggestions from code review
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
---------
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Bump actions/setup-python from 5.0.0 to 5.1.0 (#1736)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.0.0 to 5.1.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.0.0...v5.1.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-minor
...
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* Couple fixes (#1737)
* Use `is` when comparing `type` of two objects
* Unnecessary `None` provided as default
* Fix tests with Pytest 8 (#1714)
* Bump pytest version
* Use editable install when testing
---------
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Avoid redundant __contains__ (#1739)
Let's try grabbing the array.json and group.json files,
and check for `*NotFoundError`, instead of using contains first.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Array & Group: Use already loaded attributes to populate cache. (#1734)
* Array: Use already loaded attributes to populate cache.
* Group: Use already loaded attributes to populate cache.
* Fix
* Add release note
* Optimize attribute setting (#1741)
* Optimize attribute setting
* Add release note
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Make sure fs exceptions are raised if not MissingFs exceptions (clone) (#1604)
* Make sure fs exceptions are raised if not Missing
* lint
* add missing argument in tests, lint
* clear memory filesystem during test
* improve commenting
* add memory_store fixture, getitems performance
* Update release.rst
* improve FSStore.test_exception coverage
---------
Co-authored-by: Martin Durant <martin.durant@alumni.utoronto.ca>
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore(release): update changelog for 2.17.2 (#1775)
* chore(docs): reset release notes as unreleased (#1776)
* Bump codecov/codecov-action from 3 to 4 (#1647)
* Bump codecov/codecov-action from 3 to 4
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v3...v4)
---
updated-dependencies:
- dependency-name: codecov/codecov-action
dependency-type: direct:production
update-type: version-update:semver-major
...
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* Set codecov env
---------
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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Update release.rst for v2.17.2 (#1778)
* Update release.rst for v2.17.2
* Minor edits
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Deprecate the experimental v3 implementation (#1802)
* deprecate(exp-v3): Add a future warning about the pending removal of the experimental v3 implementation
* ignore warning
* add test
* chore: update pre-commit hooks (#1779)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.3.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.5...v0.3.7)
- [github.com/psf/black: 24.3.0 → 24.4.0](https://github.com/psf/black/compare/24.3.0...24.4.0)
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v4.6.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix `is_total_slice` for size-1 dimensions (#1800)
Closes #1730
Co-authored-by: Ryan Abernathey <ryan.abernathey@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* add note to the top of the release page noting the plan for 2.18.* and 3.0 (#1816)
* Bump conda-incubator/setup-miniconda from 3.0.3 to 3.0.4 (#1824)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.3 to 3.0.4.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.3...v3.0.4)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
...
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* dep(docs): deprecate experimental v3 support in docs (#1807)
* dep(docs): deprecate experimental v3 support in docs
* Apply suggestions from code review
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
---------
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Bump h5py from 3.10.0 to 3.11.0 (#1786)
Bumps [h5py](https://github.com/h5py/h5py) from 3.10.0 to 3.11.0.
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](https://github.com/h5py/h5py/compare/3.10.0...3.11.0)
---
updated-dependencies:
- dependency-name: h5py
dependency-type: direct:development
update-type: version-update:semver-minor
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Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump redis from 5.0.3 to 5.0.4 (#1810)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.3 to 5.0.4.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.3...v5.0.4)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* deprecate(stores): add deprecation warnings to stores that we plan to remove in v3 (#1801)
* deprecate(stores): add deprecation warnings to DBMStore, LMDBStore, SQLiteStore, MongoDBStore, RedisStore, and ABSStore
* filter warnings in pytest config
* more deprecation warnings in docstrings
* add release note
* use np.inf instead of PINF/NINF (#1842)
* use np.inf instead of PINF/NINF
* update release notes
* chore: update pre-commit hooks (#1825)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.1 → v0.4.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.1...v0.4.3)
- [github.com/psf/black: 24.4.0 → 24.4.2](https://github.com/psf/black/compare/24.4.0...24.4.2)
- [github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.9.0...v1.10.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Enable ruff/bugbear rules (B) and fix issues (#1702)
* Enable ruff/bugbear rules (B)
As suggested by Repo-Review.
* Fix ruff/bugbear issue (B007)
B007 Loop control variable `key` not used within loop body
https://docs.astral.sh/ruff/rules/unused-loop-control-variable/
* Fix ruff/bugbear issue (B015)
B015 Pointless comparison. Did you mean to assign a value?
Otherwise, prepend `assert` or remove it.
https://docs.astral.sh/ruff/rules/useless-comparison/
* Fix ruff/bugbear issues (B028)
B028 No explicit `stacklevel` keyword argument found
https://docs.astral.sh/ruff/rules/no-explicit-stacklevel/
* Fix ruff/bugbear issues (B904)
B904 Within an `except` clause, raise exceptions with `raise ... from err` or
`raise ... from None` to distinguish them from errors in exception handling
https://docs.astral.sh/ruff/rules/raise-without-from-inside-except/
* Document changes in docs/release.rst
* Disable ruff/bugbear rule (B017)
B017 `pytest.raises(Exception)` should be considered evil
https://docs.astral.sh/ruff/rules/assert-raises-exception/
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Release notes for 2.18.0 (#1843)
* doc: cleanup release notes for 2.18.0
* Update release.rst (#1850)
* Group dependabot updates (#1854)
* chore: update pre-commit hooks (#1876)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.3 → v0.4.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.3...v0.4.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix a regression with scalar indexing due to #1800 (#1875)
* release notes for 2.18.1 (#1885)
* reset release notes (#1886)
* Add zstd to old V3 supported codecs (#1914)
* add zstd to old V3 supported codecs
* get to full test coverage and add release note
* fix pre-commit
* doc: update release notes for 2.18.2 (#1915)
* Drop support for Python 3.9
* Revert "Drop support for Python 3.9"
This reverts commit a054afbbdaf7c8560d0ce5df77af969bc863e335.
* Update TEAM.md (#2071)
* [v2] Fix doctests with numpy 2.0 (#2073)
* Fix version number in built docs (#2044)
* Fix orthogonal indexing with scalar. (#1947)
Co-authored-by: David Stansby <dstansby@gmail.com>
* Bump the requirements group across 1 directory with 7 updates (#2092)
Bumps the requirements group with 7 updates in the / directory:
| Package | From | To |
| --- | --- | --- |
| [numpy](https://github.com/numpy/numpy) | `1.26.4` | `2.0.1` |
| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) | `8.1.2` | `8.1.3` |
| [setuptools-scm](https://github.com/pypa/setuptools_scm) | `8.0.4` | `8.1.0` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.1.1` | `8.3.2` |
| [lmdb](https://github.com/jnwatson/py-lmdb) | `1.4.1` | `1.5.1` |
| [redis](https://github.com/redis/redis-py) | `5.0.4` | `5.0.8` |
| [pymongo](https://github.com/mongodb/mongo-python-driver) | `4.6.3` | `4.8.0` |
Updates `numpy` from 1.26.4 to 2.0.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.4...v2.0.1)
Updates `ipywidgets` from 8.1.2 to 8.1.3
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.2...8.1.3)
Updates `setuptools-scm` from 8.0.4 to 8.1.0
- [Release notes](https://github.com/pypa/setuptools_scm/releases)
- [Changelog](https://github.com/pypa/setuptools_scm/blob/main/CHANGELOG.md)
- [Commits](https://github.com/pypa/setuptools_scm/compare/v8.0.4...v8.1.0)
Updates `pytest` from 8.1.1 to 8.3.2
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.1.1...8.3.2)
Updates `lmdb` from 1.4.1 to 1.5.1
- [Changelog](https://github.com/jnwatson/py-lmdb/blob/master/ChangeLog)
- [Commits](https://github.com/jnwatson/py-lmdb/compare/py-lmdb_1.4.1...py-lmdb_1.5.1)
Updates `redis` from 5.0.4 to 5.0.8
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.4...v5.0.8)
Updates `pymongo` from 4.6.3 to 4.8.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.6.3...4.8.0)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-major
dependency-group: requirements
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: setuptools-scm
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: pytest
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: lmdb
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump the actions group with 2 updates (#2087)
Bumps the actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `actions/setup-python` from 5.1.0 to 5.1.1
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.1.0...v5.1.1)
Updates `pypa/gh-action-pypi-publish` from 1.8.14 to 1.9.0
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.14...v1.9.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* [v2] Drop support for Python 3.9 (#2074)
* Drop support for Python 3.9
* Ignore B905 ruff rule
* Fix release notes
* Fix Array.__array__ for numpy 2.1 (#2106)
* Fix Array.__array__ for numpy 2.1
* Add changelog
* Depend on np.array for array coercions
* Bump test version of numcodecs (#2114)
* Bump test version of numcodecs
* Fix test for numcodecs 0.13
* fix: numpy 1.24 compat for Array.__array__ (#2123)
* Deprecate N5Store (#2103)
* deprecate(n5): add deprecation warning to N5Store
* also deprecate N5FSStore
* docs
* fix doc
* Run tests on numpy 1.23 (#2124)
* Bump the requirements group across 1 directory with 3 updates (#2129)
Bumps the requirements group with 3 updates in the / directory: [numpy](https://github.com/numpy/numpy), [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) and [azure-storage-blob](https://github.com/Azure/azure-sdk-for-python).
Updates `numpy` from 2.0.1 to 2.1.0
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.0.1...v2.1.0)
Updates `ipywidgets` from 8.1.3 to 8.1.5
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.3...8.1.5)
Updates `azure-storage-blob` from 12.16.0 to 12.21.0
- [Release notes](https://github.com/Azure/azure-sdk-for-python/releases)
- [Changelog](https://github.com/Azure/azure-sdk-for-python/blob/main/doc/esrp_release.md)
- [Commits](https://github.com/Azure/azure-sdk-for-python/compare/azure-storage-blob_12.16.0...azure-storage-blob_12.21.0)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: azure-storage-blob
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore: bump minimum numpy version to 1.24 (#2127)
* chore: bump minimum version to 1.24
* Update .github/workflows/python-package.yml
* Remove un-needed package installs in CI (#2095)
* Bump the actions group with 2 updates (#2146)
Bumps the actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `actions/setup-python` from 5.1.1 to 5.2.0
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.1.1...v5.2.0)
Updates `pypa/gh-action-pypi-publish` from 1.9.0 to 1.10.0
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.9.0...v1.10.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump numpy from 2.1.0 to 2.1.1 in the requirements group (#2151)
Bumps the requirements group with 1 update: [numpy](https://github.com/numpy/numpy).
Updates `numpy` from 2.1.0 to 2.1.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.0...v2.1.1)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore(docs): update release notes ahead of 2.18.4 (#2152)
* Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1 in the actions group (#2161)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.0 to 1.10.1
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.0...v1.10.1)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* [docs] remove primary sidebar from tutorial (#2142)
* remove primary sidebar from tutorial
* lint
* Bump pytest from 8.3.2 to 8.3.3 in the requirements group (#2172)
Bumps the requirements group with 1 update: [pytest](https://github.com/pytest-dev/pytest).
Updates `pytest` from 8.3.2 to 8.3.3
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.3.2...8.3.3)
---
updated-dependencies:
- dependency-name: pytest
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump pypa/gh-action-pypi-publish in the actions group (#2220)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.1 to 1.10.2
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.1...v1.10.2)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Update TEAM.md (#2227)
* Bump the requirements group across 1 directory with 3 updates (#2284)
Bumps the requirements group with 3 updates in the / directory: [redis](https://github.com/redis/redis-py), [pymongo](https://github.com/mongodb/mongo-python-driver) and [h5py](https://github.com/h5py/h5py).
Updates `redis` from 5.0.8 to 5.1.0
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.8...v5.1.0)
Updates `pymongo` from 4.8.0 to 4.10.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.8.0...4.10.0)
Updates `h5py` from 3.11.0 to 3.12.1
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](https://github.com/h5py/h5py/compare/3.11.0...3.12.1)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: h5py
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump pymongo from 4.10.0 to 4.10.1 in the requirements group (#2288)
Bumps the requirements group with 1 update: [pymongo](https://github.com/mongodb/mongo-python-driver).
Updates `pymongo` from 4.10.0 to 4.10.1
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.10.0...4.10.1)
---
updated-dependencies:
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Fix low contrast box titles (#2287) (#2292)
* Bump pypa/gh-action-pypi-publish in the actions group (#2304)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.2 to 1.10.3
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.2...v1.10.3)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump the requirements group with 2 updates (#2303)
Bumps the requirements group with 2 updates: [numpy](https://github.com/numpy/numpy) and [redis](https://github.com/redis/redis-py).
Updates `numpy` from 2.1.1 to 2.1.2
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.1...v2.1.2)
Updates `redis` from 5.1.0 to 5.1.1
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.1.0...v5.1.1)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump numcodecs from 0.13.0 to 0.13.1 in the requirements group (#2326)
Bumps the requirements group with 1 update: [numcodecs](https://github.com/zarr-developers/numcodecs).
Updates `numcodecs` from 0.13.0 to 0.13.1
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.rst)
- [Commits](https://github.com/zarr-developers/numcodecs/compare/v0.13.0...v0.13.1)
---
updated-dependencies:
- dependency-name: numcodecs
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* remove zarr.types from v2
---------
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Co-authored-by: David Stansby <dstansby@gmail.com>
Co-authored-by: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com>
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: jakirkham <jakirkham@gmail.com>
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Bump actions/setup-python from 4.7.1 to 5.0.0 by dependabot[bot] · Pull Request #1605 · zarr-developers/zarr-python · GitHub
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Bump actions/setup-python from 4.7.1 to 5.0.0 - #1605
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Bump actions/setup-python from 4.7.1 to 5.0.0#1605
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Bumps actions/setup-python from 4.7.1 to 5.0.0.
Release notes
Sourced from actions/setup-python's releases.
v5.0.0
What's Changed
In scope of this release, we update node version runtime from node16 to node20 (actions/setup-python#772). Besides, we update dependencies to the latest versions.
Full Changelog: actions/setup-python@v4.8.0...v5.0.0
v4.8.0
What's Changed
In scope of this release we added support for GraalPy (actions/setup-python#694). You can use this snippet to set up GraalPy:
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v4 with:
python-version: 'graalpy-22.3' - run: python my_script.py
Besides, the release contains such changes as:
New Contributors
Full Changelog: actions/setup-python@v4...v4.8.0
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@dependabot
Bump actions/setup-python from 4.7.1 to 5.0.0
cf76095
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-major
...
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Dependabot tried to merge this PR, but received the following error from GitHub:
At least 1 approving review is required by reviewers with write access.

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Bump actions/setup-python from 4.7.1 to 5.0.0 (zarr-developers#1605)
a5b4b90
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4.7.1...v5.0.0)
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jhamman added a commit
that referenced
this pull request
Oct 11, 2024
@jhamman@dependabot
@janickm@dstansby@DimitriPapadopoulos@d-v-b@joshmoore@pre-commit-ci@jakirkham@jeffpeck10x@normanrz@sanketverma1704@hoodmane@oeway@DahnJ@dcherian@itcarroll@martindurant@rabernat@sneakers-the-rat
V3 main sync w/ merge (#2335)
ce5f53e
* Bump pypa/gh-action-pypi-publish from 1.8.10 to 1.8.11 (#1586)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.10 to 1.8.11.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.10...v1.8.11)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
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* Bump conda-incubator/setup-miniconda from 2.3.0 to 3.0.1 (#1587)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 2.3.0 to 3.0.1.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v2.3.0...v3.0.1)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
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* * Cache result of FSStore._fsspec_installed (#1581)
Prevent runtime-overhead in doing this check multiple times
* Bump version of black in pre-commit (#1559)
* Use list comprehension where applicable (#1555)
Even if this is only a test, list comprehensions are faster than
repeatedly call append().
Also use tuple instead of list when possible.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Bump numcodecs from 0.11.0 to 0.12.1 (#1580)
Bumps [numcodecs](https://github.com/zarr-developers/numcodecs) from 0.11.0 to 0.12.1.
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.rst)
- [Commits](https://github.com/zarr-developers/numcodecs/compare/v0.11.0...v0.12.1)
---
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- dependency-name: numcodecs
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* Use format specification mini-language to format string (#1558)
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Single startswith() call instead of multiple ones (#1556)
It's faster and probably more readable.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump pymongo from 4.5.0 to 4.6.1 (#1585)
Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.5.0 to 4.6.1.
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.5.0...4.6.1)
---
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* Move codespell options around (#1196)
Starting with codespell 2.2.2, options can be specified in
`pyrpoject.toml` in addition to `setup.cfg`:
https://github.com/codespell-project/codespell#using-a-config-file
Specifying options in a config file instead of command line options in
`.pre-commit-config.yaml` ensures codespell uses the same options when
run as pre-commit hook or from the command line in the repository root
directory.
* Bump fsspec from 2023.10.0 to 2023.12.1 (#1600)
* Bump fsspec from 2023.10.0 to 2023.12.1
Bumps [fsspec](https://github.com/fsspec/filesystem_spec) from 2023.10.0 to 2023.12.1.
- [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.10.0...2023.12.1)
---
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- dependency-name: fsspec
dependency-type: direct:development
update-type: version-update:semver-minor
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* Update s3fs as well
* Fix s3fs
---------
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* Add type hints to zarr.create (#1536)
* Add type hints to zarr.create
* Use protocol for MetaArray
* Use protocol for Synchronizer
* Fix Path typing
* Add release note
* Fix dim separator typing
* Ignore ... in coverage reporting
* Fix chunk typing
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Remove unused mypy ignore comments (#1602)
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Bump actions/setup-python from 4.7.1 to 5.0.0 (#1605)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
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* Bump github/codeql-action from 2 to 3 (#1609)
Bumps [github/codeql-action](https://github.com/github/codeql-action) from 2 to 3.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/github/codeql-action/compare/v2...v3)
---
updated-dependencies:
- dependency-name: github/codeql-action
dependency-type: direct:production
update-type: version-update:semver-major
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* chore: update pre-commit hooks (#1448)
* chore: update pre-commit hooks
updates:
- https://github.com/charliermarsh/ruff-pre-commit → https://github.com/astral-sh/ruff-pre-commit
- [github.com/astral-sh/ruff-pre-commit: v0.0.224 → v0.1.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.224...v0.1.8)
- [github.com/psf/black: 23.10.1 → 23.12.0](https://github.com/psf/black/compare/23.10.1...23.12.0)
- [github.com/codespell-project/codespell: v2.2.5 → v2.2.6](https://github.com/codespell-project/codespell/compare/v2.2.5...v2.2.6)
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.4.0...v4.5.0)
- [github.com/pre-commit/mirrors-mypy: v1.3.0 → v1.7.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.3.0...v1.7.1)
* Attempt to fix ruff
* Use isinstance
---------
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* chore: update pre-commit hooks (#1618)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.8 → v0.1.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.8...v0.1.9)
- [github.com/psf/black: 23.12.0 → 23.12.1](https://github.com/psf/black/compare/23.12.0...23.12.1)
- [github.com/pre-commit/mirrors-mypy: v1.7.1 → v1.8.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.7.1...v1.8.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Bump fsspec from 2023.12.1 to 2023.12.2 (#1606)
* Bump fsspec from 2023.12.1 to 2023.12.2
Bumps [fsspec](https://github.com/fsspec/filesystem_spec) from 2023.12.1 to 2023.12.2.
- [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.12.1...2023.12.2)
---
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- dependency-name: fsspec
dependency-type: direct:development
update-type: version-update:semver-patch
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* Update requirements_dev_optional.txt
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* Bump pytest-doctestplus from 1.0.0 to 1.1.0 (#1619)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.0.0 to 1.1.0.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.0.0...v1.1.0)
---
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- dependency-name: pytest-doctestplus
dependency-type: direct:development
update-type: version-update:semver-minor
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* Bump pytest from 7.4.3 to 7.4.4 (#1622)
* chore: update pre-commit hooks (#1626)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.1.11](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.9...v0.1.11)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Create TEAM.md (#1628)
* Drop python 3.8 and numpy 1.20 (#1557)
* Drop 3.8 and add 3.12
* Try removing line_profiler
* Also bump the minimal numpy to 1.21
* Drop 3.12 again
* Revert "Try removing line_profiler"
This reverts commit 837854bec99a9d25aece2ead9666f01690d228cc.
* Update release.rst
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: jakirkham <jakirkham@gmail.com>
* Add Norman Rzepka to core-dev team (#1630)
* chore: update pre-commit hooks (#1633)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.11 → v0.1.13](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.11...v0.1.13)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Bump actions/download-artifact from 3 to 4 (#1611)
* Bump actions/download-artifact from 3 to 4
Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4.
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](https://github.com/actions/download-artifact/compare/v3...v4)
---
updated-dependencies:
- dependency-name: actions/download-artifact
dependency-type: direct:production
update-type: version-update:semver-major
...
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* Also bump upload-artifact
see https://github.com/actions/download-artifact?tab=readme-ov-file#breaking-changes
> Downloading artifacts that were created from action/upload-artifact@v3 and below are not supported.
---------
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Update tutorial.rst to include section about accessing Zip Files on S3 (#1615)
* Update tutorial.rst to include section about accessing Zip Files on S3
Per discussion here, add information about about accessing zip files on s3:
https://github.com/zarr-developers/zarr-python/discussions/1613
* Update release.rst
* Implement d-v-b's suggestions
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* doc(v3): add v3 roadmap and design document (#1583)
* doc(v3): add v3 roadmap and design document
* Update v3-roadmap-and-design.md
* updates after latest round of reviews
* Update v3-roadmap-and-design.md
Co-authored-by: Norman Rzepka <code@normanrz.com>
* Update v3-roadmap-and-design.md
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
---------
Co-authored-by: Norman Rzepka <code@normanrz.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore: update pre-commit hooks (#1636)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.13 → v0.1.14](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.13...v0.1.14)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix zarr sync (#1663)
This patch removes fasteners and disables zarr.sync which uses process and thread
Co-authored-by: Wei Ouyang <oeway007@gmail.com>
* Update release.rst (#1621)
* Update release.rst
* Update release.rst
* Change 2.16.2 → 2.17.0
* Update moto for test_s3
* Skip bsddb3 tests to prevent warning failure
* Fix more user warning tests
* Fix even more user warning tests
* Skip coverage for importorskips
* Move to have_X skip method for deps
* Update release.rst (PR#1663)
* Fix test_core.py 'compile' issues
* Add black formatting
* Drop Windows/3.9 build due to unrelated failures
* fix typo
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Bump numpy from 1.24.3 to 1.26.1 (#1543)
Bumps [numpy](https://github.com/numpy/numpy) from 1.24.3 to 1.26.1.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.24.3...v1.26.1)
---
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* chore: update pre-commit hooks (#1642)
* chore: update pre-commit hooks
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.14 → v0.2.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.14...v0.2.1)
- [github.com/psf/black: 23.12.1 → 24.2.0](https://github.com/psf/black/compare/23.12.1...24.2.0)
* run black incl. comments for '...'
---------
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* Bump ipywidgets from 8.1.0 to 8.1.1 (#1538)
Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.1.0 to 8.1.1.
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.0...8.1.1)
---
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- dependency-name: ipywidgets
dependency-type: direct:development
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* Proper argument for numpy.reshape (#1425)
`numpy.reshape` not only accepts a tuple of ints, but also a simple int.
Besides `(10)` is not a tuple and is identical to `10`, unlike `(10,)`.
* Bump ipywidgets from 8.1.1 to 8.1.2 (#1666)
Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.1.1 to 8.1.2.
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.1...8.1.2)
---
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- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
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* docs: ZIP-related tweaks (#1641)
* docs: use 'ZIP archive' instead of 'zip file'; clarify utility of caching in s3 + ZIP example; style
* docs: update release notes, correct spelling of greg lee's name in past release notes, and fix markup in past release notes
* docs: use 'ZIP archive' instead of 'zip file'; clarify utility of caching in s3 + ZIP example; style
* docs: update release notes, correct spelling of greg lee's name in past release notes, and fix markup in past release notes
* Bump numpy from 1.26.1 to 1.26.4 (#1669)
Bumps [numpy](https://github.com/numpy/numpy) from 1.26.1 to 1.26.4.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.1...v1.26.4)
---
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- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
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* Change occurrences of % and format() to f-strings (#1423)
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* chore: update pre-commit hooks (#1672)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.1 → v0.2.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.1...v0.2.2)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Bump pymongo from 4.6.1 to 4.6.2 (#1674)
Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.6.1 to 4.6.2.
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/4.6.2/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.6.1...4.6.2)
---
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- dependency-name: pymongo
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update-type: version-update:semver-patch
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* Bump conda-incubator/setup-miniconda from 3.0.1 to 3.0.2 (#1677)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.1 to 3.0.2.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.1...v3.0.2)
---
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- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
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* Update config.yml with Zulip
* Type dimension separator (#1620)
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Replace Gitter with new Zulip Chat link (#1685)
* Replace Gitter with Zulip
* Replace Gitter with Zulip in remaining places
* Bump redis from 5.0.1 to 5.0.2 (#1688)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.1 to 5.0.2.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.1...v5.0.2)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
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* Bump pypa/gh-action-pypi-publish from 1.8.11 to 1.8.12 (#1691)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.11 to 1.8.12.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.11...v1.8.12)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
...
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* Bump pytest-doctestplus from 1.1.0 to 1.2.0 (#1693)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.1.0 to 1.2.0.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.1.0...v1.2.0)
---
updated-dependencies:
- dependency-name: pytest-doctestplus
dependency-type: direct:development
update-type: version-update:semver-minor
...
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* Fix RTD build (#1694)
* Update release.rst for v2.17.1 (#1673)
* Update release.rst for v2.17.1
* Change the copyright year from 2023 → 2024.
* Update release.rst for v2.17.1
* Bump pytest-timeout from 2.2.0 to 2.3.1 (#1697)
Bumps [pytest-timeout](https://github.com/pytest-dev/pytest-timeout) from 2.2.0 to 2.3.1.
- [Commits](https://github.com/pytest-dev/pytest-timeout/compare/2.2.0...2.3.1)
---
updated-dependencies:
- dependency-name: pytest-timeout
dependency-type: direct:development
update-type: version-update:semver-minor
...
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* Bump conda-incubator/setup-miniconda from 3.0.2 to 3.0.3 (#1690)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.2 to 3.0.3.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.2...v3.0.3)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
...
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Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* docs(tutorial.rst): fix link to GCSMap (#1689)
* Update installation.rst stating version support policy (#1665)
* Update installation.rst stating version support policy
* Update docs/installation.rst
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Update docs/installation.rst
---------
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Bump pypa/gh-action-pypi-publish from 1.8.12 to 1.8.14 (#1700)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.12 to 1.8.14.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.12...v1.8.14)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
...
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* Bump pytest-doctestplus from 1.2.0 to 1.2.1 (#1699)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.2.0 to 1.2.1.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.2.0...v1.2.1)
---
updated-dependencies:
- dependency-name: pytest-doctestplus
dependency-type: direct:development
update-type: version-update:semver-patch
...
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Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Bump redis from 5.0.2 to 5.0.3 (#1698)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.2 to 5.0.3.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.2...v5.0.3)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* Add Python 3.12 to CI (#1719)
* Update python-package.yml
* bump numpy versions
* bump min python version
* Update release.rst
* Bump pytest-cov from 4.1.0 to 5.0.0 (#1722)
Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 4.1.0 to 5.0.0.
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest-cov/compare/v4.1.0...v5.0.0)
---
updated-dependencies:
- dependency-name: pytest-cov
dependency-type: direct:development
update-type: version-update:semver-major
...
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* chore: update pre-commit hooks (#1708)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.2 → v0.3.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.2...v0.3.3)
- [github.com/psf/black: 24.2.0 → 24.3.0](https://github.com/psf/black/compare/24.2.0...24.3.0)
- [github.com/pre-commit/mirrors-mypy: v1.8.0 → v1.9.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.8.0...v1.9.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore: update pre-commit hooks (#1723)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.3 → v0.3.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.3...v0.3.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix release notes (following #1719) (#1725)
* Override ipython repr methods. (#1724)
Closes #1716
This avoids expensive lookups against object stores.
* Bump pymongo from 4.6.2 to 4.6.3 (#1729)
* Remove v1 and v2 specification (#1582)
* Remove v1 and v2 specification
* fix warning
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* chore: update pre-commit hooks (#1738)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.4 → v0.3.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.4...v0.3.5)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Optimize Array.info and Group.info (#1733)
* Optimize Array.info.
Avoid repeated computes of the same value (getsize)
* Don't have InfoReporter query items twice.
Apparently IPython will run both __repr__ and _repr_html_
so we were calling `getsize` twice.
* Group too
* Apply suggestions from code review
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
---------
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Bump actions/setup-python from 5.0.0 to 5.1.0 (#1736)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.0.0 to 5.1.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.0.0...v5.1.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-minor
...
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* Couple fixes (#1737)
* Use `is` when comparing `type` of two objects
* Unnecessary `None` provided as default
* Fix tests with Pytest 8 (#1714)
* Bump pytest version
* Use editable install when testing
---------
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Avoid redundant __contains__ (#1739)
Let's try grabbing the array.json and group.json files,
and check for `*NotFoundError`, instead of using contains first.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Array & Group: Use already loaded attributes to populate cache. (#1734)
* Array: Use already loaded attributes to populate cache.
* Group: Use already loaded attributes to populate cache.
* Fix
* Add release note
* Optimize attribute setting (#1741)
* Optimize attribute setting
* Add release note
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Make sure fs exceptions are raised if not MissingFs exceptions (clone) (#1604)
* Make sure fs exceptions are raised if not Missing
* lint
* add missing argument in tests, lint
* clear memory filesystem during test
* improve commenting
* add memory_store fixture, getitems performance
* Update release.rst
* improve FSStore.test_exception coverage
---------
Co-authored-by: Martin Durant <martin.durant@alumni.utoronto.ca>
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore(release): update changelog for 2.17.2 (#1775)
* chore(docs): reset release notes as unreleased (#1776)
* Bump codecov/codecov-action from 3 to 4 (#1647)
* Bump codecov/codecov-action from 3 to 4
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v3...v4)
---
updated-dependencies:
- dependency-name: codecov/codecov-action
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
* Set codecov env
---------
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Update release.rst for v2.17.2 (#1778)
* Update release.rst for v2.17.2
* Minor edits
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Deprecate the experimental v3 implementation (#1802)
* deprecate(exp-v3): Add a future warning about the pending removal of the experimental v3 implementation
* ignore warning
* add test
* chore: update pre-commit hooks (#1779)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.3.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.5...v0.3.7)
- [github.com/psf/black: 24.3.0 → 24.4.0](https://github.com/psf/black/compare/24.3.0...24.4.0)
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v4.6.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix `is_total_slice` for size-1 dimensions (#1800)
Closes #1730
Co-authored-by: Ryan Abernathey <ryan.abernathey@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* add note to the top of the release page noting the plan for 2.18.* and 3.0 (#1816)
* Bump conda-incubator/setup-miniconda from 3.0.3 to 3.0.4 (#1824)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.3 to 3.0.4.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.3...v3.0.4)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
...
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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* dep(docs): deprecate experimental v3 support in docs (#1807)
* dep(docs): deprecate experimental v3 support in docs
* Apply suggestions from code review
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
---------
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Bump h5py from 3.10.0 to 3.11.0 (#1786)
Bumps [h5py](https://github.com/h5py/h5py) from 3.10.0 to 3.11.0.
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](https://github.com/h5py/h5py/compare/3.10.0...3.11.0)
---
updated-dependencies:
- dependency-name: h5py
dependency-type: direct:development
update-type: version-update:semver-minor
...
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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump redis from 5.0.3 to 5.0.4 (#1810)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.3 to 5.0.4.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.3...v5.0.4)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* deprecate(stores): add deprecation warnings to stores that we plan to remove in v3 (#1801)
* deprecate(stores): add deprecation warnings to DBMStore, LMDBStore, SQLiteStore, MongoDBStore, RedisStore, and ABSStore
* filter warnings in pytest config
* more deprecation warnings in docstrings
* add release note
* use np.inf instead of PINF/NINF (#1842)
* use np.inf instead of PINF/NINF
* update release notes
* chore: update pre-commit hooks (#1825)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.1 → v0.4.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.1...v0.4.3)
- [github.com/psf/black: 24.4.0 → 24.4.2](https://github.com/psf/black/compare/24.4.0...24.4.2)
- [github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.9.0...v1.10.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Enable ruff/bugbear rules (B) and fix issues (#1702)
* Enable ruff/bugbear rules (B)
As suggested by Repo-Review.
* Fix ruff/bugbear issue (B007)
B007 Loop control variable `key` not used within loop body
https://docs.astral.sh/ruff/rules/unused-loop-control-variable/
* Fix ruff/bugbear issue (B015)
B015 Pointless comparison. Did you mean to assign a value?
Otherwise, prepend `assert` or remove it.
https://docs.astral.sh/ruff/rules/useless-comparison/
* Fix ruff/bugbear issues (B028)
B028 No explicit `stacklevel` keyword argument found
https://docs.astral.sh/ruff/rules/no-explicit-stacklevel/
* Fix ruff/bugbear issues (B904)
B904 Within an `except` clause, raise exceptions with `raise ... from err` or
`raise ... from None` to distinguish them from errors in exception handling
https://docs.astral.sh/ruff/rules/raise-without-from-inside-except/
* Document changes in docs/release.rst
* Disable ruff/bugbear rule (B017)
B017 `pytest.raises(Exception)` should be considered evil
https://docs.astral.sh/ruff/rules/assert-raises-exception/
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Release notes for 2.18.0 (#1843)
* doc: cleanup release notes for 2.18.0
* Update release.rst (#1850)
* Group dependabot updates (#1854)
* chore: update pre-commit hooks (#1876)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.3 → v0.4.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.3...v0.4.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix a regression with scalar indexing due to #1800 (#1875)
* release notes for 2.18.1 (#1885)
* reset release notes (#1886)
* Add zstd to old V3 supported codecs (#1914)
* add zstd to old V3 supported codecs
* get to full test coverage and add release note
* fix pre-commit
* doc: update release notes for 2.18.2 (#1915)
* Drop support for Python 3.9
* Revert "Drop support for Python 3.9"
This reverts commit a054afbbdaf7c8560d0ce5df77af969bc863e335.
* Update TEAM.md (#2071)
* [v2] Fix doctests with numpy 2.0 (#2073)
* Fix version number in built docs (#2044)
* Fix orthogonal indexing with scalar. (#1947)
Co-authored-by: David Stansby <dstansby@gmail.com>
* Bump the requirements group across 1 directory with 7 updates (#2092)
Bumps the requirements group with 7 updates in the / directory:
| Package | From | To |
| --- | --- | --- |
| [numpy](https://github.com/numpy/numpy) | `1.26.4` | `2.0.1` |
| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) | `8.1.2` | `8.1.3` |
| [setuptools-scm](https://github.com/pypa/setuptools_scm) | `8.0.4` | `8.1.0` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.1.1` | `8.3.2` |
| [lmdb](https://github.com/jnwatson/py-lmdb) | `1.4.1` | `1.5.1` |
| [redis](https://github.com/redis/redis-py) | `5.0.4` | `5.0.8` |
| [pymongo](https://github.com/mongodb/mongo-python-driver) | `4.6.3` | `4.8.0` |
Updates `numpy` from 1.26.4 to 2.0.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.4...v2.0.1)
Updates `ipywidgets` from 8.1.2 to 8.1.3
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.2...8.1.3)
Updates `setuptools-scm` from 8.0.4 to 8.1.0
- [Release notes](https://github.com/pypa/setuptools_scm/releases)
- [Changelog](https://github.com/pypa/setuptools_scm/blob/main/CHANGELOG.md)
- [Commits](https://github.com/pypa/setuptools_scm/compare/v8.0.4...v8.1.0)
Updates `pytest` from 8.1.1 to 8.3.2
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.1.1...8.3.2)
Updates `lmdb` from 1.4.1 to 1.5.1
- [Changelog](https://github.com/jnwatson/py-lmdb/blob/master/ChangeLog)
- [Commits](https://github.com/jnwatson/py-lmdb/compare/py-lmdb_1.4.1...py-lmdb_1.5.1)
Updates `redis` from 5.0.4 to 5.0.8
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.4...v5.0.8)
Updates `pymongo` from 4.6.3 to 4.8.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.6.3...4.8.0)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-major
dependency-group: requirements
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: setuptools-scm
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: pytest
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: lmdb
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump the actions group with 2 updates (#2087)
Bumps the actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `actions/setup-python` from 5.1.0 to 5.1.1
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.1.0...v5.1.1)
Updates `pypa/gh-action-pypi-publish` from 1.8.14 to 1.9.0
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.14...v1.9.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* [v2] Drop support for Python 3.9 (#2074)
* Drop support for Python 3.9
* Ignore B905 ruff rule
* Fix release notes
* Fix Array.__array__ for numpy 2.1 (#2106)
* Fix Array.__array__ for numpy 2.1
* Add changelog
* Depend on np.array for array coercions
* Bump test version of numcodecs (#2114)
* Bump test version of numcodecs
* Fix test for numcodecs 0.13
* fix: numpy 1.24 compat for Array.__array__ (#2123)
* Deprecate N5Store (#2103)
* deprecate(n5): add deprecation warning to N5Store
* also deprecate N5FSStore
* docs
* fix doc
* Run tests on numpy 1.23 (#2124)
* Bump the requirements group across 1 directory with 3 updates (#2129)
Bumps the requirements group with 3 updates in the / directory: [numpy](https://github.com/numpy/numpy), [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) and [azure-storage-blob](https://github.com/Azure/azure-sdk-for-python).
Updates `numpy` from 2.0.1 to 2.1.0
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.0.1...v2.1.0)
Updates `ipywidgets` from 8.1.3 to 8.1.5
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.3...8.1.5)
Updates `azure-storage-blob` from 12.16.0 to 12.21.0
- [Release notes](https://github.com/Azure/azure-sdk-for-python/releases)
- [Changelog](https://github.com/Azure/azure-sdk-for-python/blob/main/doc/esrp_release.md)
- [Commits](https://github.com/Azure/azure-sdk-for-python/compare/azure-storage-blob_12.16.0...azure-storage-blob_12.21.0)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: azure-storage-blob
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore: bump minimum numpy version to 1.24 (#2127)
* chore: bump minimum version to 1.24
* Update .github/workflows/python-package.yml
* Remove un-needed package installs in CI (#2095)
* Bump the actions group with 2 updates (#2146)
Bumps the actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `actions/setup-python` from 5.1.1 to 5.2.0
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.1.1...v5.2.0)
Updates `pypa/gh-action-pypi-publish` from 1.9.0 to 1.10.0
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.9.0...v1.10.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump numpy from 2.1.0 to 2.1.1 in the requirements group (#2151)
Bumps the requirements group with 1 update: [numpy](https://github.com/numpy/numpy).
Updates `numpy` from 2.1.0 to 2.1.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.0...v2.1.1)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore(docs): update release notes ahead of 2.18.4 (#2152)
* Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1 in the actions group (#2161)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.0 to 1.10.1
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.0...v1.10.1)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* [docs] remove primary sidebar from tutorial (#2142)
* remove primary sidebar from tutorial
* lint
* Bump pytest from 8.3.2 to 8.3.3 in the requirements group (#2172)
Bumps the requirements group with 1 update: [pytest](https://github.com/pytest-dev/pytest).
Updates `pytest` from 8.3.2 to 8.3.3
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.3.2...8.3.3)
---
updated-dependencies:
- dependency-name: pytest
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump pypa/gh-action-pypi-publish in the actions group (#2220)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.1 to 1.10.2
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.1...v1.10.2)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Update TEAM.md (#2227)
* Bump the requirements group across 1 directory with 3 updates (#2284)
Bumps the requirements group with 3 updates in the / directory: [redis](https://github.com/redis/redis-py), [pymongo](https://github.com/mongodb/mongo-python-driver) and [h5py](https://github.com/h5py/h5py).
Updates `redis` from 5.0.8 to 5.1.0
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.8...v5.1.0)
Updates `pymongo` from 4.8.0 to 4.10.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.8.0...4.10.0)
Updates `h5py` from 3.11.0 to 3.12.1
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](https://github.com/h5py/h5py/compare/3.11.0...3.12.1)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: h5py
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump pymongo from 4.10.0 to 4.10.1 in the requirements group (#2288)
Bumps the requirements group with 1 update: [pymongo](https://github.com/mongodb/mongo-python-driver).
Updates `pymongo` from 4.10.0 to 4.10.1
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.10.0...4.10.1)
---
updated-dependencies:
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Fix low contrast box titles (#2287) (#2292)
* Bump pypa/gh-action-pypi-publish in the actions group (#2304)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.2 to 1.10.3
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.2...v1.10.3)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump the requirements group with 2 updates (#2303)
Bumps the requirements group with 2 updates: [numpy](https://github.com/numpy/numpy) and [redis](https://github.com/redis/redis-py).
Updates `numpy` from 2.1.1 to 2.1.2
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.1...v2.1.2)
Updates `redis` from 5.1.0 to 5.1.1
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.1.0...v5.1.1)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump numcodecs from 0.13.0 to 0.13.1 in the requirements group (#2326)
Bumps the requirements group with 1 update: [numcodecs](https://github.com/zarr-developers/numcodecs).
Updates `numcodecs` from 0.13.0 to 0.13.1
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.rst)
- [Commits](https://github.com/zarr-developers/numcodecs/compare/v0.13.0...v0.13.1)
---
updated-dependencies:
- dependency-name: numcodecs
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* remove zarr.types from v2
---------
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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Janick Martinez Esturo <janick@jme.pub>
Co-authored-by: David Stansby <dstansby@gmail.com>
Co-authored-by: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com>
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: jakirkham <jakirkham@gmail.com>
Co-authored-by: Jeff Peck <jeffrey.peck@10xgenomics.com>
Co-authored-by: Norman Rzepka <code@normanrz.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
Co-authored-by: Hood Chatham <roberthoodchatham@gmail.com>
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Co-authored-by: Daniel Jahn (dahn) <dahnjahn@gmail.com>
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Co-authored-by: Martin Durant <martin.durant@alumni.utoronto.ca>
Co-authored-by: Ryan Abernathey <ryan.abernathey@gmail.com>
Co-authored-by: Jonny Saunders <sneakers-the-rat@protonmail.com>
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Bump actions/setup-python from 4.7.1 to 5.0.0 by dependabot[bot] · Pull Request #1605 · zarr-developers/zarr-python · GitHub
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Bump actions/setup-python from 4.7.1 to 5.0.0 - #1605
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Bump actions/setup-python from 4.7.1 to 5.0.0#1605
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Bumps actions/setup-python from 4.7.1 to 5.0.0.
Release notes
Sourced from actions/setup-python's releases.
v5.0.0
What's Changed
In scope of this release, we update node version runtime from node16 to node20 (actions/setup-python#772). Besides, we update dependencies to the latest versions.
Full Changelog: actions/setup-python@v4.8.0...v5.0.0
v4.8.0
What's Changed
In scope of this release we added support for GraalPy (actions/setup-python#694). You can use this snippet to set up GraalPy:
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v4 with:
python-version: 'graalpy-22.3' - run: python my_script.py
Besides, the release contains such changes as:
New Contributors
Full Changelog: actions/setup-python@v4...v4.8.0
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@dependabot
Bump actions/setup-python from 4.7.1 to 5.0.0
cf76095
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-major
...
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Dependabot tried to merge this PR, but received the following error from GitHub:
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Bump actions/setup-python from 4.7.1 to 5.0.0 (zarr-developers#1605)
a5b4b90
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
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Oct 11, 2024
@jhamman@dependabot
@janickm@dstansby@DimitriPapadopoulos@d-v-b@joshmoore@pre-commit-ci@jakirkham@jeffpeck10x@normanrz@sanketverma1704@hoodmane@oeway@DahnJ@dcherian@itcarroll@martindurant@rabernat@sneakers-the-rat
V3 main sync w/ merge (#2335)
ce5f53e
* Bump pypa/gh-action-pypi-publish from 1.8.10 to 1.8.11 (#1586)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.10 to 1.8.11.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.10...v1.8.11)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
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* Bump conda-incubator/setup-miniconda from 2.3.0 to 3.0.1 (#1587)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 2.3.0 to 3.0.1.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v2.3.0...v3.0.1)
---
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- dependency-name: conda-incubator/setup-miniconda
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* * Cache result of FSStore._fsspec_installed (#1581)
Prevent runtime-overhead in doing this check multiple times
* Bump version of black in pre-commit (#1559)
* Use list comprehension where applicable (#1555)
Even if this is only a test, list comprehensions are faster than
repeatedly call append().
Also use tuple instead of list when possible.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Bump numcodecs from 0.11.0 to 0.12.1 (#1580)
Bumps [numcodecs](https://github.com/zarr-developers/numcodecs) from 0.11.0 to 0.12.1.
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.rst)
- [Commits](https://github.com/zarr-developers/numcodecs/compare/v0.11.0...v0.12.1)
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- dependency-name: numcodecs
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* Use format specification mini-language to format string (#1558)
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Single startswith() call instead of multiple ones (#1556)
It's faster and probably more readable.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump pymongo from 4.5.0 to 4.6.1 (#1585)
Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.5.0 to 4.6.1.
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.5.0...4.6.1)
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* Move codespell options around (#1196)
Starting with codespell 2.2.2, options can be specified in
`pyrpoject.toml` in addition to `setup.cfg`:
https://github.com/codespell-project/codespell#using-a-config-file
Specifying options in a config file instead of command line options in
`.pre-commit-config.yaml` ensures codespell uses the same options when
run as pre-commit hook or from the command line in the repository root
directory.
* Bump fsspec from 2023.10.0 to 2023.12.1 (#1600)
* Bump fsspec from 2023.10.0 to 2023.12.1
Bumps [fsspec](https://github.com/fsspec/filesystem_spec) from 2023.10.0 to 2023.12.1.
- [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.10.0...2023.12.1)
---
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- dependency-name: fsspec
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* Update s3fs as well
* Fix s3fs
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* Add type hints to zarr.create (#1536)
* Add type hints to zarr.create
* Use protocol for MetaArray
* Use protocol for Synchronizer
* Fix Path typing
* Add release note
* Fix dim separator typing
* Ignore ... in coverage reporting
* Fix chunk typing
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Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Remove unused mypy ignore comments (#1602)
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Bump actions/setup-python from 4.7.1 to 5.0.0 (#1605)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v4.7.1...v5.0.0)
---
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* Bump github/codeql-action from 2 to 3 (#1609)
Bumps [github/codeql-action](https://github.com/github/codeql-action) from 2 to 3.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/github/codeql-action/compare/v2...v3)
---
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- dependency-name: github/codeql-action
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* chore: update pre-commit hooks (#1448)
* chore: update pre-commit hooks
updates:
- https://github.com/charliermarsh/ruff-pre-commit → https://github.com/astral-sh/ruff-pre-commit
- [github.com/astral-sh/ruff-pre-commit: v0.0.224 → v0.1.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.224...v0.1.8)
- [github.com/psf/black: 23.10.1 → 23.12.0](https://github.com/psf/black/compare/23.10.1...23.12.0)
- [github.com/codespell-project/codespell: v2.2.5 → v2.2.6](https://github.com/codespell-project/codespell/compare/v2.2.5...v2.2.6)
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.4.0...v4.5.0)
- [github.com/pre-commit/mirrors-mypy: v1.3.0 → v1.7.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.3.0...v1.7.1)
* Attempt to fix ruff
* Use isinstance
---------
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* chore: update pre-commit hooks (#1618)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.8 → v0.1.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.8...v0.1.9)
- [github.com/psf/black: 23.12.0 → 23.12.1](https://github.com/psf/black/compare/23.12.0...23.12.1)
- [github.com/pre-commit/mirrors-mypy: v1.7.1 → v1.8.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.7.1...v1.8.0)
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* Bump fsspec from 2023.12.1 to 2023.12.2 (#1606)
* Bump fsspec from 2023.12.1 to 2023.12.2
Bumps [fsspec](https://github.com/fsspec/filesystem_spec) from 2023.12.1 to 2023.12.2.
- [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.12.1...2023.12.2)
---
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* Update requirements_dev_optional.txt
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* Bump pytest-doctestplus from 1.0.0 to 1.1.0 (#1619)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.0.0 to 1.1.0.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.0.0...v1.1.0)
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* Bump pytest from 7.4.3 to 7.4.4 (#1622)
* chore: update pre-commit hooks (#1626)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.1.11](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.9...v0.1.11)
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* Create TEAM.md (#1628)
* Drop python 3.8 and numpy 1.20 (#1557)
* Drop 3.8 and add 3.12
* Try removing line_profiler
* Also bump the minimal numpy to 1.21
* Drop 3.12 again
* Revert "Try removing line_profiler"
This reverts commit 837854bec99a9d25aece2ead9666f01690d228cc.
* Update release.rst
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: jakirkham <jakirkham@gmail.com>
* Add Norman Rzepka to core-dev team (#1630)
* chore: update pre-commit hooks (#1633)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.11 → v0.1.13](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.11...v0.1.13)
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* Bump actions/download-artifact from 3 to 4 (#1611)
* Bump actions/download-artifact from 3 to 4
Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4.
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](https://github.com/actions/download-artifact/compare/v3...v4)
---
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- dependency-name: actions/download-artifact
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* Also bump upload-artifact
see https://github.com/actions/download-artifact?tab=readme-ov-file#breaking-changes
> Downloading artifacts that were created from action/upload-artifact@v3 and below are not supported.
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* Update tutorial.rst to include section about accessing Zip Files on S3 (#1615)
* Update tutorial.rst to include section about accessing Zip Files on S3
Per discussion here, add information about about accessing zip files on s3:
https://github.com/zarr-developers/zarr-python/discussions/1613
* Update release.rst
* Implement d-v-b's suggestions
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* doc(v3): add v3 roadmap and design document (#1583)
* doc(v3): add v3 roadmap and design document
* Update v3-roadmap-and-design.md
* updates after latest round of reviews
* Update v3-roadmap-and-design.md
Co-authored-by: Norman Rzepka <code@normanrz.com>
* Update v3-roadmap-and-design.md
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
---------
Co-authored-by: Norman Rzepka <code@normanrz.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore: update pre-commit hooks (#1636)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.13 → v0.1.14](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.13...v0.1.14)
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* Fix zarr sync (#1663)
This patch removes fasteners and disables zarr.sync which uses process and thread
Co-authored-by: Wei Ouyang <oeway007@gmail.com>
* Update release.rst (#1621)
* Update release.rst
* Update release.rst
* Change 2.16.2 → 2.17.0
* Update moto for test_s3
* Skip bsddb3 tests to prevent warning failure
* Fix more user warning tests
* Fix even more user warning tests
* Skip coverage for importorskips
* Move to have_X skip method for deps
* Update release.rst (PR#1663)
* Fix test_core.py 'compile' issues
* Add black formatting
* Drop Windows/3.9 build due to unrelated failures
* fix typo
---------
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Bump numpy from 1.24.3 to 1.26.1 (#1543)
Bumps [numpy](https://github.com/numpy/numpy) from 1.24.3 to 1.26.1.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.24.3...v1.26.1)
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* chore: update pre-commit hooks (#1642)
* chore: update pre-commit hooks
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.14 → v0.2.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.14...v0.2.1)
- [github.com/psf/black: 23.12.1 → 24.2.0](https://github.com/psf/black/compare/23.12.1...24.2.0)
* run black incl. comments for '...'
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* Bump ipywidgets from 8.1.0 to 8.1.1 (#1538)
Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.1.0 to 8.1.1.
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.0...8.1.1)
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* Proper argument for numpy.reshape (#1425)
`numpy.reshape` not only accepts a tuple of ints, but also a simple int.
Besides `(10)` is not a tuple and is identical to `10`, unlike `(10,)`.
* Bump ipywidgets from 8.1.1 to 8.1.2 (#1666)
Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.1.1 to 8.1.2.
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.1...8.1.2)
---
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- dependency-name: ipywidgets
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* docs: ZIP-related tweaks (#1641)
* docs: use 'ZIP archive' instead of 'zip file'; clarify utility of caching in s3 + ZIP example; style
* docs: update release notes, correct spelling of greg lee's name in past release notes, and fix markup in past release notes
* docs: use 'ZIP archive' instead of 'zip file'; clarify utility of caching in s3 + ZIP example; style
* docs: update release notes, correct spelling of greg lee's name in past release notes, and fix markup in past release notes
* Bump numpy from 1.26.1 to 1.26.4 (#1669)
Bumps [numpy](https://github.com/numpy/numpy) from 1.26.1 to 1.26.4.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.1...v1.26.4)
---
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* Change occurrences of % and format() to f-strings (#1423)
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* chore: update pre-commit hooks (#1672)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.1 → v0.2.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.1...v0.2.2)
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* Bump pymongo from 4.6.1 to 4.6.2 (#1674)
Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.6.1 to 4.6.2.
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/4.6.2/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.6.1...4.6.2)
---
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- dependency-name: pymongo
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* Bump conda-incubator/setup-miniconda from 3.0.1 to 3.0.2 (#1677)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.1 to 3.0.2.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.1...v3.0.2)
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- dependency-name: conda-incubator/setup-miniconda
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* Update config.yml with Zulip
* Type dimension separator (#1620)
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Replace Gitter with new Zulip Chat link (#1685)
* Replace Gitter with Zulip
* Replace Gitter with Zulip in remaining places
* Bump redis from 5.0.1 to 5.0.2 (#1688)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.1 to 5.0.2.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.1...v5.0.2)
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- dependency-name: redis
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* Bump pypa/gh-action-pypi-publish from 1.8.11 to 1.8.12 (#1691)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.11 to 1.8.12.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.11...v1.8.12)
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* Bump pytest-doctestplus from 1.1.0 to 1.2.0 (#1693)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.1.0 to 1.2.0.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.1.0...v1.2.0)
---
updated-dependencies:
- dependency-name: pytest-doctestplus
dependency-type: direct:development
update-type: version-update:semver-minor
...
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* Fix RTD build (#1694)
* Update release.rst for v2.17.1 (#1673)
* Update release.rst for v2.17.1
* Change the copyright year from 2023 → 2024.
* Update release.rst for v2.17.1
* Bump pytest-timeout from 2.2.0 to 2.3.1 (#1697)
Bumps [pytest-timeout](https://github.com/pytest-dev/pytest-timeout) from 2.2.0 to 2.3.1.
- [Commits](https://github.com/pytest-dev/pytest-timeout/compare/2.2.0...2.3.1)
---
updated-dependencies:
- dependency-name: pytest-timeout
dependency-type: direct:development
update-type: version-update:semver-minor
...
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* Bump conda-incubator/setup-miniconda from 3.0.2 to 3.0.3 (#1690)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.2 to 3.0.3.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.2...v3.0.3)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
...
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Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* docs(tutorial.rst): fix link to GCSMap (#1689)
* Update installation.rst stating version support policy (#1665)
* Update installation.rst stating version support policy
* Update docs/installation.rst
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Update docs/installation.rst
---------
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Bump pypa/gh-action-pypi-publish from 1.8.12 to 1.8.14 (#1700)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.12 to 1.8.14.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.12...v1.8.14)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
...
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* Bump pytest-doctestplus from 1.2.0 to 1.2.1 (#1699)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.2.0 to 1.2.1.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.2.0...v1.2.1)
---
updated-dependencies:
- dependency-name: pytest-doctestplus
dependency-type: direct:development
update-type: version-update:semver-patch
...
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Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Bump redis from 5.0.2 to 5.0.3 (#1698)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.2 to 5.0.3.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.2...v5.0.3)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* Add Python 3.12 to CI (#1719)
* Update python-package.yml
* bump numpy versions
* bump min python version
* Update release.rst
* Bump pytest-cov from 4.1.0 to 5.0.0 (#1722)
Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 4.1.0 to 5.0.0.
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest-cov/compare/v4.1.0...v5.0.0)
---
updated-dependencies:
- dependency-name: pytest-cov
dependency-type: direct:development
update-type: version-update:semver-major
...
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* chore: update pre-commit hooks (#1708)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.2 → v0.3.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.2...v0.3.3)
- [github.com/psf/black: 24.2.0 → 24.3.0](https://github.com/psf/black/compare/24.2.0...24.3.0)
- [github.com/pre-commit/mirrors-mypy: v1.8.0 → v1.9.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.8.0...v1.9.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore: update pre-commit hooks (#1723)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.3 → v0.3.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.3...v0.3.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix release notes (following #1719) (#1725)
* Override ipython repr methods. (#1724)
Closes #1716
This avoids expensive lookups against object stores.
* Bump pymongo from 4.6.2 to 4.6.3 (#1729)
* Remove v1 and v2 specification (#1582)
* Remove v1 and v2 specification
* fix warning
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* chore: update pre-commit hooks (#1738)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.4 → v0.3.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.4...v0.3.5)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Optimize Array.info and Group.info (#1733)
* Optimize Array.info.
Avoid repeated computes of the same value (getsize)
* Don't have InfoReporter query items twice.
Apparently IPython will run both __repr__ and _repr_html_
so we were calling `getsize` twice.
* Group too
* Apply suggestions from code review
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
---------
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Bump actions/setup-python from 5.0.0 to 5.1.0 (#1736)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.0.0 to 5.1.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.0.0...v5.1.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-minor
...
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* Couple fixes (#1737)
* Use `is` when comparing `type` of two objects
* Unnecessary `None` provided as default
* Fix tests with Pytest 8 (#1714)
* Bump pytest version
* Use editable install when testing
---------
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Avoid redundant __contains__ (#1739)
Let's try grabbing the array.json and group.json files,
and check for `*NotFoundError`, instead of using contains first.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Array & Group: Use already loaded attributes to populate cache. (#1734)
* Array: Use already loaded attributes to populate cache.
* Group: Use already loaded attributes to populate cache.
* Fix
* Add release note
* Optimize attribute setting (#1741)
* Optimize attribute setting
* Add release note
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Make sure fs exceptions are raised if not MissingFs exceptions (clone) (#1604)
* Make sure fs exceptions are raised if not Missing
* lint
* add missing argument in tests, lint
* clear memory filesystem during test
* improve commenting
* add memory_store fixture, getitems performance
* Update release.rst
* improve FSStore.test_exception coverage
---------
Co-authored-by: Martin Durant <martin.durant@alumni.utoronto.ca>
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore(release): update changelog for 2.17.2 (#1775)
* chore(docs): reset release notes as unreleased (#1776)
* Bump codecov/codecov-action from 3 to 4 (#1647)
* Bump codecov/codecov-action from 3 to 4
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v3...v4)
---
updated-dependencies:
- dependency-name: codecov/codecov-action
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
* Set codecov env
---------
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Update release.rst for v2.17.2 (#1778)
* Update release.rst for v2.17.2
* Minor edits
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Deprecate the experimental v3 implementation (#1802)
* deprecate(exp-v3): Add a future warning about the pending removal of the experimental v3 implementation
* ignore warning
* add test
* chore: update pre-commit hooks (#1779)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.3.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.5...v0.3.7)
- [github.com/psf/black: 24.3.0 → 24.4.0](https://github.com/psf/black/compare/24.3.0...24.4.0)
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v4.6.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix `is_total_slice` for size-1 dimensions (#1800)
Closes #1730
Co-authored-by: Ryan Abernathey <ryan.abernathey@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* add note to the top of the release page noting the plan for 2.18.* and 3.0 (#1816)
* Bump conda-incubator/setup-miniconda from 3.0.3 to 3.0.4 (#1824)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.3 to 3.0.4.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.3...v3.0.4)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
...
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* dep(docs): deprecate experimental v3 support in docs (#1807)
* dep(docs): deprecate experimental v3 support in docs
* Apply suggestions from code review
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
---------
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Bump h5py from 3.10.0 to 3.11.0 (#1786)
Bumps [h5py](https://github.com/h5py/h5py) from 3.10.0 to 3.11.0.
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](https://github.com/h5py/h5py/compare/3.10.0...3.11.0)
---
updated-dependencies:
- dependency-name: h5py
dependency-type: direct:development
update-type: version-update:semver-minor
...
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Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump redis from 5.0.3 to 5.0.4 (#1810)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.3 to 5.0.4.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.3...v5.0.4)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* deprecate(stores): add deprecation warnings to stores that we plan to remove in v3 (#1801)
* deprecate(stores): add deprecation warnings to DBMStore, LMDBStore, SQLiteStore, MongoDBStore, RedisStore, and ABSStore
* filter warnings in pytest config
* more deprecation warnings in docstrings
* add release note
* use np.inf instead of PINF/NINF (#1842)
* use np.inf instead of PINF/NINF
* update release notes
* chore: update pre-commit hooks (#1825)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.1 → v0.4.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.1...v0.4.3)
- [github.com/psf/black: 24.4.0 → 24.4.2](https://github.com/psf/black/compare/24.4.0...24.4.2)
- [github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.9.0...v1.10.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Enable ruff/bugbear rules (B) and fix issues (#1702)
* Enable ruff/bugbear rules (B)
As suggested by Repo-Review.
* Fix ruff/bugbear issue (B007)
B007 Loop control variable `key` not used within loop body
https://docs.astral.sh/ruff/rules/unused-loop-control-variable/
* Fix ruff/bugbear issue (B015)
B015 Pointless comparison. Did you mean to assign a value?
Otherwise, prepend `assert` or remove it.
https://docs.astral.sh/ruff/rules/useless-comparison/
* Fix ruff/bugbear issues (B028)
B028 No explicit `stacklevel` keyword argument found
https://docs.astral.sh/ruff/rules/no-explicit-stacklevel/
* Fix ruff/bugbear issues (B904)
B904 Within an `except` clause, raise exceptions with `raise ... from err` or
`raise ... from None` to distinguish them from errors in exception handling
https://docs.astral.sh/ruff/rules/raise-without-from-inside-except/
* Document changes in docs/release.rst
* Disable ruff/bugbear rule (B017)
B017 `pytest.raises(Exception)` should be considered evil
https://docs.astral.sh/ruff/rules/assert-raises-exception/
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Release notes for 2.18.0 (#1843)
* doc: cleanup release notes for 2.18.0
* Update release.rst (#1850)
* Group dependabot updates (#1854)
* chore: update pre-commit hooks (#1876)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.3 → v0.4.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.3...v0.4.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix a regression with scalar indexing due to #1800 (#1875)
* release notes for 2.18.1 (#1885)
* reset release notes (#1886)
* Add zstd to old V3 supported codecs (#1914)
* add zstd to old V3 supported codecs
* get to full test coverage and add release note
* fix pre-commit
* doc: update release notes for 2.18.2 (#1915)
* Drop support for Python 3.9
* Revert "Drop support for Python 3.9"
This reverts commit a054afbbdaf7c8560d0ce5df77af969bc863e335.
* Update TEAM.md (#2071)
* [v2] Fix doctests with numpy 2.0 (#2073)
* Fix version number in built docs (#2044)
* Fix orthogonal indexing with scalar. (#1947)
Co-authored-by: David Stansby <dstansby@gmail.com>
* Bump the requirements group across 1 directory with 7 updates (#2092)
Bumps the requirements group with 7 updates in the / directory:
| Package | From | To |
| --- | --- | --- |
| [numpy](https://github.com/numpy/numpy) | `1.26.4` | `2.0.1` |
| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) | `8.1.2` | `8.1.3` |
| [setuptools-scm](https://github.com/pypa/setuptools_scm) | `8.0.4` | `8.1.0` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.1.1` | `8.3.2` |
| [lmdb](https://github.com/jnwatson/py-lmdb) | `1.4.1` | `1.5.1` |
| [redis](https://github.com/redis/redis-py) | `5.0.4` | `5.0.8` |
| [pymongo](https://github.com/mongodb/mongo-python-driver) | `4.6.3` | `4.8.0` |
Updates `numpy` from 1.26.4 to 2.0.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.4...v2.0.1)
Updates `ipywidgets` from 8.1.2 to 8.1.3
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.2...8.1.3)
Updates `setuptools-scm` from 8.0.4 to 8.1.0
- [Release notes](https://github.com/pypa/setuptools_scm/releases)
- [Changelog](https://github.com/pypa/setuptools_scm/blob/main/CHANGELOG.md)
- [Commits](https://github.com/pypa/setuptools_scm/compare/v8.0.4...v8.1.0)
Updates `pytest` from 8.1.1 to 8.3.2
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.1.1...8.3.2)
Updates `lmdb` from 1.4.1 to 1.5.1
- [Changelog](https://github.com/jnwatson/py-lmdb/blob/master/ChangeLog)
- [Commits](https://github.com/jnwatson/py-lmdb/compare/py-lmdb_1.4.1...py-lmdb_1.5.1)
Updates `redis` from 5.0.4 to 5.0.8
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.4...v5.0.8)
Updates `pymongo` from 4.6.3 to 4.8.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.6.3...4.8.0)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-major
dependency-group: requirements
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: setuptools-scm
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: pytest
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: lmdb
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump the actions group with 2 updates (#2087)
Bumps the actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `actions/setup-python` from 5.1.0 to 5.1.1
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.1.0...v5.1.1)
Updates `pypa/gh-action-pypi-publish` from 1.8.14 to 1.9.0
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.14...v1.9.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* [v2] Drop support for Python 3.9 (#2074)
* Drop support for Python 3.9
* Ignore B905 ruff rule
* Fix release notes
* Fix Array.__array__ for numpy 2.1 (#2106)
* Fix Array.__array__ for numpy 2.1
* Add changelog
* Depend on np.array for array coercions
* Bump test version of numcodecs (#2114)
* Bump test version of numcodecs
* Fix test for numcodecs 0.13
* fix: numpy 1.24 compat for Array.__array__ (#2123)
* Deprecate N5Store (#2103)
* deprecate(n5): add deprecation warning to N5Store
* also deprecate N5FSStore
* docs
* fix doc
* Run tests on numpy 1.23 (#2124)
* Bump the requirements group across 1 directory with 3 updates (#2129)
Bumps the requirements group with 3 updates in the / directory: [numpy](https://github.com/numpy/numpy), [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) and [azure-storage-blob](https://github.com/Azure/azure-sdk-for-python).
Updates `numpy` from 2.0.1 to 2.1.0
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.0.1...v2.1.0)
Updates `ipywidgets` from 8.1.3 to 8.1.5
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.3...8.1.5)
Updates `azure-storage-blob` from 12.16.0 to 12.21.0
- [Release notes](https://github.com/Azure/azure-sdk-for-python/releases)
- [Changelog](https://github.com/Azure/azure-sdk-for-python/blob/main/doc/esrp_release.md)
- [Commits](https://github.com/Azure/azure-sdk-for-python/compare/azure-storage-blob_12.16.0...azure-storage-blob_12.21.0)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: azure-storage-blob
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore: bump minimum numpy version to 1.24 (#2127)
* chore: bump minimum version to 1.24
* Update .github/workflows/python-package.yml
* Remove un-needed package installs in CI (#2095)
* Bump the actions group with 2 updates (#2146)
Bumps the actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `actions/setup-python` from 5.1.1 to 5.2.0
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.1.1...v5.2.0)
Updates `pypa/gh-action-pypi-publish` from 1.9.0 to 1.10.0
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.9.0...v1.10.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump numpy from 2.1.0 to 2.1.1 in the requirements group (#2151)
Bumps the requirements group with 1 update: [numpy](https://github.com/numpy/numpy).
Updates `numpy` from 2.1.0 to 2.1.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.0...v2.1.1)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore(docs): update release notes ahead of 2.18.4 (#2152)
* Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1 in the actions group (#2161)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.0 to 1.10.1
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.0...v1.10.1)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* [docs] remove primary sidebar from tutorial (#2142)
* remove primary sidebar from tutorial
* lint
* Bump pytest from 8.3.2 to 8.3.3 in the requirements group (#2172)
Bumps the requirements group with 1 update: [pytest](https://github.com/pytest-dev/pytest).
Updates `pytest` from 8.3.2 to 8.3.3
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.3.2...8.3.3)
---
updated-dependencies:
- dependency-name: pytest
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump pypa/gh-action-pypi-publish in the actions group (#2220)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.1 to 1.10.2
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.1...v1.10.2)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Update TEAM.md (#2227)
* Bump the requirements group across 1 directory with 3 updates (#2284)
Bumps the requirements group with 3 updates in the / directory: [redis](https://github.com/redis/redis-py), [pymongo](https://github.com/mongodb/mongo-python-driver) and [h5py](https://github.com/h5py/h5py).
Updates `redis` from 5.0.8 to 5.1.0
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.8...v5.1.0)
Updates `pymongo` from 4.8.0 to 4.10.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.8.0...4.10.0)
Updates `h5py` from 3.11.0 to 3.12.1
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](https://github.com/h5py/h5py/compare/3.11.0...3.12.1)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: h5py
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump pymongo from 4.10.0 to 4.10.1 in the requirements group (#2288)
Bumps the requirements group with 1 update: [pymongo](https://github.com/mongodb/mongo-python-driver).
Updates `pymongo` from 4.10.0 to 4.10.1
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.10.0...4.10.1)
---
updated-dependencies:
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Fix low contrast box titles (#2287) (#2292)
* Bump pypa/gh-action-pypi-publish in the actions group (#2304)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.2 to 1.10.3
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.2...v1.10.3)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump the requirements group with 2 updates (#2303)
Bumps the requirements group with 2 updates: [numpy](https://github.com/numpy/numpy) and [redis](https://github.com/redis/redis-py).
Updates `numpy` from 2.1.1 to 2.1.2
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.1...v2.1.2)
Updates `redis` from 5.1.0 to 5.1.1
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.1.0...v5.1.1)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump numcodecs from 0.13.0 to 0.13.1 in the requirements group (#2326)
Bumps the requirements group with 1 update: [numcodecs](https://github.com/zarr-developers/numcodecs).
Updates `numcodecs` from 0.13.0 to 0.13.1
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.rst)
- [Commits](https://github.com/zarr-developers/numcodecs/compare/v0.13.0...v0.13.1)
---
updated-dependencies:
- dependency-name: numcodecs
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* remove zarr.types from v2
---------
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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Janick Martinez Esturo <janick@jme.pub>
Co-authored-by: David Stansby <dstansby@gmail.com>
Co-authored-by: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com>
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: jakirkham <jakirkham@gmail.com>
Co-authored-by: Jeff Peck <jeffrey.peck@10xgenomics.com>
Co-authored-by: Norman Rzepka <code@normanrz.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
Co-authored-by: Hood Chatham <roberthoodchatham@gmail.com>
Co-authored-by: Wei Ouyang <oeway007@gmail.com>
Co-authored-by: Daniel Jahn (dahn) <dahnjahn@gmail.com>
Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com>
Co-authored-by: Ian Carroll <carroll.ian@gmail.com>
Co-authored-by: Martin Durant <martin.durant@alumni.utoronto.ca>
Co-authored-by: Ryan Abernathey <ryan.abernathey@gmail.com>
Co-authored-by: Jonny Saunders <sneakers-the-rat@protonmail.com>
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Bump actions/setup-python from 4.7.1 to 5.0.0 by dependabot[bot] · Pull Request #1605 · zarr-developers/zarr-python · GitHub
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Bump actions/setup-python from 4.7.1 to 5.0.0 - #1605
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Bump actions/setup-python from 4.7.1 to 5.0.0#1605
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Bumps actions/setup-python from 4.7.1 to 5.0.0.
Release notes
Sourced from actions/setup-python's releases.
v5.0.0
What's Changed
In scope of this release, we update node version runtime from node16 to node20 (actions/setup-python#772). Besides, we update dependencies to the latest versions.
Full Changelog: actions/setup-python@v4.8.0...v5.0.0
v4.8.0
What's Changed
In scope of this release we added support for GraalPy (actions/setup-python#694). You can use this snippet to set up GraalPy:
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v4 with:
python-version: 'graalpy-22.3' - run: python my_script.py
Besides, the release contains such changes as:
New Contributors
Full Changelog: actions/setup-python@v4...v4.8.0
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@dependabot
Bump actions/setup-python from 4.7.1 to 5.0.0
cf76095
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
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Dependabot tried to merge this PR, but received the following error from GitHub:
At least 1 approving review is required by reviewers with write access.

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@dependabot@jhamman
Bump actions/setup-python from 4.7.1 to 5.0.0 (zarr-developers#1605)
a5b4b90
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
jhamman added a commit
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@jhamman@dependabot
@janickm@dstansby@DimitriPapadopoulos@d-v-b@joshmoore@pre-commit-ci@jakirkham@jeffpeck10x@normanrz@sanketverma1704@hoodmane@oeway@DahnJ@dcherian@itcarroll@martindurant@rabernat@sneakers-the-rat
V3 main sync w/ merge (#2335)
ce5f53e
* Bump pypa/gh-action-pypi-publish from 1.8.10 to 1.8.11 (#1586)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.10 to 1.8.11.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.10...v1.8.11)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump conda-incubator/setup-miniconda from 2.3.0 to 3.0.1 (#1587)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 2.3.0 to 3.0.1.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v2.3.0...v3.0.1)
---
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* * Cache result of FSStore._fsspec_installed (#1581)
Prevent runtime-overhead in doing this check multiple times
* Bump version of black in pre-commit (#1559)
* Use list comprehension where applicable (#1555)
Even if this is only a test, list comprehensions are faster than
repeatedly call append().
Also use tuple instead of list when possible.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Bump numcodecs from 0.11.0 to 0.12.1 (#1580)
Bumps [numcodecs](https://github.com/zarr-developers/numcodecs) from 0.11.0 to 0.12.1.
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.rst)
- [Commits](https://github.com/zarr-developers/numcodecs/compare/v0.11.0...v0.12.1)
---
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- dependency-name: numcodecs
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* Use format specification mini-language to format string (#1558)
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Single startswith() call instead of multiple ones (#1556)
It's faster and probably more readable.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump pymongo from 4.5.0 to 4.6.1 (#1585)
Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.5.0 to 4.6.1.
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.5.0...4.6.1)
---
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* Move codespell options around (#1196)
Starting with codespell 2.2.2, options can be specified in
`pyrpoject.toml` in addition to `setup.cfg`:
https://github.com/codespell-project/codespell#using-a-config-file
Specifying options in a config file instead of command line options in
`.pre-commit-config.yaml` ensures codespell uses the same options when
run as pre-commit hook or from the command line in the repository root
directory.
* Bump fsspec from 2023.10.0 to 2023.12.1 (#1600)
* Bump fsspec from 2023.10.0 to 2023.12.1
Bumps [fsspec](https://github.com/fsspec/filesystem_spec) from 2023.10.0 to 2023.12.1.
- [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.10.0...2023.12.1)
---
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- dependency-name: fsspec
dependency-type: direct:development
update-type: version-update:semver-minor
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* Update s3fs as well
* Fix s3fs
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* Add type hints to zarr.create (#1536)
* Add type hints to zarr.create
* Use protocol for MetaArray
* Use protocol for Synchronizer
* Fix Path typing
* Add release note
* Fix dim separator typing
* Ignore ... in coverage reporting
* Fix chunk typing
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Remove unused mypy ignore comments (#1602)
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Bump actions/setup-python from 4.7.1 to 5.0.0 (#1605)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
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* Bump github/codeql-action from 2 to 3 (#1609)
Bumps [github/codeql-action](https://github.com/github/codeql-action) from 2 to 3.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/github/codeql-action/compare/v2...v3)
---
updated-dependencies:
- dependency-name: github/codeql-action
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* chore: update pre-commit hooks (#1448)
* chore: update pre-commit hooks
updates:
- https://github.com/charliermarsh/ruff-pre-commit → https://github.com/astral-sh/ruff-pre-commit
- [github.com/astral-sh/ruff-pre-commit: v0.0.224 → v0.1.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.224...v0.1.8)
- [github.com/psf/black: 23.10.1 → 23.12.0](https://github.com/psf/black/compare/23.10.1...23.12.0)
- [github.com/codespell-project/codespell: v2.2.5 → v2.2.6](https://github.com/codespell-project/codespell/compare/v2.2.5...v2.2.6)
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.4.0...v4.5.0)
- [github.com/pre-commit/mirrors-mypy: v1.3.0 → v1.7.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.3.0...v1.7.1)
* Attempt to fix ruff
* Use isinstance
---------
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* chore: update pre-commit hooks (#1618)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.8 → v0.1.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.8...v0.1.9)
- [github.com/psf/black: 23.12.0 → 23.12.1](https://github.com/psf/black/compare/23.12.0...23.12.1)
- [github.com/pre-commit/mirrors-mypy: v1.7.1 → v1.8.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.7.1...v1.8.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Bump fsspec from 2023.12.1 to 2023.12.2 (#1606)
* Bump fsspec from 2023.12.1 to 2023.12.2
Bumps [fsspec](https://github.com/fsspec/filesystem_spec) from 2023.12.1 to 2023.12.2.
- [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.12.1...2023.12.2)
---
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* Update requirements_dev_optional.txt
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* Bump pytest-doctestplus from 1.0.0 to 1.1.0 (#1619)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.0.0 to 1.1.0.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.0.0...v1.1.0)
---
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* Bump pytest from 7.4.3 to 7.4.4 (#1622)
* chore: update pre-commit hooks (#1626)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.1.11](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.9...v0.1.11)
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* Create TEAM.md (#1628)
* Drop python 3.8 and numpy 1.20 (#1557)
* Drop 3.8 and add 3.12
* Try removing line_profiler
* Also bump the minimal numpy to 1.21
* Drop 3.12 again
* Revert "Try removing line_profiler"
This reverts commit 837854bec99a9d25aece2ead9666f01690d228cc.
* Update release.rst
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: jakirkham <jakirkham@gmail.com>
* Add Norman Rzepka to core-dev team (#1630)
* chore: update pre-commit hooks (#1633)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.11 → v0.1.13](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.11...v0.1.13)
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* Bump actions/download-artifact from 3 to 4 (#1611)
* Bump actions/download-artifact from 3 to 4
Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4.
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](https://github.com/actions/download-artifact/compare/v3...v4)
---
updated-dependencies:
- dependency-name: actions/download-artifact
dependency-type: direct:production
update-type: version-update:semver-major
...
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* Also bump upload-artifact
see https://github.com/actions/download-artifact?tab=readme-ov-file#breaking-changes
> Downloading artifacts that were created from action/upload-artifact@v3 and below are not supported.
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Update tutorial.rst to include section about accessing Zip Files on S3 (#1615)
* Update tutorial.rst to include section about accessing Zip Files on S3
Per discussion here, add information about about accessing zip files on s3:
https://github.com/zarr-developers/zarr-python/discussions/1613
* Update release.rst
* Implement d-v-b's suggestions
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* doc(v3): add v3 roadmap and design document (#1583)
* doc(v3): add v3 roadmap and design document
* Update v3-roadmap-and-design.md
* updates after latest round of reviews
* Update v3-roadmap-and-design.md
Co-authored-by: Norman Rzepka <code@normanrz.com>
* Update v3-roadmap-and-design.md
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
---------
Co-authored-by: Norman Rzepka <code@normanrz.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore: update pre-commit hooks (#1636)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.13 → v0.1.14](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.13...v0.1.14)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix zarr sync (#1663)
This patch removes fasteners and disables zarr.sync which uses process and thread
Co-authored-by: Wei Ouyang <oeway007@gmail.com>
* Update release.rst (#1621)
* Update release.rst
* Update release.rst
* Change 2.16.2 → 2.17.0
* Update moto for test_s3
* Skip bsddb3 tests to prevent warning failure
* Fix more user warning tests
* Fix even more user warning tests
* Skip coverage for importorskips
* Move to have_X skip method for deps
* Update release.rst (PR#1663)
* Fix test_core.py 'compile' issues
* Add black formatting
* Drop Windows/3.9 build due to unrelated failures
* fix typo
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Bump numpy from 1.24.3 to 1.26.1 (#1543)
Bumps [numpy](https://github.com/numpy/numpy) from 1.24.3 to 1.26.1.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.24.3...v1.26.1)
---
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Co-authored-by: Joe Hamman <joe@earthmover.io>
* chore: update pre-commit hooks (#1642)
* chore: update pre-commit hooks
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.14 → v0.2.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.14...v0.2.1)
- [github.com/psf/black: 23.12.1 → 24.2.0](https://github.com/psf/black/compare/23.12.1...24.2.0)
* run black incl. comments for '...'
---------
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* Bump ipywidgets from 8.1.0 to 8.1.1 (#1538)
Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.1.0 to 8.1.1.
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.0...8.1.1)
---
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- dependency-name: ipywidgets
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* Proper argument for numpy.reshape (#1425)
`numpy.reshape` not only accepts a tuple of ints, but also a simple int.
Besides `(10)` is not a tuple and is identical to `10`, unlike `(10,)`.
* Bump ipywidgets from 8.1.1 to 8.1.2 (#1666)
Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.1.1 to 8.1.2.
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.1...8.1.2)
---
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- dependency-name: ipywidgets
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* docs: ZIP-related tweaks (#1641)
* docs: use 'ZIP archive' instead of 'zip file'; clarify utility of caching in s3 + ZIP example; style
* docs: update release notes, correct spelling of greg lee's name in past release notes, and fix markup in past release notes
* docs: use 'ZIP archive' instead of 'zip file'; clarify utility of caching in s3 + ZIP example; style
* docs: update release notes, correct spelling of greg lee's name in past release notes, and fix markup in past release notes
* Bump numpy from 1.26.1 to 1.26.4 (#1669)
Bumps [numpy](https://github.com/numpy/numpy) from 1.26.1 to 1.26.4.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.1...v1.26.4)
---
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- dependency-name: numpy
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update-type: version-update:semver-patch
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* Change occurrences of % and format() to f-strings (#1423)
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* chore: update pre-commit hooks (#1672)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.1 → v0.2.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.1...v0.2.2)
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* Bump pymongo from 4.6.1 to 4.6.2 (#1674)
Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.6.1 to 4.6.2.
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/4.6.2/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.6.1...4.6.2)
---
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- dependency-name: pymongo
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* Bump conda-incubator/setup-miniconda from 3.0.1 to 3.0.2 (#1677)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.1 to 3.0.2.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.1...v3.0.2)
---
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- dependency-name: conda-incubator/setup-miniconda
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* Update config.yml with Zulip
* Type dimension separator (#1620)
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Replace Gitter with new Zulip Chat link (#1685)
* Replace Gitter with Zulip
* Replace Gitter with Zulip in remaining places
* Bump redis from 5.0.1 to 5.0.2 (#1688)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.1 to 5.0.2.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.1...v5.0.2)
---
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- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
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* Bump pypa/gh-action-pypi-publish from 1.8.11 to 1.8.12 (#1691)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.11 to 1.8.12.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.11...v1.8.12)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
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* Bump pytest-doctestplus from 1.1.0 to 1.2.0 (#1693)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.1.0 to 1.2.0.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.1.0...v1.2.0)
---
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- dependency-name: pytest-doctestplus
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* Fix RTD build (#1694)
* Update release.rst for v2.17.1 (#1673)
* Update release.rst for v2.17.1
* Change the copyright year from 2023 → 2024.
* Update release.rst for v2.17.1
* Bump pytest-timeout from 2.2.0 to 2.3.1 (#1697)
Bumps [pytest-timeout](https://github.com/pytest-dev/pytest-timeout) from 2.2.0 to 2.3.1.
- [Commits](https://github.com/pytest-dev/pytest-timeout/compare/2.2.0...2.3.1)
---
updated-dependencies:
- dependency-name: pytest-timeout
dependency-type: direct:development
update-type: version-update:semver-minor
...
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* Bump conda-incubator/setup-miniconda from 3.0.2 to 3.0.3 (#1690)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.2 to 3.0.3.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.2...v3.0.3)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
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* docs(tutorial.rst): fix link to GCSMap (#1689)
* Update installation.rst stating version support policy (#1665)
* Update installation.rst stating version support policy
* Update docs/installation.rst
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Update docs/installation.rst
---------
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Bump pypa/gh-action-pypi-publish from 1.8.12 to 1.8.14 (#1700)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.12 to 1.8.14.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.12...v1.8.14)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
...
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* Bump pytest-doctestplus from 1.2.0 to 1.2.1 (#1699)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.2.0 to 1.2.1.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.2.0...v1.2.1)
---
updated-dependencies:
- dependency-name: pytest-doctestplus
dependency-type: direct:development
update-type: version-update:semver-patch
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* Bump redis from 5.0.2 to 5.0.3 (#1698)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.2 to 5.0.3.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.2...v5.0.3)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
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* Add Python 3.12 to CI (#1719)
* Update python-package.yml
* bump numpy versions
* bump min python version
* Update release.rst
* Bump pytest-cov from 4.1.0 to 5.0.0 (#1722)
Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 4.1.0 to 5.0.0.
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest-cov/compare/v4.1.0...v5.0.0)
---
updated-dependencies:
- dependency-name: pytest-cov
dependency-type: direct:development
update-type: version-update:semver-major
...
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* chore: update pre-commit hooks (#1708)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.2 → v0.3.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.2...v0.3.3)
- [github.com/psf/black: 24.2.0 → 24.3.0](https://github.com/psf/black/compare/24.2.0...24.3.0)
- [github.com/pre-commit/mirrors-mypy: v1.8.0 → v1.9.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.8.0...v1.9.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore: update pre-commit hooks (#1723)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.3 → v0.3.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.3...v0.3.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix release notes (following #1719) (#1725)
* Override ipython repr methods. (#1724)
Closes #1716
This avoids expensive lookups against object stores.
* Bump pymongo from 4.6.2 to 4.6.3 (#1729)
* Remove v1 and v2 specification (#1582)
* Remove v1 and v2 specification
* fix warning
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* chore: update pre-commit hooks (#1738)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.4 → v0.3.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.4...v0.3.5)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Optimize Array.info and Group.info (#1733)
* Optimize Array.info.
Avoid repeated computes of the same value (getsize)
* Don't have InfoReporter query items twice.
Apparently IPython will run both __repr__ and _repr_html_
so we were calling `getsize` twice.
* Group too
* Apply suggestions from code review
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
---------
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Bump actions/setup-python from 5.0.0 to 5.1.0 (#1736)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.0.0 to 5.1.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.0.0...v5.1.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-minor
...
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* Couple fixes (#1737)
* Use `is` when comparing `type` of two objects
* Unnecessary `None` provided as default
* Fix tests with Pytest 8 (#1714)
* Bump pytest version
* Use editable install when testing
---------
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Avoid redundant __contains__ (#1739)
Let's try grabbing the array.json and group.json files,
and check for `*NotFoundError`, instead of using contains first.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Array & Group: Use already loaded attributes to populate cache. (#1734)
* Array: Use already loaded attributes to populate cache.
* Group: Use already loaded attributes to populate cache.
* Fix
* Add release note
* Optimize attribute setting (#1741)
* Optimize attribute setting
* Add release note
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Make sure fs exceptions are raised if not MissingFs exceptions (clone) (#1604)
* Make sure fs exceptions are raised if not Missing
* lint
* add missing argument in tests, lint
* clear memory filesystem during test
* improve commenting
* add memory_store fixture, getitems performance
* Update release.rst
* improve FSStore.test_exception coverage
---------
Co-authored-by: Martin Durant <martin.durant@alumni.utoronto.ca>
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore(release): update changelog for 2.17.2 (#1775)
* chore(docs): reset release notes as unreleased (#1776)
* Bump codecov/codecov-action from 3 to 4 (#1647)
* Bump codecov/codecov-action from 3 to 4
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v3...v4)
---
updated-dependencies:
- dependency-name: codecov/codecov-action
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
* Set codecov env
---------
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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Update release.rst for v2.17.2 (#1778)
* Update release.rst for v2.17.2
* Minor edits
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Deprecate the experimental v3 implementation (#1802)
* deprecate(exp-v3): Add a future warning about the pending removal of the experimental v3 implementation
* ignore warning
* add test
* chore: update pre-commit hooks (#1779)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.3.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.5...v0.3.7)
- [github.com/psf/black: 24.3.0 → 24.4.0](https://github.com/psf/black/compare/24.3.0...24.4.0)
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v4.6.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix `is_total_slice` for size-1 dimensions (#1800)
Closes #1730
Co-authored-by: Ryan Abernathey <ryan.abernathey@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* add note to the top of the release page noting the plan for 2.18.* and 3.0 (#1816)
* Bump conda-incubator/setup-miniconda from 3.0.3 to 3.0.4 (#1824)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.3 to 3.0.4.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.3...v3.0.4)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
...
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* dep(docs): deprecate experimental v3 support in docs (#1807)
* dep(docs): deprecate experimental v3 support in docs
* Apply suggestions from code review
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
---------
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Bump h5py from 3.10.0 to 3.11.0 (#1786)
Bumps [h5py](https://github.com/h5py/h5py) from 3.10.0 to 3.11.0.
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](https://github.com/h5py/h5py/compare/3.10.0...3.11.0)
---
updated-dependencies:
- dependency-name: h5py
dependency-type: direct:development
update-type: version-update:semver-minor
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Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump redis from 5.0.3 to 5.0.4 (#1810)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.3 to 5.0.4.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.3...v5.0.4)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* deprecate(stores): add deprecation warnings to stores that we plan to remove in v3 (#1801)
* deprecate(stores): add deprecation warnings to DBMStore, LMDBStore, SQLiteStore, MongoDBStore, RedisStore, and ABSStore
* filter warnings in pytest config
* more deprecation warnings in docstrings
* add release note
* use np.inf instead of PINF/NINF (#1842)
* use np.inf instead of PINF/NINF
* update release notes
* chore: update pre-commit hooks (#1825)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.1 → v0.4.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.1...v0.4.3)
- [github.com/psf/black: 24.4.0 → 24.4.2](https://github.com/psf/black/compare/24.4.0...24.4.2)
- [github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.9.0...v1.10.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Enable ruff/bugbear rules (B) and fix issues (#1702)
* Enable ruff/bugbear rules (B)
As suggested by Repo-Review.
* Fix ruff/bugbear issue (B007)
B007 Loop control variable `key` not used within loop body
https://docs.astral.sh/ruff/rules/unused-loop-control-variable/
* Fix ruff/bugbear issue (B015)
B015 Pointless comparison. Did you mean to assign a value?
Otherwise, prepend `assert` or remove it.
https://docs.astral.sh/ruff/rules/useless-comparison/
* Fix ruff/bugbear issues (B028)
B028 No explicit `stacklevel` keyword argument found
https://docs.astral.sh/ruff/rules/no-explicit-stacklevel/
* Fix ruff/bugbear issues (B904)
B904 Within an `except` clause, raise exceptions with `raise ... from err` or
`raise ... from None` to distinguish them from errors in exception handling
https://docs.astral.sh/ruff/rules/raise-without-from-inside-except/
* Document changes in docs/release.rst
* Disable ruff/bugbear rule (B017)
B017 `pytest.raises(Exception)` should be considered evil
https://docs.astral.sh/ruff/rules/assert-raises-exception/
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Release notes for 2.18.0 (#1843)
* doc: cleanup release notes for 2.18.0
* Update release.rst (#1850)
* Group dependabot updates (#1854)
* chore: update pre-commit hooks (#1876)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.3 → v0.4.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.3...v0.4.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix a regression with scalar indexing due to #1800 (#1875)
* release notes for 2.18.1 (#1885)
* reset release notes (#1886)
* Add zstd to old V3 supported codecs (#1914)
* add zstd to old V3 supported codecs
* get to full test coverage and add release note
* fix pre-commit
* doc: update release notes for 2.18.2 (#1915)
* Drop support for Python 3.9
* Revert "Drop support for Python 3.9"
This reverts commit a054afbbdaf7c8560d0ce5df77af969bc863e335.
* Update TEAM.md (#2071)
* [v2] Fix doctests with numpy 2.0 (#2073)
* Fix version number in built docs (#2044)
* Fix orthogonal indexing with scalar. (#1947)
Co-authored-by: David Stansby <dstansby@gmail.com>
* Bump the requirements group across 1 directory with 7 updates (#2092)
Bumps the requirements group with 7 updates in the / directory:
| Package | From | To |
| --- | --- | --- |
| [numpy](https://github.com/numpy/numpy) | `1.26.4` | `2.0.1` |
| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) | `8.1.2` | `8.1.3` |
| [setuptools-scm](https://github.com/pypa/setuptools_scm) | `8.0.4` | `8.1.0` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.1.1` | `8.3.2` |
| [lmdb](https://github.com/jnwatson/py-lmdb) | `1.4.1` | `1.5.1` |
| [redis](https://github.com/redis/redis-py) | `5.0.4` | `5.0.8` |
| [pymongo](https://github.com/mongodb/mongo-python-driver) | `4.6.3` | `4.8.0` |
Updates `numpy` from 1.26.4 to 2.0.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.4...v2.0.1)
Updates `ipywidgets` from 8.1.2 to 8.1.3
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.2...8.1.3)
Updates `setuptools-scm` from 8.0.4 to 8.1.0
- [Release notes](https://github.com/pypa/setuptools_scm/releases)
- [Changelog](https://github.com/pypa/setuptools_scm/blob/main/CHANGELOG.md)
- [Commits](https://github.com/pypa/setuptools_scm/compare/v8.0.4...v8.1.0)
Updates `pytest` from 8.1.1 to 8.3.2
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.1.1...8.3.2)
Updates `lmdb` from 1.4.1 to 1.5.1
- [Changelog](https://github.com/jnwatson/py-lmdb/blob/master/ChangeLog)
- [Commits](https://github.com/jnwatson/py-lmdb/compare/py-lmdb_1.4.1...py-lmdb_1.5.1)
Updates `redis` from 5.0.4 to 5.0.8
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.4...v5.0.8)
Updates `pymongo` from 4.6.3 to 4.8.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.6.3...4.8.0)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-major
dependency-group: requirements
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: setuptools-scm
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: pytest
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: lmdb
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
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* Bump the actions group with 2 updates (#2087)
Bumps the actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `actions/setup-python` from 5.1.0 to 5.1.1
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.1.0...v5.1.1)
Updates `pypa/gh-action-pypi-publish` from 1.8.14 to 1.9.0
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.14...v1.9.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
...
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* [v2] Drop support for Python 3.9 (#2074)
* Drop support for Python 3.9
* Ignore B905 ruff rule
* Fix release notes
* Fix Array.__array__ for numpy 2.1 (#2106)
* Fix Array.__array__ for numpy 2.1
* Add changelog
* Depend on np.array for array coercions
* Bump test version of numcodecs (#2114)
* Bump test version of numcodecs
* Fix test for numcodecs 0.13
* fix: numpy 1.24 compat for Array.__array__ (#2123)
* Deprecate N5Store (#2103)
* deprecate(n5): add deprecation warning to N5Store
* also deprecate N5FSStore
* docs
* fix doc
* Run tests on numpy 1.23 (#2124)
* Bump the requirements group across 1 directory with 3 updates (#2129)
Bumps the requirements group with 3 updates in the / directory: [numpy](https://github.com/numpy/numpy), [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) and [azure-storage-blob](https://github.com/Azure/azure-sdk-for-python).
Updates `numpy` from 2.0.1 to 2.1.0
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.0.1...v2.1.0)
Updates `ipywidgets` from 8.1.3 to 8.1.5
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.3...8.1.5)
Updates `azure-storage-blob` from 12.16.0 to 12.21.0
- [Release notes](https://github.com/Azure/azure-sdk-for-python/releases)
- [Changelog](https://github.com/Azure/azure-sdk-for-python/blob/main/doc/esrp_release.md)
- [Commits](https://github.com/Azure/azure-sdk-for-python/compare/azure-storage-blob_12.16.0...azure-storage-blob_12.21.0)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: azure-storage-blob
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore: bump minimum numpy version to 1.24 (#2127)
* chore: bump minimum version to 1.24
* Update .github/workflows/python-package.yml
* Remove un-needed package installs in CI (#2095)
* Bump the actions group with 2 updates (#2146)
Bumps the actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `actions/setup-python` from 5.1.1 to 5.2.0
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.1.1...v5.2.0)
Updates `pypa/gh-action-pypi-publish` from 1.9.0 to 1.10.0
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.9.0...v1.10.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump numpy from 2.1.0 to 2.1.1 in the requirements group (#2151)
Bumps the requirements group with 1 update: [numpy](https://github.com/numpy/numpy).
Updates `numpy` from 2.1.0 to 2.1.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.0...v2.1.1)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore(docs): update release notes ahead of 2.18.4 (#2152)
* Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1 in the actions group (#2161)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.0 to 1.10.1
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.0...v1.10.1)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* [docs] remove primary sidebar from tutorial (#2142)
* remove primary sidebar from tutorial
* lint
* Bump pytest from 8.3.2 to 8.3.3 in the requirements group (#2172)
Bumps the requirements group with 1 update: [pytest](https://github.com/pytest-dev/pytest).
Updates `pytest` from 8.3.2 to 8.3.3
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.3.2...8.3.3)
---
updated-dependencies:
- dependency-name: pytest
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump pypa/gh-action-pypi-publish in the actions group (#2220)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.1 to 1.10.2
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.1...v1.10.2)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Update TEAM.md (#2227)
* Bump the requirements group across 1 directory with 3 updates (#2284)
Bumps the requirements group with 3 updates in the / directory: [redis](https://github.com/redis/redis-py), [pymongo](https://github.com/mongodb/mongo-python-driver) and [h5py](https://github.com/h5py/h5py).
Updates `redis` from 5.0.8 to 5.1.0
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.8...v5.1.0)
Updates `pymongo` from 4.8.0 to 4.10.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.8.0...4.10.0)
Updates `h5py` from 3.11.0 to 3.12.1
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](https://github.com/h5py/h5py/compare/3.11.0...3.12.1)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: h5py
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump pymongo from 4.10.0 to 4.10.1 in the requirements group (#2288)
Bumps the requirements group with 1 update: [pymongo](https://github.com/mongodb/mongo-python-driver).
Updates `pymongo` from 4.10.0 to 4.10.1
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.10.0...4.10.1)
---
updated-dependencies:
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Fix low contrast box titles (#2287) (#2292)
* Bump pypa/gh-action-pypi-publish in the actions group (#2304)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.2 to 1.10.3
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.2...v1.10.3)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump the requirements group with 2 updates (#2303)
Bumps the requirements group with 2 updates: [numpy](https://github.com/numpy/numpy) and [redis](https://github.com/redis/redis-py).
Updates `numpy` from 2.1.1 to 2.1.2
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.1...v2.1.2)
Updates `redis` from 5.1.0 to 5.1.1
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.1.0...v5.1.1)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump numcodecs from 0.13.0 to 0.13.1 in the requirements group (#2326)
Bumps the requirements group with 1 update: [numcodecs](https://github.com/zarr-developers/numcodecs).
Updates `numcodecs` from 0.13.0 to 0.13.1
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.rst)
- [Commits](https://github.com/zarr-developers/numcodecs/compare/v0.13.0...v0.13.1)
---
updated-dependencies:
- dependency-name: numcodecs
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* remove zarr.types from v2
---------
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Janick Martinez Esturo <janick@jme.pub>
Co-authored-by: David Stansby <dstansby@gmail.com>
Co-authored-by: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com>
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: jakirkham <jakirkham@gmail.com>
Co-authored-by: Jeff Peck <jeffrey.peck@10xgenomics.com>
Co-authored-by: Norman Rzepka <code@normanrz.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
Co-authored-by: Hood Chatham <roberthoodchatham@gmail.com>
Co-authored-by: Wei Ouyang <oeway007@gmail.com>
Co-authored-by: Daniel Jahn (dahn) <dahnjahn@gmail.com>
Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com>
Co-authored-by: Ian Carroll <carroll.ian@gmail.com>
Co-authored-by: Martin Durant <martin.durant@alumni.utoronto.ca>
Co-authored-by: Ryan Abernathey <ryan.abernathey@gmail.com>
Co-authored-by: Jonny Saunders <sneakers-the-rat@protonmail.com>
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Bump actions/setup-python from 4.7.1 to 5.0.0 by dependabot[bot] · Pull Request #1605 · zarr-developers/zarr-python · GitHub
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Bump actions/setup-python from 4.7.1 to 5.0.0 - #1605
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Bump actions/setup-python from 4.7.1 to 5.0.0#1605
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Bumps actions/setup-python from 4.7.1 to 5.0.0.
Release notes
Sourced from actions/setup-python's releases.
v5.0.0
What's Changed
In scope of this release, we update node version runtime from node16 to node20 (actions/setup-python#772). Besides, we update dependencies to the latest versions.
Full Changelog: actions/setup-python@v4.8.0...v5.0.0
v4.8.0
What's Changed
In scope of this release we added support for GraalPy (actions/setup-python#694). You can use this snippet to set up GraalPy:
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v4 with:
python-version: 'graalpy-22.3' - run: python my_script.py
Besides, the release contains such changes as:
New Contributors
Full Changelog: actions/setup-python@v4...v4.8.0
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@dependabot
Bump actions/setup-python from 4.7.1 to 5.0.0
cf76095
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
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Dependabot tried to merge this PR, but received the following error from GitHub:
At least 1 approving review is required by reviewers with write access.

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@dependabot@jhamman
Bump actions/setup-python from 4.7.1 to 5.0.0 (zarr-developers#1605)
a5b4b90
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
jhamman added a commit
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@jhamman@dependabot
@janickm@dstansby@DimitriPapadopoulos@d-v-b@joshmoore@pre-commit-ci@jakirkham@jeffpeck10x@normanrz@sanketverma1704@hoodmane@oeway@DahnJ@dcherian@itcarroll@martindurant@rabernat@sneakers-the-rat
V3 main sync w/ merge (#2335)
ce5f53e
* Bump pypa/gh-action-pypi-publish from 1.8.10 to 1.8.11 (#1586)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.10 to 1.8.11.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.10...v1.8.11)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump conda-incubator/setup-miniconda from 2.3.0 to 3.0.1 (#1587)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 2.3.0 to 3.0.1.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v2.3.0...v3.0.1)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* * Cache result of FSStore._fsspec_installed (#1581)
Prevent runtime-overhead in doing this check multiple times
* Bump version of black in pre-commit (#1559)
* Use list comprehension where applicable (#1555)
Even if this is only a test, list comprehensions are faster than
repeatedly call append().
Also use tuple instead of list when possible.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Bump numcodecs from 0.11.0 to 0.12.1 (#1580)
Bumps [numcodecs](https://github.com/zarr-developers/numcodecs) from 0.11.0 to 0.12.1.
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.rst)
- [Commits](https://github.com/zarr-developers/numcodecs/compare/v0.11.0...v0.12.1)
---
updated-dependencies:
- dependency-name: numcodecs
dependency-type: direct:development
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Use format specification mini-language to format string (#1558)
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Single startswith() call instead of multiple ones (#1556)
It's faster and probably more readable.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump pymongo from 4.5.0 to 4.6.1 (#1585)
Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.5.0 to 4.6.1.
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.5.0...4.6.1)
---
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* Move codespell options around (#1196)
Starting with codespell 2.2.2, options can be specified in
`pyrpoject.toml` in addition to `setup.cfg`:
https://github.com/codespell-project/codespell#using-a-config-file
Specifying options in a config file instead of command line options in
`.pre-commit-config.yaml` ensures codespell uses the same options when
run as pre-commit hook or from the command line in the repository root
directory.
* Bump fsspec from 2023.10.0 to 2023.12.1 (#1600)
* Bump fsspec from 2023.10.0 to 2023.12.1
Bumps [fsspec](https://github.com/fsspec/filesystem_spec) from 2023.10.0 to 2023.12.1.
- [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.10.0...2023.12.1)
---
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- dependency-name: fsspec
dependency-type: direct:development
update-type: version-update:semver-minor
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* Update s3fs as well
* Fix s3fs
---------
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* Add type hints to zarr.create (#1536)
* Add type hints to zarr.create
* Use protocol for MetaArray
* Use protocol for Synchronizer
* Fix Path typing
* Add release note
* Fix dim separator typing
* Ignore ... in coverage reporting
* Fix chunk typing
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Remove unused mypy ignore comments (#1602)
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Bump actions/setup-python from 4.7.1 to 5.0.0 (#1605)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
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* Bump github/codeql-action from 2 to 3 (#1609)
Bumps [github/codeql-action](https://github.com/github/codeql-action) from 2 to 3.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/github/codeql-action/compare/v2...v3)
---
updated-dependencies:
- dependency-name: github/codeql-action
dependency-type: direct:production
update-type: version-update:semver-major
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* chore: update pre-commit hooks (#1448)
* chore: update pre-commit hooks
updates:
- https://github.com/charliermarsh/ruff-pre-commit → https://github.com/astral-sh/ruff-pre-commit
- [github.com/astral-sh/ruff-pre-commit: v0.0.224 → v0.1.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.224...v0.1.8)
- [github.com/psf/black: 23.10.1 → 23.12.0](https://github.com/psf/black/compare/23.10.1...23.12.0)
- [github.com/codespell-project/codespell: v2.2.5 → v2.2.6](https://github.com/codespell-project/codespell/compare/v2.2.5...v2.2.6)
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.4.0...v4.5.0)
- [github.com/pre-commit/mirrors-mypy: v1.3.0 → v1.7.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.3.0...v1.7.1)
* Attempt to fix ruff
* Use isinstance
---------
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* chore: update pre-commit hooks (#1618)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.8 → v0.1.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.8...v0.1.9)
- [github.com/psf/black: 23.12.0 → 23.12.1](https://github.com/psf/black/compare/23.12.0...23.12.1)
- [github.com/pre-commit/mirrors-mypy: v1.7.1 → v1.8.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.7.1...v1.8.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Bump fsspec from 2023.12.1 to 2023.12.2 (#1606)
* Bump fsspec from 2023.12.1 to 2023.12.2
Bumps [fsspec](https://github.com/fsspec/filesystem_spec) from 2023.12.1 to 2023.12.2.
- [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.12.1...2023.12.2)
---
updated-dependencies:
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* Update requirements_dev_optional.txt
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* Bump pytest-doctestplus from 1.0.0 to 1.1.0 (#1619)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.0.0 to 1.1.0.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.0.0...v1.1.0)
---
updated-dependencies:
- dependency-name: pytest-doctestplus
dependency-type: direct:development
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* Bump pytest from 7.4.3 to 7.4.4 (#1622)
* chore: update pre-commit hooks (#1626)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.1.11](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.9...v0.1.11)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Create TEAM.md (#1628)
* Drop python 3.8 and numpy 1.20 (#1557)
* Drop 3.8 and add 3.12
* Try removing line_profiler
* Also bump the minimal numpy to 1.21
* Drop 3.12 again
* Revert "Try removing line_profiler"
This reverts commit 837854bec99a9d25aece2ead9666f01690d228cc.
* Update release.rst
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: jakirkham <jakirkham@gmail.com>
* Add Norman Rzepka to core-dev team (#1630)
* chore: update pre-commit hooks (#1633)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.11 → v0.1.13](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.11...v0.1.13)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Bump actions/download-artifact from 3 to 4 (#1611)
* Bump actions/download-artifact from 3 to 4
Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4.
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](https://github.com/actions/download-artifact/compare/v3...v4)
---
updated-dependencies:
- dependency-name: actions/download-artifact
dependency-type: direct:production
update-type: version-update:semver-major
...
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* Also bump upload-artifact
see https://github.com/actions/download-artifact?tab=readme-ov-file#breaking-changes
> Downloading artifacts that were created from action/upload-artifact@v3 and below are not supported.
---------
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Update tutorial.rst to include section about accessing Zip Files on S3 (#1615)
* Update tutorial.rst to include section about accessing Zip Files on S3
Per discussion here, add information about about accessing zip files on s3:
https://github.com/zarr-developers/zarr-python/discussions/1613
* Update release.rst
* Implement d-v-b's suggestions
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* doc(v3): add v3 roadmap and design document (#1583)
* doc(v3): add v3 roadmap and design document
* Update v3-roadmap-and-design.md
* updates after latest round of reviews
* Update v3-roadmap-and-design.md
Co-authored-by: Norman Rzepka <code@normanrz.com>
* Update v3-roadmap-and-design.md
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
---------
Co-authored-by: Norman Rzepka <code@normanrz.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore: update pre-commit hooks (#1636)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.13 → v0.1.14](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.13...v0.1.14)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix zarr sync (#1663)
This patch removes fasteners and disables zarr.sync which uses process and thread
Co-authored-by: Wei Ouyang <oeway007@gmail.com>
* Update release.rst (#1621)
* Update release.rst
* Update release.rst
* Change 2.16.2 → 2.17.0
* Update moto for test_s3
* Skip bsddb3 tests to prevent warning failure
* Fix more user warning tests
* Fix even more user warning tests
* Skip coverage for importorskips
* Move to have_X skip method for deps
* Update release.rst (PR#1663)
* Fix test_core.py 'compile' issues
* Add black formatting
* Drop Windows/3.9 build due to unrelated failures
* fix typo
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Bump numpy from 1.24.3 to 1.26.1 (#1543)
Bumps [numpy](https://github.com/numpy/numpy) from 1.24.3 to 1.26.1.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.24.3...v1.26.1)
---
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dependency-type: direct:development
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* chore: update pre-commit hooks (#1642)
* chore: update pre-commit hooks
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.14 → v0.2.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.14...v0.2.1)
- [github.com/psf/black: 23.12.1 → 24.2.0](https://github.com/psf/black/compare/23.12.1...24.2.0)
* run black incl. comments for '...'
---------
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Bump ipywidgets from 8.1.0 to 8.1.1 (#1538)
Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.1.0 to 8.1.1.
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.0...8.1.1)
---
updated-dependencies:
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
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* Proper argument for numpy.reshape (#1425)
`numpy.reshape` not only accepts a tuple of ints, but also a simple int.
Besides `(10)` is not a tuple and is identical to `10`, unlike `(10,)`.
* Bump ipywidgets from 8.1.1 to 8.1.2 (#1666)
Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.1.1 to 8.1.2.
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.1...8.1.2)
---
updated-dependencies:
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* docs: ZIP-related tweaks (#1641)
* docs: use 'ZIP archive' instead of 'zip file'; clarify utility of caching in s3 + ZIP example; style
* docs: update release notes, correct spelling of greg lee's name in past release notes, and fix markup in past release notes
* docs: use 'ZIP archive' instead of 'zip file'; clarify utility of caching in s3 + ZIP example; style
* docs: update release notes, correct spelling of greg lee's name in past release notes, and fix markup in past release notes
* Bump numpy from 1.26.1 to 1.26.4 (#1669)
Bumps [numpy](https://github.com/numpy/numpy) from 1.26.1 to 1.26.4.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.1...v1.26.4)
---
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- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* Change occurrences of % and format() to f-strings (#1423)
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* chore: update pre-commit hooks (#1672)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.1 → v0.2.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.1...v0.2.2)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Bump pymongo from 4.6.1 to 4.6.2 (#1674)
Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.6.1 to 4.6.2.
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/4.6.2/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.6.1...4.6.2)
---
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- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* Bump conda-incubator/setup-miniconda from 3.0.1 to 3.0.2 (#1677)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.1 to 3.0.2.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.1...v3.0.2)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
...
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* Update config.yml with Zulip
* Type dimension separator (#1620)
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Replace Gitter with new Zulip Chat link (#1685)
* Replace Gitter with Zulip
* Replace Gitter with Zulip in remaining places
* Bump redis from 5.0.1 to 5.0.2 (#1688)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.1 to 5.0.2.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.1...v5.0.2)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* Bump pypa/gh-action-pypi-publish from 1.8.11 to 1.8.12 (#1691)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.11 to 1.8.12.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.11...v1.8.12)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
...
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* Bump pytest-doctestplus from 1.1.0 to 1.2.0 (#1693)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.1.0 to 1.2.0.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.1.0...v1.2.0)
---
updated-dependencies:
- dependency-name: pytest-doctestplus
dependency-type: direct:development
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* Fix RTD build (#1694)
* Update release.rst for v2.17.1 (#1673)
* Update release.rst for v2.17.1
* Change the copyright year from 2023 → 2024.
* Update release.rst for v2.17.1
* Bump pytest-timeout from 2.2.0 to 2.3.1 (#1697)
Bumps [pytest-timeout](https://github.com/pytest-dev/pytest-timeout) from 2.2.0 to 2.3.1.
- [Commits](https://github.com/pytest-dev/pytest-timeout/compare/2.2.0...2.3.1)
---
updated-dependencies:
- dependency-name: pytest-timeout
dependency-type: direct:development
update-type: version-update:semver-minor
...
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* Bump conda-incubator/setup-miniconda from 3.0.2 to 3.0.3 (#1690)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.2 to 3.0.3.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.2...v3.0.3)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
...
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Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* docs(tutorial.rst): fix link to GCSMap (#1689)
* Update installation.rst stating version support policy (#1665)
* Update installation.rst stating version support policy
* Update docs/installation.rst
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Update docs/installation.rst
---------
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Bump pypa/gh-action-pypi-publish from 1.8.12 to 1.8.14 (#1700)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.12 to 1.8.14.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.12...v1.8.14)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
...
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* Bump pytest-doctestplus from 1.2.0 to 1.2.1 (#1699)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.2.0 to 1.2.1.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.2.0...v1.2.1)
---
updated-dependencies:
- dependency-name: pytest-doctestplus
dependency-type: direct:development
update-type: version-update:semver-patch
...
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Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Bump redis from 5.0.2 to 5.0.3 (#1698)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.2 to 5.0.3.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.2...v5.0.3)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
...
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Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Add Python 3.12 to CI (#1719)
* Update python-package.yml
* bump numpy versions
* bump min python version
* Update release.rst
* Bump pytest-cov from 4.1.0 to 5.0.0 (#1722)
Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 4.1.0 to 5.0.0.
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest-cov/compare/v4.1.0...v5.0.0)
---
updated-dependencies:
- dependency-name: pytest-cov
dependency-type: direct:development
update-type: version-update:semver-major
...
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* chore: update pre-commit hooks (#1708)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.2 → v0.3.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.2...v0.3.3)
- [github.com/psf/black: 24.2.0 → 24.3.0](https://github.com/psf/black/compare/24.2.0...24.3.0)
- [github.com/pre-commit/mirrors-mypy: v1.8.0 → v1.9.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.8.0...v1.9.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore: update pre-commit hooks (#1723)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.3 → v0.3.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.3...v0.3.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix release notes (following #1719) (#1725)
* Override ipython repr methods. (#1724)
Closes #1716
This avoids expensive lookups against object stores.
* Bump pymongo from 4.6.2 to 4.6.3 (#1729)
* Remove v1 and v2 specification (#1582)
* Remove v1 and v2 specification
* fix warning
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* chore: update pre-commit hooks (#1738)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.4 → v0.3.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.4...v0.3.5)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Optimize Array.info and Group.info (#1733)
* Optimize Array.info.
Avoid repeated computes of the same value (getsize)
* Don't have InfoReporter query items twice.
Apparently IPython will run both __repr__ and _repr_html_
so we were calling `getsize` twice.
* Group too
* Apply suggestions from code review
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
---------
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Bump actions/setup-python from 5.0.0 to 5.1.0 (#1736)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.0.0 to 5.1.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.0.0...v5.1.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
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* Couple fixes (#1737)
* Use `is` when comparing `type` of two objects
* Unnecessary `None` provided as default
* Fix tests with Pytest 8 (#1714)
* Bump pytest version
* Use editable install when testing
---------
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Avoid redundant __contains__ (#1739)
Let's try grabbing the array.json and group.json files,
and check for `*NotFoundError`, instead of using contains first.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Array & Group: Use already loaded attributes to populate cache. (#1734)
* Array: Use already loaded attributes to populate cache.
* Group: Use already loaded attributes to populate cache.
* Fix
* Add release note
* Optimize attribute setting (#1741)
* Optimize attribute setting
* Add release note
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Make sure fs exceptions are raised if not MissingFs exceptions (clone) (#1604)
* Make sure fs exceptions are raised if not Missing
* lint
* add missing argument in tests, lint
* clear memory filesystem during test
* improve commenting
* add memory_store fixture, getitems performance
* Update release.rst
* improve FSStore.test_exception coverage
---------
Co-authored-by: Martin Durant <martin.durant@alumni.utoronto.ca>
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore(release): update changelog for 2.17.2 (#1775)
* chore(docs): reset release notes as unreleased (#1776)
* Bump codecov/codecov-action from 3 to 4 (#1647)
* Bump codecov/codecov-action from 3 to 4
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v3...v4)
---
updated-dependencies:
- dependency-name: codecov/codecov-action
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
* Set codecov env
---------
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Update release.rst for v2.17.2 (#1778)
* Update release.rst for v2.17.2
* Minor edits
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Deprecate the experimental v3 implementation (#1802)
* deprecate(exp-v3): Add a future warning about the pending removal of the experimental v3 implementation
* ignore warning
* add test
* chore: update pre-commit hooks (#1779)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.3.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.5...v0.3.7)
- [github.com/psf/black: 24.3.0 → 24.4.0](https://github.com/psf/black/compare/24.3.0...24.4.0)
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v4.6.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix `is_total_slice` for size-1 dimensions (#1800)
Closes #1730
Co-authored-by: Ryan Abernathey <ryan.abernathey@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* add note to the top of the release page noting the plan for 2.18.* and 3.0 (#1816)
* Bump conda-incubator/setup-miniconda from 3.0.3 to 3.0.4 (#1824)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.3 to 3.0.4.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.3...v3.0.4)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* dep(docs): deprecate experimental v3 support in docs (#1807)
* dep(docs): deprecate experimental v3 support in docs
* Apply suggestions from code review
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
---------
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Bump h5py from 3.10.0 to 3.11.0 (#1786)
Bumps [h5py](https://github.com/h5py/h5py) from 3.10.0 to 3.11.0.
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](https://github.com/h5py/h5py/compare/3.10.0...3.11.0)
---
updated-dependencies:
- dependency-name: h5py
dependency-type: direct:development
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump redis from 5.0.3 to 5.0.4 (#1810)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.3 to 5.0.4.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.3...v5.0.4)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* deprecate(stores): add deprecation warnings to stores that we plan to remove in v3 (#1801)
* deprecate(stores): add deprecation warnings to DBMStore, LMDBStore, SQLiteStore, MongoDBStore, RedisStore, and ABSStore
* filter warnings in pytest config
* more deprecation warnings in docstrings
* add release note
* use np.inf instead of PINF/NINF (#1842)
* use np.inf instead of PINF/NINF
* update release notes
* chore: update pre-commit hooks (#1825)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.1 → v0.4.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.1...v0.4.3)
- [github.com/psf/black: 24.4.0 → 24.4.2](https://github.com/psf/black/compare/24.4.0...24.4.2)
- [github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.9.0...v1.10.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Enable ruff/bugbear rules (B) and fix issues (#1702)
* Enable ruff/bugbear rules (B)
As suggested by Repo-Review.
* Fix ruff/bugbear issue (B007)
B007 Loop control variable `key` not used within loop body
https://docs.astral.sh/ruff/rules/unused-loop-control-variable/
* Fix ruff/bugbear issue (B015)
B015 Pointless comparison. Did you mean to assign a value?
Otherwise, prepend `assert` or remove it.
https://docs.astral.sh/ruff/rules/useless-comparison/
* Fix ruff/bugbear issues (B028)
B028 No explicit `stacklevel` keyword argument found
https://docs.astral.sh/ruff/rules/no-explicit-stacklevel/
* Fix ruff/bugbear issues (B904)
B904 Within an `except` clause, raise exceptions with `raise ... from err` or
`raise ... from None` to distinguish them from errors in exception handling
https://docs.astral.sh/ruff/rules/raise-without-from-inside-except/
* Document changes in docs/release.rst
* Disable ruff/bugbear rule (B017)
B017 `pytest.raises(Exception)` should be considered evil
https://docs.astral.sh/ruff/rules/assert-raises-exception/
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Release notes for 2.18.0 (#1843)
* doc: cleanup release notes for 2.18.0
* Update release.rst (#1850)
* Group dependabot updates (#1854)
* chore: update pre-commit hooks (#1876)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.3 → v0.4.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.3...v0.4.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix a regression with scalar indexing due to #1800 (#1875)
* release notes for 2.18.1 (#1885)
* reset release notes (#1886)
* Add zstd to old V3 supported codecs (#1914)
* add zstd to old V3 supported codecs
* get to full test coverage and add release note
* fix pre-commit
* doc: update release notes for 2.18.2 (#1915)
* Drop support for Python 3.9
* Revert "Drop support for Python 3.9"
This reverts commit a054afbbdaf7c8560d0ce5df77af969bc863e335.
* Update TEAM.md (#2071)
* [v2] Fix doctests with numpy 2.0 (#2073)
* Fix version number in built docs (#2044)
* Fix orthogonal indexing with scalar. (#1947)
Co-authored-by: David Stansby <dstansby@gmail.com>
* Bump the requirements group across 1 directory with 7 updates (#2092)
Bumps the requirements group with 7 updates in the / directory:
| Package | From | To |
| --- | --- | --- |
| [numpy](https://github.com/numpy/numpy) | `1.26.4` | `2.0.1` |
| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) | `8.1.2` | `8.1.3` |
| [setuptools-scm](https://github.com/pypa/setuptools_scm) | `8.0.4` | `8.1.0` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.1.1` | `8.3.2` |
| [lmdb](https://github.com/jnwatson/py-lmdb) | `1.4.1` | `1.5.1` |
| [redis](https://github.com/redis/redis-py) | `5.0.4` | `5.0.8` |
| [pymongo](https://github.com/mongodb/mongo-python-driver) | `4.6.3` | `4.8.0` |
Updates `numpy` from 1.26.4 to 2.0.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.4...v2.0.1)
Updates `ipywidgets` from 8.1.2 to 8.1.3
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.2...8.1.3)
Updates `setuptools-scm` from 8.0.4 to 8.1.0
- [Release notes](https://github.com/pypa/setuptools_scm/releases)
- [Changelog](https://github.com/pypa/setuptools_scm/blob/main/CHANGELOG.md)
- [Commits](https://github.com/pypa/setuptools_scm/compare/v8.0.4...v8.1.0)
Updates `pytest` from 8.1.1 to 8.3.2
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.1.1...8.3.2)
Updates `lmdb` from 1.4.1 to 1.5.1
- [Changelog](https://github.com/jnwatson/py-lmdb/blob/master/ChangeLog)
- [Commits](https://github.com/jnwatson/py-lmdb/compare/py-lmdb_1.4.1...py-lmdb_1.5.1)
Updates `redis` from 5.0.4 to 5.0.8
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.4...v5.0.8)
Updates `pymongo` from 4.6.3 to 4.8.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.6.3...4.8.0)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-major
dependency-group: requirements
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: setuptools-scm
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: pytest
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: lmdb
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump the actions group with 2 updates (#2087)
Bumps the actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `actions/setup-python` from 5.1.0 to 5.1.1
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.1.0...v5.1.1)
Updates `pypa/gh-action-pypi-publish` from 1.8.14 to 1.9.0
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.14...v1.9.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* [v2] Drop support for Python 3.9 (#2074)
* Drop support for Python 3.9
* Ignore B905 ruff rule
* Fix release notes
* Fix Array.__array__ for numpy 2.1 (#2106)
* Fix Array.__array__ for numpy 2.1
* Add changelog
* Depend on np.array for array coercions
* Bump test version of numcodecs (#2114)
* Bump test version of numcodecs
* Fix test for numcodecs 0.13
* fix: numpy 1.24 compat for Array.__array__ (#2123)
* Deprecate N5Store (#2103)
* deprecate(n5): add deprecation warning to N5Store
* also deprecate N5FSStore
* docs
* fix doc
* Run tests on numpy 1.23 (#2124)
* Bump the requirements group across 1 directory with 3 updates (#2129)
Bumps the requirements group with 3 updates in the / directory: [numpy](https://github.com/numpy/numpy), [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) and [azure-storage-blob](https://github.com/Azure/azure-sdk-for-python).
Updates `numpy` from 2.0.1 to 2.1.0
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.0.1...v2.1.0)
Updates `ipywidgets` from 8.1.3 to 8.1.5
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.3...8.1.5)
Updates `azure-storage-blob` from 12.16.0 to 12.21.0
- [Release notes](https://github.com/Azure/azure-sdk-for-python/releases)
- [Changelog](https://github.com/Azure/azure-sdk-for-python/blob/main/doc/esrp_release.md)
- [Commits](https://github.com/Azure/azure-sdk-for-python/compare/azure-storage-blob_12.16.0...azure-storage-blob_12.21.0)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: azure-storage-blob
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore: bump minimum numpy version to 1.24 (#2127)
* chore: bump minimum version to 1.24
* Update .github/workflows/python-package.yml
* Remove un-needed package installs in CI (#2095)
* Bump the actions group with 2 updates (#2146)
Bumps the actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `actions/setup-python` from 5.1.1 to 5.2.0
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.1.1...v5.2.0)
Updates `pypa/gh-action-pypi-publish` from 1.9.0 to 1.10.0
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.9.0...v1.10.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump numpy from 2.1.0 to 2.1.1 in the requirements group (#2151)
Bumps the requirements group with 1 update: [numpy](https://github.com/numpy/numpy).
Updates `numpy` from 2.1.0 to 2.1.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.0...v2.1.1)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore(docs): update release notes ahead of 2.18.4 (#2152)
* Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1 in the actions group (#2161)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.0 to 1.10.1
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.0...v1.10.1)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* [docs] remove primary sidebar from tutorial (#2142)
* remove primary sidebar from tutorial
* lint
* Bump pytest from 8.3.2 to 8.3.3 in the requirements group (#2172)
Bumps the requirements group with 1 update: [pytest](https://github.com/pytest-dev/pytest).
Updates `pytest` from 8.3.2 to 8.3.3
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.3.2...8.3.3)
---
updated-dependencies:
- dependency-name: pytest
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump pypa/gh-action-pypi-publish in the actions group (#2220)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.1 to 1.10.2
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.1...v1.10.2)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Update TEAM.md (#2227)
* Bump the requirements group across 1 directory with 3 updates (#2284)
Bumps the requirements group with 3 updates in the / directory: [redis](https://github.com/redis/redis-py), [pymongo](https://github.com/mongodb/mongo-python-driver) and [h5py](https://github.com/h5py/h5py).
Updates `redis` from 5.0.8 to 5.1.0
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.8...v5.1.0)
Updates `pymongo` from 4.8.0 to 4.10.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.8.0...4.10.0)
Updates `h5py` from 3.11.0 to 3.12.1
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](https://github.com/h5py/h5py/compare/3.11.0...3.12.1)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: h5py
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump pymongo from 4.10.0 to 4.10.1 in the requirements group (#2288)
Bumps the requirements group with 1 update: [pymongo](https://github.com/mongodb/mongo-python-driver).
Updates `pymongo` from 4.10.0 to 4.10.1
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.10.0...4.10.1)
---
updated-dependencies:
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Fix low contrast box titles (#2287) (#2292)
* Bump pypa/gh-action-pypi-publish in the actions group (#2304)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.2 to 1.10.3
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.2...v1.10.3)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump the requirements group with 2 updates (#2303)
Bumps the requirements group with 2 updates: [numpy](https://github.com/numpy/numpy) and [redis](https://github.com/redis/redis-py).
Updates `numpy` from 2.1.1 to 2.1.2
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.1...v2.1.2)
Updates `redis` from 5.1.0 to 5.1.1
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.1.0...v5.1.1)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump numcodecs from 0.13.0 to 0.13.1 in the requirements group (#2326)
Bumps the requirements group with 1 update: [numcodecs](https://github.com/zarr-developers/numcodecs).
Updates `numcodecs` from 0.13.0 to 0.13.1
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.rst)
- [Commits](https://github.com/zarr-developers/numcodecs/compare/v0.13.0...v0.13.1)
---
updated-dependencies:
- dependency-name: numcodecs
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* remove zarr.types from v2
---------
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Janick Martinez Esturo <janick@jme.pub>
Co-authored-by: David Stansby <dstansby@gmail.com>
Co-authored-by: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com>
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: jakirkham <jakirkham@gmail.com>
Co-authored-by: Jeff Peck <jeffrey.peck@10xgenomics.com>
Co-authored-by: Norman Rzepka <code@normanrz.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
Co-authored-by: Hood Chatham <roberthoodchatham@gmail.com>
Co-authored-by: Wei Ouyang <oeway007@gmail.com>
Co-authored-by: Daniel Jahn (dahn) <dahnjahn@gmail.com>
Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com>
Co-authored-by: Ian Carroll <carroll.ian@gmail.com>
Co-authored-by: Martin Durant <martin.durant@alumni.utoronto.ca>
Co-authored-by: Ryan Abernathey <ryan.abernathey@gmail.com>
Co-authored-by: Jonny Saunders <sneakers-the-rat@protonmail.com>
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Bump actions/setup-python from 4.7.1 to 5.0.0 by dependabot[bot] · Pull Request #1605 · zarr-developers/zarr-python · GitHub
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Bump actions/setup-python from 4.7.1 to 5.0.0 - #1605
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Bump actions/setup-python from 4.7.1 to 5.0.0#1605
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Bumps actions/setup-python from 4.7.1 to 5.0.0.
Release notes
Sourced from actions/setup-python's releases.
v5.0.0
What's Changed
In scope of this release, we update node version runtime from node16 to node20 (actions/setup-python#772). Besides, we update dependencies to the latest versions.
Full Changelog: actions/setup-python@v4.8.0...v5.0.0
v4.8.0
What's Changed
In scope of this release we added support for GraalPy (actions/setup-python#694). You can use this snippet to set up GraalPy:
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v4 with:
python-version: 'graalpy-22.3' - run: python my_script.py
Besides, the release contains such changes as:
New Contributors
Full Changelog: actions/setup-python@v4...v4.8.0
Commits

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@dependabot
Bump actions/setup-python from 4.7.1 to 5.0.0
cf76095
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
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Dependabot tried to merge this PR, but received the following error from GitHub:
At least 1 approving review is required by reviewers with write access.

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@dependabot@jhamman
Bump actions/setup-python from 4.7.1 to 5.0.0 (zarr-developers#1605)
a5b4b90
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
jhamman added a commit
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@jhamman@dependabot
@janickm@dstansby@DimitriPapadopoulos@d-v-b@joshmoore@pre-commit-ci@jakirkham@jeffpeck10x@normanrz@sanketverma1704@hoodmane@oeway@DahnJ@dcherian@itcarroll@martindurant@rabernat@sneakers-the-rat
V3 main sync w/ merge (#2335)
ce5f53e
* Bump pypa/gh-action-pypi-publish from 1.8.10 to 1.8.11 (#1586)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.10 to 1.8.11.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.10...v1.8.11)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump conda-incubator/setup-miniconda from 2.3.0 to 3.0.1 (#1587)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 2.3.0 to 3.0.1.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v2.3.0...v3.0.1)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* * Cache result of FSStore._fsspec_installed (#1581)
Prevent runtime-overhead in doing this check multiple times
* Bump version of black in pre-commit (#1559)
* Use list comprehension where applicable (#1555)
Even if this is only a test, list comprehensions are faster than
repeatedly call append().
Also use tuple instead of list when possible.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Bump numcodecs from 0.11.0 to 0.12.1 (#1580)
Bumps [numcodecs](https://github.com/zarr-developers/numcodecs) from 0.11.0 to 0.12.1.
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.rst)
- [Commits](https://github.com/zarr-developers/numcodecs/compare/v0.11.0...v0.12.1)
---
updated-dependencies:
- dependency-name: numcodecs
dependency-type: direct:development
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Use format specification mini-language to format string (#1558)
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Single startswith() call instead of multiple ones (#1556)
It's faster and probably more readable.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump pymongo from 4.5.0 to 4.6.1 (#1585)
Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.5.0 to 4.6.1.
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.5.0...4.6.1)
---
updated-dependencies:
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Move codespell options around (#1196)
Starting with codespell 2.2.2, options can be specified in
`pyrpoject.toml` in addition to `setup.cfg`:
https://github.com/codespell-project/codespell#using-a-config-file
Specifying options in a config file instead of command line options in
`.pre-commit-config.yaml` ensures codespell uses the same options when
run as pre-commit hook or from the command line in the repository root
directory.
* Bump fsspec from 2023.10.0 to 2023.12.1 (#1600)
* Bump fsspec from 2023.10.0 to 2023.12.1
Bumps [fsspec](https://github.com/fsspec/filesystem_spec) from 2023.10.0 to 2023.12.1.
- [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.10.0...2023.12.1)
---
updated-dependencies:
- dependency-name: fsspec
dependency-type: direct:development
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
* Update s3fs as well
* Fix s3fs
---------
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Add type hints to zarr.create (#1536)
* Add type hints to zarr.create
* Use protocol for MetaArray
* Use protocol for Synchronizer
* Fix Path typing
* Add release note
* Fix dim separator typing
* Ignore ... in coverage reporting
* Fix chunk typing
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Remove unused mypy ignore comments (#1602)
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Bump actions/setup-python from 4.7.1 to 5.0.0 (#1605)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v4.7.1...v5.0.0)
---
updated-dependencies:
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* Bump github/codeql-action from 2 to 3 (#1609)
Bumps [github/codeql-action](https://github.com/github/codeql-action) from 2 to 3.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/github/codeql-action/compare/v2...v3)
---
updated-dependencies:
- dependency-name: github/codeql-action
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* chore: update pre-commit hooks (#1448)
* chore: update pre-commit hooks
updates:
- https://github.com/charliermarsh/ruff-pre-commit → https://github.com/astral-sh/ruff-pre-commit
- [github.com/astral-sh/ruff-pre-commit: v0.0.224 → v0.1.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.224...v0.1.8)
- [github.com/psf/black: 23.10.1 → 23.12.0](https://github.com/psf/black/compare/23.10.1...23.12.0)
- [github.com/codespell-project/codespell: v2.2.5 → v2.2.6](https://github.com/codespell-project/codespell/compare/v2.2.5...v2.2.6)
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.4.0...v4.5.0)
- [github.com/pre-commit/mirrors-mypy: v1.3.0 → v1.7.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.3.0...v1.7.1)
* Attempt to fix ruff
* Use isinstance
---------
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* chore: update pre-commit hooks (#1618)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.8 → v0.1.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.8...v0.1.9)
- [github.com/psf/black: 23.12.0 → 23.12.1](https://github.com/psf/black/compare/23.12.0...23.12.1)
- [github.com/pre-commit/mirrors-mypy: v1.7.1 → v1.8.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.7.1...v1.8.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Bump fsspec from 2023.12.1 to 2023.12.2 (#1606)
* Bump fsspec from 2023.12.1 to 2023.12.2
Bumps [fsspec](https://github.com/fsspec/filesystem_spec) from 2023.12.1 to 2023.12.2.
- [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.12.1...2023.12.2)
---
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* Update requirements_dev_optional.txt
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* Bump pytest-doctestplus from 1.0.0 to 1.1.0 (#1619)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.0.0 to 1.1.0.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.0.0...v1.1.0)
---
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* Bump pytest from 7.4.3 to 7.4.4 (#1622)
* chore: update pre-commit hooks (#1626)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.1.11](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.9...v0.1.11)
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* Create TEAM.md (#1628)
* Drop python 3.8 and numpy 1.20 (#1557)
* Drop 3.8 and add 3.12
* Try removing line_profiler
* Also bump the minimal numpy to 1.21
* Drop 3.12 again
* Revert "Try removing line_profiler"
This reverts commit 837854bec99a9d25aece2ead9666f01690d228cc.
* Update release.rst
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: jakirkham <jakirkham@gmail.com>
* Add Norman Rzepka to core-dev team (#1630)
* chore: update pre-commit hooks (#1633)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.11 → v0.1.13](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.11...v0.1.13)
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* Bump actions/download-artifact from 3 to 4 (#1611)
* Bump actions/download-artifact from 3 to 4
Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4.
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](https://github.com/actions/download-artifact/compare/v3...v4)
---
updated-dependencies:
- dependency-name: actions/download-artifact
dependency-type: direct:production
update-type: version-update:semver-major
...
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* Also bump upload-artifact
see https://github.com/actions/download-artifact?tab=readme-ov-file#breaking-changes
> Downloading artifacts that were created from action/upload-artifact@v3 and below are not supported.
---------
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Update tutorial.rst to include section about accessing Zip Files on S3 (#1615)
* Update tutorial.rst to include section about accessing Zip Files on S3
Per discussion here, add information about about accessing zip files on s3:
https://github.com/zarr-developers/zarr-python/discussions/1613
* Update release.rst
* Implement d-v-b's suggestions
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* doc(v3): add v3 roadmap and design document (#1583)
* doc(v3): add v3 roadmap and design document
* Update v3-roadmap-and-design.md
* updates after latest round of reviews
* Update v3-roadmap-and-design.md
Co-authored-by: Norman Rzepka <code@normanrz.com>
* Update v3-roadmap-and-design.md
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
---------
Co-authored-by: Norman Rzepka <code@normanrz.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore: update pre-commit hooks (#1636)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.13 → v0.1.14](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.13...v0.1.14)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix zarr sync (#1663)
This patch removes fasteners and disables zarr.sync which uses process and thread
Co-authored-by: Wei Ouyang <oeway007@gmail.com>
* Update release.rst (#1621)
* Update release.rst
* Update release.rst
* Change 2.16.2 → 2.17.0
* Update moto for test_s3
* Skip bsddb3 tests to prevent warning failure
* Fix more user warning tests
* Fix even more user warning tests
* Skip coverage for importorskips
* Move to have_X skip method for deps
* Update release.rst (PR#1663)
* Fix test_core.py 'compile' issues
* Add black formatting
* Drop Windows/3.9 build due to unrelated failures
* fix typo
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Bump numpy from 1.24.3 to 1.26.1 (#1543)
Bumps [numpy](https://github.com/numpy/numpy) from 1.24.3 to 1.26.1.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.24.3...v1.26.1)
---
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- dependency-name: numpy
dependency-type: direct:development
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* chore: update pre-commit hooks (#1642)
* chore: update pre-commit hooks
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.14 → v0.2.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.14...v0.2.1)
- [github.com/psf/black: 23.12.1 → 24.2.0](https://github.com/psf/black/compare/23.12.1...24.2.0)
* run black incl. comments for '...'
---------
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Bump ipywidgets from 8.1.0 to 8.1.1 (#1538)
Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.1.0 to 8.1.1.
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.0...8.1.1)
---
updated-dependencies:
- dependency-name: ipywidgets
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update-type: version-update:semver-patch
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Proper argument for numpy.reshape (#1425)
`numpy.reshape` not only accepts a tuple of ints, but also a simple int.
Besides `(10)` is not a tuple and is identical to `10`, unlike `(10,)`.
* Bump ipywidgets from 8.1.1 to 8.1.2 (#1666)
Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.1.1 to 8.1.2.
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.1...8.1.2)
---
updated-dependencies:
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* docs: ZIP-related tweaks (#1641)
* docs: use 'ZIP archive' instead of 'zip file'; clarify utility of caching in s3 + ZIP example; style
* docs: update release notes, correct spelling of greg lee's name in past release notes, and fix markup in past release notes
* docs: use 'ZIP archive' instead of 'zip file'; clarify utility of caching in s3 + ZIP example; style
* docs: update release notes, correct spelling of greg lee's name in past release notes, and fix markup in past release notes
* Bump numpy from 1.26.1 to 1.26.4 (#1669)
Bumps [numpy](https://github.com/numpy/numpy) from 1.26.1 to 1.26.4.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.1...v1.26.4)
---
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- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* Change occurrences of % and format() to f-strings (#1423)
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* chore: update pre-commit hooks (#1672)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.1 → v0.2.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.1...v0.2.2)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Bump pymongo from 4.6.1 to 4.6.2 (#1674)
Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.6.1 to 4.6.2.
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/4.6.2/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.6.1...4.6.2)
---
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- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* Bump conda-incubator/setup-miniconda from 3.0.1 to 3.0.2 (#1677)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.1 to 3.0.2.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.1...v3.0.2)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
...
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* Update config.yml with Zulip
* Type dimension separator (#1620)
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Replace Gitter with new Zulip Chat link (#1685)
* Replace Gitter with Zulip
* Replace Gitter with Zulip in remaining places
* Bump redis from 5.0.1 to 5.0.2 (#1688)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.1 to 5.0.2.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.1...v5.0.2)
---
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- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* Bump pypa/gh-action-pypi-publish from 1.8.11 to 1.8.12 (#1691)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.11 to 1.8.12.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.11...v1.8.12)
---
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- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
...
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* Bump pytest-doctestplus from 1.1.0 to 1.2.0 (#1693)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.1.0 to 1.2.0.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.1.0...v1.2.0)
---
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- dependency-name: pytest-doctestplus
dependency-type: direct:development
update-type: version-update:semver-minor
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* Fix RTD build (#1694)
* Update release.rst for v2.17.1 (#1673)
* Update release.rst for v2.17.1
* Change the copyright year from 2023 → 2024.
* Update release.rst for v2.17.1
* Bump pytest-timeout from 2.2.0 to 2.3.1 (#1697)
Bumps [pytest-timeout](https://github.com/pytest-dev/pytest-timeout) from 2.2.0 to 2.3.1.
- [Commits](https://github.com/pytest-dev/pytest-timeout/compare/2.2.0...2.3.1)
---
updated-dependencies:
- dependency-name: pytest-timeout
dependency-type: direct:development
update-type: version-update:semver-minor
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* Bump conda-incubator/setup-miniconda from 3.0.2 to 3.0.3 (#1690)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.2 to 3.0.3.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.2...v3.0.3)
---
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- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
...
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Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* docs(tutorial.rst): fix link to GCSMap (#1689)
* Update installation.rst stating version support policy (#1665)
* Update installation.rst stating version support policy
* Update docs/installation.rst
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Update docs/installation.rst
---------
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Bump pypa/gh-action-pypi-publish from 1.8.12 to 1.8.14 (#1700)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.12 to 1.8.14.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.12...v1.8.14)
---
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- dependency-name: pypa/gh-action-pypi-publish
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update-type: version-update:semver-patch
...
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* Bump pytest-doctestplus from 1.2.0 to 1.2.1 (#1699)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.2.0 to 1.2.1.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.2.0...v1.2.1)
---
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- dependency-name: pytest-doctestplus
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* Bump redis from 5.0.2 to 5.0.3 (#1698)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.2 to 5.0.3.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.2...v5.0.3)
---
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* Add Python 3.12 to CI (#1719)
* Update python-package.yml
* bump numpy versions
* bump min python version
* Update release.rst
* Bump pytest-cov from 4.1.0 to 5.0.0 (#1722)
Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 4.1.0 to 5.0.0.
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest-cov/compare/v4.1.0...v5.0.0)
---
updated-dependencies:
- dependency-name: pytest-cov
dependency-type: direct:development
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore: update pre-commit hooks (#1708)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.2 → v0.3.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.2...v0.3.3)
- [github.com/psf/black: 24.2.0 → 24.3.0](https://github.com/psf/black/compare/24.2.0...24.3.0)
- [github.com/pre-commit/mirrors-mypy: v1.8.0 → v1.9.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.8.0...v1.9.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore: update pre-commit hooks (#1723)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.3 → v0.3.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.3...v0.3.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix release notes (following #1719) (#1725)
* Override ipython repr methods. (#1724)
Closes #1716
This avoids expensive lookups against object stores.
* Bump pymongo from 4.6.2 to 4.6.3 (#1729)
* Remove v1 and v2 specification (#1582)
* Remove v1 and v2 specification
* fix warning
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* chore: update pre-commit hooks (#1738)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.4 → v0.3.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.4...v0.3.5)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Optimize Array.info and Group.info (#1733)
* Optimize Array.info.
Avoid repeated computes of the same value (getsize)
* Don't have InfoReporter query items twice.
Apparently IPython will run both __repr__ and _repr_html_
so we were calling `getsize` twice.
* Group too
* Apply suggestions from code review
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
---------
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Bump actions/setup-python from 5.0.0 to 5.1.0 (#1736)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.0.0 to 5.1.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.0.0...v5.1.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Couple fixes (#1737)
* Use `is` when comparing `type` of two objects
* Unnecessary `None` provided as default
* Fix tests with Pytest 8 (#1714)
* Bump pytest version
* Use editable install when testing
---------
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Avoid redundant __contains__ (#1739)
Let's try grabbing the array.json and group.json files,
and check for `*NotFoundError`, instead of using contains first.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Array & Group: Use already loaded attributes to populate cache. (#1734)
* Array: Use already loaded attributes to populate cache.
* Group: Use already loaded attributes to populate cache.
* Fix
* Add release note
* Optimize attribute setting (#1741)
* Optimize attribute setting
* Add release note
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Make sure fs exceptions are raised if not MissingFs exceptions (clone) (#1604)
* Make sure fs exceptions are raised if not Missing
* lint
* add missing argument in tests, lint
* clear memory filesystem during test
* improve commenting
* add memory_store fixture, getitems performance
* Update release.rst
* improve FSStore.test_exception coverage
---------
Co-authored-by: Martin Durant <martin.durant@alumni.utoronto.ca>
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore(release): update changelog for 2.17.2 (#1775)
* chore(docs): reset release notes as unreleased (#1776)
* Bump codecov/codecov-action from 3 to 4 (#1647)
* Bump codecov/codecov-action from 3 to 4
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v3...v4)
---
updated-dependencies:
- dependency-name: codecov/codecov-action
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
* Set codecov env
---------
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Update release.rst for v2.17.2 (#1778)
* Update release.rst for v2.17.2
* Minor edits
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Deprecate the experimental v3 implementation (#1802)
* deprecate(exp-v3): Add a future warning about the pending removal of the experimental v3 implementation
* ignore warning
* add test
* chore: update pre-commit hooks (#1779)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.3.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.5...v0.3.7)
- [github.com/psf/black: 24.3.0 → 24.4.0](https://github.com/psf/black/compare/24.3.0...24.4.0)
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v4.6.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix `is_total_slice` for size-1 dimensions (#1800)
Closes #1730
Co-authored-by: Ryan Abernathey <ryan.abernathey@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* add note to the top of the release page noting the plan for 2.18.* and 3.0 (#1816)
* Bump conda-incubator/setup-miniconda from 3.0.3 to 3.0.4 (#1824)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.3 to 3.0.4.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.3...v3.0.4)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* dep(docs): deprecate experimental v3 support in docs (#1807)
* dep(docs): deprecate experimental v3 support in docs
* Apply suggestions from code review
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
---------
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Bump h5py from 3.10.0 to 3.11.0 (#1786)
Bumps [h5py](https://github.com/h5py/h5py) from 3.10.0 to 3.11.0.
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](https://github.com/h5py/h5py/compare/3.10.0...3.11.0)
---
updated-dependencies:
- dependency-name: h5py
dependency-type: direct:development
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump redis from 5.0.3 to 5.0.4 (#1810)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.3 to 5.0.4.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.3...v5.0.4)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* deprecate(stores): add deprecation warnings to stores that we plan to remove in v3 (#1801)
* deprecate(stores): add deprecation warnings to DBMStore, LMDBStore, SQLiteStore, MongoDBStore, RedisStore, and ABSStore
* filter warnings in pytest config
* more deprecation warnings in docstrings
* add release note
* use np.inf instead of PINF/NINF (#1842)
* use np.inf instead of PINF/NINF
* update release notes
* chore: update pre-commit hooks (#1825)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.1 → v0.4.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.1...v0.4.3)
- [github.com/psf/black: 24.4.0 → 24.4.2](https://github.com/psf/black/compare/24.4.0...24.4.2)
- [github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.9.0...v1.10.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Enable ruff/bugbear rules (B) and fix issues (#1702)
* Enable ruff/bugbear rules (B)
As suggested by Repo-Review.
* Fix ruff/bugbear issue (B007)
B007 Loop control variable `key` not used within loop body
https://docs.astral.sh/ruff/rules/unused-loop-control-variable/
* Fix ruff/bugbear issue (B015)
B015 Pointless comparison. Did you mean to assign a value?
Otherwise, prepend `assert` or remove it.
https://docs.astral.sh/ruff/rules/useless-comparison/
* Fix ruff/bugbear issues (B028)
B028 No explicit `stacklevel` keyword argument found
https://docs.astral.sh/ruff/rules/no-explicit-stacklevel/
* Fix ruff/bugbear issues (B904)
B904 Within an `except` clause, raise exceptions with `raise ... from err` or
`raise ... from None` to distinguish them from errors in exception handling
https://docs.astral.sh/ruff/rules/raise-without-from-inside-except/
* Document changes in docs/release.rst
* Disable ruff/bugbear rule (B017)
B017 `pytest.raises(Exception)` should be considered evil
https://docs.astral.sh/ruff/rules/assert-raises-exception/
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Release notes for 2.18.0 (#1843)
* doc: cleanup release notes for 2.18.0
* Update release.rst (#1850)
* Group dependabot updates (#1854)
* chore: update pre-commit hooks (#1876)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.3 → v0.4.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.3...v0.4.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix a regression with scalar indexing due to #1800 (#1875)
* release notes for 2.18.1 (#1885)
* reset release notes (#1886)
* Add zstd to old V3 supported codecs (#1914)
* add zstd to old V3 supported codecs
* get to full test coverage and add release note
* fix pre-commit
* doc: update release notes for 2.18.2 (#1915)
* Drop support for Python 3.9
* Revert "Drop support for Python 3.9"
This reverts commit a054afbbdaf7c8560d0ce5df77af969bc863e335.
* Update TEAM.md (#2071)
* [v2] Fix doctests with numpy 2.0 (#2073)
* Fix version number in built docs (#2044)
* Fix orthogonal indexing with scalar. (#1947)
Co-authored-by: David Stansby <dstansby@gmail.com>
* Bump the requirements group across 1 directory with 7 updates (#2092)
Bumps the requirements group with 7 updates in the / directory:
| Package | From | To |
| --- | --- | --- |
| [numpy](https://github.com/numpy/numpy) | `1.26.4` | `2.0.1` |
| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) | `8.1.2` | `8.1.3` |
| [setuptools-scm](https://github.com/pypa/setuptools_scm) | `8.0.4` | `8.1.0` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.1.1` | `8.3.2` |
| [lmdb](https://github.com/jnwatson/py-lmdb) | `1.4.1` | `1.5.1` |
| [redis](https://github.com/redis/redis-py) | `5.0.4` | `5.0.8` |
| [pymongo](https://github.com/mongodb/mongo-python-driver) | `4.6.3` | `4.8.0` |
Updates `numpy` from 1.26.4 to 2.0.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.4...v2.0.1)
Updates `ipywidgets` from 8.1.2 to 8.1.3
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.2...8.1.3)
Updates `setuptools-scm` from 8.0.4 to 8.1.0
- [Release notes](https://github.com/pypa/setuptools_scm/releases)
- [Changelog](https://github.com/pypa/setuptools_scm/blob/main/CHANGELOG.md)
- [Commits](https://github.com/pypa/setuptools_scm/compare/v8.0.4...v8.1.0)
Updates `pytest` from 8.1.1 to 8.3.2
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.1.1...8.3.2)
Updates `lmdb` from 1.4.1 to 1.5.1
- [Changelog](https://github.com/jnwatson/py-lmdb/blob/master/ChangeLog)
- [Commits](https://github.com/jnwatson/py-lmdb/compare/py-lmdb_1.4.1...py-lmdb_1.5.1)
Updates `redis` from 5.0.4 to 5.0.8
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.4...v5.0.8)
Updates `pymongo` from 4.6.3 to 4.8.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.6.3...4.8.0)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-major
dependency-group: requirements
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: setuptools-scm
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: pytest
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: lmdb
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump the actions group with 2 updates (#2087)
Bumps the actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `actions/setup-python` from 5.1.0 to 5.1.1
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.1.0...v5.1.1)
Updates `pypa/gh-action-pypi-publish` from 1.8.14 to 1.9.0
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.14...v1.9.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* [v2] Drop support for Python 3.9 (#2074)
* Drop support for Python 3.9
* Ignore B905 ruff rule
* Fix release notes
* Fix Array.__array__ for numpy 2.1 (#2106)
* Fix Array.__array__ for numpy 2.1
* Add changelog
* Depend on np.array for array coercions
* Bump test version of numcodecs (#2114)
* Bump test version of numcodecs
* Fix test for numcodecs 0.13
* fix: numpy 1.24 compat for Array.__array__ (#2123)
* Deprecate N5Store (#2103)
* deprecate(n5): add deprecation warning to N5Store
* also deprecate N5FSStore
* docs
* fix doc
* Run tests on numpy 1.23 (#2124)
* Bump the requirements group across 1 directory with 3 updates (#2129)
Bumps the requirements group with 3 updates in the / directory: [numpy](https://github.com/numpy/numpy), [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) and [azure-storage-blob](https://github.com/Azure/azure-sdk-for-python).
Updates `numpy` from 2.0.1 to 2.1.0
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.0.1...v2.1.0)
Updates `ipywidgets` from 8.1.3 to 8.1.5
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.3...8.1.5)
Updates `azure-storage-blob` from 12.16.0 to 12.21.0
- [Release notes](https://github.com/Azure/azure-sdk-for-python/releases)
- [Changelog](https://github.com/Azure/azure-sdk-for-python/blob/main/doc/esrp_release.md)
- [Commits](https://github.com/Azure/azure-sdk-for-python/compare/azure-storage-blob_12.16.0...azure-storage-blob_12.21.0)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: azure-storage-blob
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore: bump minimum numpy version to 1.24 (#2127)
* chore: bump minimum version to 1.24
* Update .github/workflows/python-package.yml
* Remove un-needed package installs in CI (#2095)
* Bump the actions group with 2 updates (#2146)
Bumps the actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `actions/setup-python` from 5.1.1 to 5.2.0
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.1.1...v5.2.0)
Updates `pypa/gh-action-pypi-publish` from 1.9.0 to 1.10.0
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.9.0...v1.10.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump numpy from 2.1.0 to 2.1.1 in the requirements group (#2151)
Bumps the requirements group with 1 update: [numpy](https://github.com/numpy/numpy).
Updates `numpy` from 2.1.0 to 2.1.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.0...v2.1.1)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore(docs): update release notes ahead of 2.18.4 (#2152)
* Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1 in the actions group (#2161)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.0 to 1.10.1
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.0...v1.10.1)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* [docs] remove primary sidebar from tutorial (#2142)
* remove primary sidebar from tutorial
* lint
* Bump pytest from 8.3.2 to 8.3.3 in the requirements group (#2172)
Bumps the requirements group with 1 update: [pytest](https://github.com/pytest-dev/pytest).
Updates `pytest` from 8.3.2 to 8.3.3
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.3.2...8.3.3)
---
updated-dependencies:
- dependency-name: pytest
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump pypa/gh-action-pypi-publish in the actions group (#2220)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.1 to 1.10.2
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.1...v1.10.2)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Update TEAM.md (#2227)
* Bump the requirements group across 1 directory with 3 updates (#2284)
Bumps the requirements group with 3 updates in the / directory: [redis](https://github.com/redis/redis-py), [pymongo](https://github.com/mongodb/mongo-python-driver) and [h5py](https://github.com/h5py/h5py).
Updates `redis` from 5.0.8 to 5.1.0
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.8...v5.1.0)
Updates `pymongo` from 4.8.0 to 4.10.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.8.0...4.10.0)
Updates `h5py` from 3.11.0 to 3.12.1
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](https://github.com/h5py/h5py/compare/3.11.0...3.12.1)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: h5py
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump pymongo from 4.10.0 to 4.10.1 in the requirements group (#2288)
Bumps the requirements group with 1 update: [pymongo](https://github.com/mongodb/mongo-python-driver).
Updates `pymongo` from 4.10.0 to 4.10.1
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.10.0...4.10.1)
---
updated-dependencies:
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Fix low contrast box titles (#2287) (#2292)
* Bump pypa/gh-action-pypi-publish in the actions group (#2304)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.2 to 1.10.3
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.2...v1.10.3)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump the requirements group with 2 updates (#2303)
Bumps the requirements group with 2 updates: [numpy](https://github.com/numpy/numpy) and [redis](https://github.com/redis/redis-py).
Updates `numpy` from 2.1.1 to 2.1.2
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.1...v2.1.2)
Updates `redis` from 5.1.0 to 5.1.1
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.1.0...v5.1.1)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump numcodecs from 0.13.0 to 0.13.1 in the requirements group (#2326)
Bumps the requirements group with 1 update: [numcodecs](https://github.com/zarr-developers/numcodecs).
Updates `numcodecs` from 0.13.0 to 0.13.1
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.rst)
- [Commits](https://github.com/zarr-developers/numcodecs/compare/v0.13.0...v0.13.1)
---
updated-dependencies:
- dependency-name: numcodecs
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* remove zarr.types from v2
---------
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Janick Martinez Esturo <janick@jme.pub>
Co-authored-by: David Stansby <dstansby@gmail.com>
Co-authored-by: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com>
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: jakirkham <jakirkham@gmail.com>
Co-authored-by: Jeff Peck <jeffrey.peck@10xgenomics.com>
Co-authored-by: Norman Rzepka <code@normanrz.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
Co-authored-by: Hood Chatham <roberthoodchatham@gmail.com>
Co-authored-by: Wei Ouyang <oeway007@gmail.com>
Co-authored-by: Daniel Jahn (dahn) <dahnjahn@gmail.com>
Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com>
Co-authored-by: Ian Carroll <carroll.ian@gmail.com>
Co-authored-by: Martin Durant <martin.durant@alumni.utoronto.ca>
Co-authored-by: Ryan Abernathey <ryan.abernathey@gmail.com>
Co-authored-by: Jonny Saunders <sneakers-the-rat@protonmail.com>
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Bump actions/setup-python from 4.7.1 to 5.0.0 by dependabot[bot] · Pull Request #1605 · zarr-developers/zarr-python · GitHub
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Bump actions/setup-python from 4.7.1 to 5.0.0 - #1605
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Bump actions/setup-python from 4.7.1 to 5.0.0#1605
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Bumps actions/setup-python from 4.7.1 to 5.0.0.
Release notes
Sourced from actions/setup-python's releases.
v5.0.0
What's Changed
In scope of this release, we update node version runtime from node16 to node20 (actions/setup-python#772). Besides, we update dependencies to the latest versions.
Full Changelog: actions/setup-python@v4.8.0...v5.0.0
v4.8.0
What's Changed
In scope of this release we added support for GraalPy (actions/setup-python#694). You can use this snippet to set up GraalPy:
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v4 with:
python-version: 'graalpy-22.3' - run: python my_script.py
Besides, the release contains such changes as:
New Contributors
Full Changelog: actions/setup-python@v4...v4.8.0
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@dependabot
Bump actions/setup-python from 4.7.1 to 5.0.0
cf76095
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
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Dependabot tried to merge this PR, but received the following error from GitHub:
At least 1 approving review is required by reviewers with write access.

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@dependabot@jhamman
Bump actions/setup-python from 4.7.1 to 5.0.0 (zarr-developers#1605)
a5b4b90
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4.7.1...v5.0.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
jhamman added a commit
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@jhamman@dependabot
@janickm@dstansby@DimitriPapadopoulos@d-v-b@joshmoore@pre-commit-ci@jakirkham@jeffpeck10x@normanrz@sanketverma1704@hoodmane@oeway@DahnJ@dcherian@itcarroll@martindurant@rabernat@sneakers-the-rat
V3 main sync w/ merge (#2335)
ce5f53e
* Bump pypa/gh-action-pypi-publish from 1.8.10 to 1.8.11 (#1586)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.10 to 1.8.11.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.10...v1.8.11)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump conda-incubator/setup-miniconda from 2.3.0 to 3.0.1 (#1587)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 2.3.0 to 3.0.1.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v2.3.0...v3.0.1)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* * Cache result of FSStore._fsspec_installed (#1581)
Prevent runtime-overhead in doing this check multiple times
* Bump version of black in pre-commit (#1559)
* Use list comprehension where applicable (#1555)
Even if this is only a test, list comprehensions are faster than
repeatedly call append().
Also use tuple instead of list when possible.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Bump numcodecs from 0.11.0 to 0.12.1 (#1580)
Bumps [numcodecs](https://github.com/zarr-developers/numcodecs) from 0.11.0 to 0.12.1.
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.rst)
- [Commits](https://github.com/zarr-developers/numcodecs/compare/v0.11.0...v0.12.1)
---
updated-dependencies:
- dependency-name: numcodecs
dependency-type: direct:development
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Use format specification mini-language to format string (#1558)
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Single startswith() call instead of multiple ones (#1556)
It's faster and probably more readable.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump pymongo from 4.5.0 to 4.6.1 (#1585)
Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.5.0 to 4.6.1.
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.5.0...4.6.1)
---
updated-dependencies:
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Move codespell options around (#1196)
Starting with codespell 2.2.2, options can be specified in
`pyrpoject.toml` in addition to `setup.cfg`:
https://github.com/codespell-project/codespell#using-a-config-file
Specifying options in a config file instead of command line options in
`.pre-commit-config.yaml` ensures codespell uses the same options when
run as pre-commit hook or from the command line in the repository root
directory.
* Bump fsspec from 2023.10.0 to 2023.12.1 (#1600)
* Bump fsspec from 2023.10.0 to 2023.12.1
Bumps [fsspec](https://github.com/fsspec/filesystem_spec) from 2023.10.0 to 2023.12.1.
- [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.10.0...2023.12.1)
---
updated-dependencies:
- dependency-name: fsspec
dependency-type: direct:development
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
* Update s3fs as well
* Fix s3fs
---------
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Add type hints to zarr.create (#1536)
* Add type hints to zarr.create
* Use protocol for MetaArray
* Use protocol for Synchronizer
* Fix Path typing
* Add release note
* Fix dim separator typing
* Ignore ... in coverage reporting
* Fix chunk typing
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Remove unused mypy ignore comments (#1602)
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Bump actions/setup-python from 4.7.1 to 5.0.0 (#1605)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v4.7.1...v5.0.0)
---
updated-dependencies:
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* Bump github/codeql-action from 2 to 3 (#1609)
Bumps [github/codeql-action](https://github.com/github/codeql-action) from 2 to 3.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/github/codeql-action/compare/v2...v3)
---
updated-dependencies:
- dependency-name: github/codeql-action
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* chore: update pre-commit hooks (#1448)
* chore: update pre-commit hooks
updates:
- https://github.com/charliermarsh/ruff-pre-commit → https://github.com/astral-sh/ruff-pre-commit
- [github.com/astral-sh/ruff-pre-commit: v0.0.224 → v0.1.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.224...v0.1.8)
- [github.com/psf/black: 23.10.1 → 23.12.0](https://github.com/psf/black/compare/23.10.1...23.12.0)
- [github.com/codespell-project/codespell: v2.2.5 → v2.2.6](https://github.com/codespell-project/codespell/compare/v2.2.5...v2.2.6)
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.4.0...v4.5.0)
- [github.com/pre-commit/mirrors-mypy: v1.3.0 → v1.7.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.3.0...v1.7.1)
* Attempt to fix ruff
* Use isinstance
---------
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* chore: update pre-commit hooks (#1618)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.8 → v0.1.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.8...v0.1.9)
- [github.com/psf/black: 23.12.0 → 23.12.1](https://github.com/psf/black/compare/23.12.0...23.12.1)
- [github.com/pre-commit/mirrors-mypy: v1.7.1 → v1.8.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.7.1...v1.8.0)
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* Bump fsspec from 2023.12.1 to 2023.12.2 (#1606)
* Bump fsspec from 2023.12.1 to 2023.12.2
Bumps [fsspec](https://github.com/fsspec/filesystem_spec) from 2023.12.1 to 2023.12.2.
- [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.12.1...2023.12.2)
---
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* Update requirements_dev_optional.txt
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* Bump pytest-doctestplus from 1.0.0 to 1.1.0 (#1619)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.0.0 to 1.1.0.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.0.0...v1.1.0)
---
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* Bump pytest from 7.4.3 to 7.4.4 (#1622)
* chore: update pre-commit hooks (#1626)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.1.11](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.9...v0.1.11)
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* Create TEAM.md (#1628)
* Drop python 3.8 and numpy 1.20 (#1557)
* Drop 3.8 and add 3.12
* Try removing line_profiler
* Also bump the minimal numpy to 1.21
* Drop 3.12 again
* Revert "Try removing line_profiler"
This reverts commit 837854bec99a9d25aece2ead9666f01690d228cc.
* Update release.rst
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: jakirkham <jakirkham@gmail.com>
* Add Norman Rzepka to core-dev team (#1630)
* chore: update pre-commit hooks (#1633)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.11 → v0.1.13](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.11...v0.1.13)
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* Bump actions/download-artifact from 3 to 4 (#1611)
* Bump actions/download-artifact from 3 to 4
Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4.
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](https://github.com/actions/download-artifact/compare/v3...v4)
---
updated-dependencies:
- dependency-name: actions/download-artifact
dependency-type: direct:production
update-type: version-update:semver-major
...
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* Also bump upload-artifact
see https://github.com/actions/download-artifact?tab=readme-ov-file#breaking-changes
> Downloading artifacts that were created from action/upload-artifact@v3 and below are not supported.
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Update tutorial.rst to include section about accessing Zip Files on S3 (#1615)
* Update tutorial.rst to include section about accessing Zip Files on S3
Per discussion here, add information about about accessing zip files on s3:
https://github.com/zarr-developers/zarr-python/discussions/1613
* Update release.rst
* Implement d-v-b's suggestions
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* doc(v3): add v3 roadmap and design document (#1583)
* doc(v3): add v3 roadmap and design document
* Update v3-roadmap-and-design.md
* updates after latest round of reviews
* Update v3-roadmap-and-design.md
Co-authored-by: Norman Rzepka <code@normanrz.com>
* Update v3-roadmap-and-design.md
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
---------
Co-authored-by: Norman Rzepka <code@normanrz.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore: update pre-commit hooks (#1636)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.13 → v0.1.14](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.13...v0.1.14)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix zarr sync (#1663)
This patch removes fasteners and disables zarr.sync which uses process and thread
Co-authored-by: Wei Ouyang <oeway007@gmail.com>
* Update release.rst (#1621)
* Update release.rst
* Update release.rst
* Change 2.16.2 → 2.17.0
* Update moto for test_s3
* Skip bsddb3 tests to prevent warning failure
* Fix more user warning tests
* Fix even more user warning tests
* Skip coverage for importorskips
* Move to have_X skip method for deps
* Update release.rst (PR#1663)
* Fix test_core.py 'compile' issues
* Add black formatting
* Drop Windows/3.9 build due to unrelated failures
* fix typo
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Bump numpy from 1.24.3 to 1.26.1 (#1543)
Bumps [numpy](https://github.com/numpy/numpy) from 1.24.3 to 1.26.1.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.24.3...v1.26.1)
---
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- dependency-name: numpy
dependency-type: direct:development
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* chore: update pre-commit hooks (#1642)
* chore: update pre-commit hooks
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.14 → v0.2.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.14...v0.2.1)
- [github.com/psf/black: 23.12.1 → 24.2.0](https://github.com/psf/black/compare/23.12.1...24.2.0)
* run black incl. comments for '...'
---------
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Bump ipywidgets from 8.1.0 to 8.1.1 (#1538)
Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.1.0 to 8.1.1.
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.0...8.1.1)
---
updated-dependencies:
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
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Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Proper argument for numpy.reshape (#1425)
`numpy.reshape` not only accepts a tuple of ints, but also a simple int.
Besides `(10)` is not a tuple and is identical to `10`, unlike `(10,)`.
* Bump ipywidgets from 8.1.1 to 8.1.2 (#1666)
Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.1.1 to 8.1.2.
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.1...8.1.2)
---
updated-dependencies:
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
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* docs: ZIP-related tweaks (#1641)
* docs: use 'ZIP archive' instead of 'zip file'; clarify utility of caching in s3 + ZIP example; style
* docs: update release notes, correct spelling of greg lee's name in past release notes, and fix markup in past release notes
* docs: use 'ZIP archive' instead of 'zip file'; clarify utility of caching in s3 + ZIP example; style
* docs: update release notes, correct spelling of greg lee's name in past release notes, and fix markup in past release notes
* Bump numpy from 1.26.1 to 1.26.4 (#1669)
Bumps [numpy](https://github.com/numpy/numpy) from 1.26.1 to 1.26.4.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.1...v1.26.4)
---
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- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* Change occurrences of % and format() to f-strings (#1423)
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* chore: update pre-commit hooks (#1672)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.1 → v0.2.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.1...v0.2.2)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Bump pymongo from 4.6.1 to 4.6.2 (#1674)
Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.6.1 to 4.6.2.
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/4.6.2/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.6.1...4.6.2)
---
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- dependency-name: pymongo
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update-type: version-update:semver-patch
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* Bump conda-incubator/setup-miniconda from 3.0.1 to 3.0.2 (#1677)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.1 to 3.0.2.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.1...v3.0.2)
---
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- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
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* Update config.yml with Zulip
* Type dimension separator (#1620)
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Replace Gitter with new Zulip Chat link (#1685)
* Replace Gitter with Zulip
* Replace Gitter with Zulip in remaining places
* Bump redis from 5.0.1 to 5.0.2 (#1688)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.1 to 5.0.2.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.1...v5.0.2)
---
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- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
...
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* Bump pypa/gh-action-pypi-publish from 1.8.11 to 1.8.12 (#1691)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.11 to 1.8.12.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.11...v1.8.12)
---
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- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
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* Bump pytest-doctestplus from 1.1.0 to 1.2.0 (#1693)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.1.0 to 1.2.0.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.1.0...v1.2.0)
---
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- dependency-name: pytest-doctestplus
dependency-type: direct:development
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* Fix RTD build (#1694)
* Update release.rst for v2.17.1 (#1673)
* Update release.rst for v2.17.1
* Change the copyright year from 2023 → 2024.
* Update release.rst for v2.17.1
* Bump pytest-timeout from 2.2.0 to 2.3.1 (#1697)
Bumps [pytest-timeout](https://github.com/pytest-dev/pytest-timeout) from 2.2.0 to 2.3.1.
- [Commits](https://github.com/pytest-dev/pytest-timeout/compare/2.2.0...2.3.1)
---
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- dependency-name: pytest-timeout
dependency-type: direct:development
update-type: version-update:semver-minor
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* Bump conda-incubator/setup-miniconda from 3.0.2 to 3.0.3 (#1690)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.2 to 3.0.3.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.2...v3.0.3)
---
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- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
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* docs(tutorial.rst): fix link to GCSMap (#1689)
* Update installation.rst stating version support policy (#1665)
* Update installation.rst stating version support policy
* Update docs/installation.rst
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Update docs/installation.rst
---------
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Bump pypa/gh-action-pypi-publish from 1.8.12 to 1.8.14 (#1700)
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.12 to 1.8.14.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.12...v1.8.14)
---
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- dependency-name: pypa/gh-action-pypi-publish
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update-type: version-update:semver-patch
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* Bump pytest-doctestplus from 1.2.0 to 1.2.1 (#1699)
Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.2.0 to 1.2.1.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.2.0...v1.2.1)
---
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* Bump redis from 5.0.2 to 5.0.3 (#1698)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.2 to 5.0.3.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.2...v5.0.3)
---
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* Add Python 3.12 to CI (#1719)
* Update python-package.yml
* bump numpy versions
* bump min python version
* Update release.rst
* Bump pytest-cov from 4.1.0 to 5.0.0 (#1722)
Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 4.1.0 to 5.0.0.
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest-cov/compare/v4.1.0...v5.0.0)
---
updated-dependencies:
- dependency-name: pytest-cov
dependency-type: direct:development
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore: update pre-commit hooks (#1708)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.2 → v0.3.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.2...v0.3.3)
- [github.com/psf/black: 24.2.0 → 24.3.0](https://github.com/psf/black/compare/24.2.0...24.3.0)
- [github.com/pre-commit/mirrors-mypy: v1.8.0 → v1.9.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.8.0...v1.9.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore: update pre-commit hooks (#1723)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.3 → v0.3.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.3...v0.3.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix release notes (following #1719) (#1725)
* Override ipython repr methods. (#1724)
Closes #1716
This avoids expensive lookups against object stores.
* Bump pymongo from 4.6.2 to 4.6.3 (#1729)
* Remove v1 and v2 specification (#1582)
* Remove v1 and v2 specification
* fix warning
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* chore: update pre-commit hooks (#1738)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.4 → v0.3.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.4...v0.3.5)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Optimize Array.info and Group.info (#1733)
* Optimize Array.info.
Avoid repeated computes of the same value (getsize)
* Don't have InfoReporter query items twice.
Apparently IPython will run both __repr__ and _repr_html_
so we were calling `getsize` twice.
* Group too
* Apply suggestions from code review
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
---------
Co-authored-by: Joe Hamman <jhamman1@gmail.com>
* Bump actions/setup-python from 5.0.0 to 5.1.0 (#1736)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.0.0 to 5.1.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.0.0...v5.1.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Couple fixes (#1737)
* Use `is` when comparing `type` of two objects
* Unnecessary `None` provided as default
* Fix tests with Pytest 8 (#1714)
* Bump pytest version
* Use editable install when testing
---------
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Avoid redundant __contains__ (#1739)
Let's try grabbing the array.json and group.json files,
and check for `*NotFoundError`, instead of using contains first.
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Array & Group: Use already loaded attributes to populate cache. (#1734)
* Array: Use already loaded attributes to populate cache.
* Group: Use already loaded attributes to populate cache.
* Fix
* Add release note
* Optimize attribute setting (#1741)
* Optimize attribute setting
* Add release note
---------
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
* Make sure fs exceptions are raised if not MissingFs exceptions (clone) (#1604)
* Make sure fs exceptions are raised if not Missing
* lint
* add missing argument in tests, lint
* clear memory filesystem during test
* improve commenting
* add memory_store fixture, getitems performance
* Update release.rst
* improve FSStore.test_exception coverage
---------
Co-authored-by: Martin Durant <martin.durant@alumni.utoronto.ca>
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* chore(release): update changelog for 2.17.2 (#1775)
* chore(docs): reset release notes as unreleased (#1776)
* Bump codecov/codecov-action from 3 to 4 (#1647)
* Bump codecov/codecov-action from 3 to 4
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v3...v4)
---
updated-dependencies:
- dependency-name: codecov/codecov-action
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com>
* Set codecov env
---------
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
* Update release.rst for v2.17.2 (#1778)
* Update release.rst for v2.17.2
* Minor edits
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Deprecate the experimental v3 implementation (#1802)
* deprecate(exp-v3): Add a future warning about the pending removal of the experimental v3 implementation
* ignore warning
* add test
* chore: update pre-commit hooks (#1779)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.3.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.5...v0.3.7)
- [github.com/psf/black: 24.3.0 → 24.4.0](https://github.com/psf/black/compare/24.3.0...24.4.0)
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v4.6.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix `is_total_slice` for size-1 dimensions (#1800)
Closes #1730
Co-authored-by: Ryan Abernathey <ryan.abernathey@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* add note to the top of the release page noting the plan for 2.18.* and 3.0 (#1816)
* Bump conda-incubator/setup-miniconda from 3.0.3 to 3.0.4 (#1824)
Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.3 to 3.0.4.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.3...v3.0.4)
---
updated-dependencies:
- dependency-name: conda-incubator/setup-miniconda
dependency-type: direct:production
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* dep(docs): deprecate experimental v3 support in docs (#1807)
* dep(docs): deprecate experimental v3 support in docs
* Apply suggestions from code review
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
---------
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
* Bump h5py from 3.10.0 to 3.11.0 (#1786)
Bumps [h5py](https://github.com/h5py/h5py) from 3.10.0 to 3.11.0.
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](https://github.com/h5py/h5py/compare/3.10.0...3.11.0)
---
updated-dependencies:
- dependency-name: h5py
dependency-type: direct:development
update-type: version-update:semver-minor
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Bump redis from 5.0.3 to 5.0.4 (#1810)
Bumps [redis](https://github.com/redis/redis-py) from 5.0.3 to 5.0.4.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.3...v5.0.4)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* deprecate(stores): add deprecation warnings to stores that we plan to remove in v3 (#1801)
* deprecate(stores): add deprecation warnings to DBMStore, LMDBStore, SQLiteStore, MongoDBStore, RedisStore, and ABSStore
* filter warnings in pytest config
* more deprecation warnings in docstrings
* add release note
* use np.inf instead of PINF/NINF (#1842)
* use np.inf instead of PINF/NINF
* update release notes
* chore: update pre-commit hooks (#1825)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.1 → v0.4.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.1...v0.4.3)
- [github.com/psf/black: 24.4.0 → 24.4.2](https://github.com/psf/black/compare/24.4.0...24.4.2)
- [github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.9.0...v1.10.0)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Enable ruff/bugbear rules (B) and fix issues (#1702)
* Enable ruff/bugbear rules (B)
As suggested by Repo-Review.
* Fix ruff/bugbear issue (B007)
B007 Loop control variable `key` not used within loop body
https://docs.astral.sh/ruff/rules/unused-loop-control-variable/
* Fix ruff/bugbear issue (B015)
B015 Pointless comparison. Did you mean to assign a value?
Otherwise, prepend `assert` or remove it.
https://docs.astral.sh/ruff/rules/useless-comparison/
* Fix ruff/bugbear issues (B028)
B028 No explicit `stacklevel` keyword argument found
https://docs.astral.sh/ruff/rules/no-explicit-stacklevel/
* Fix ruff/bugbear issues (B904)
B904 Within an `except` clause, raise exceptions with `raise ... from err` or
`raise ... from None` to distinguish them from errors in exception handling
https://docs.astral.sh/ruff/rules/raise-without-from-inside-except/
* Document changes in docs/release.rst
* Disable ruff/bugbear rule (B017)
B017 `pytest.raises(Exception)` should be considered evil
https://docs.astral.sh/ruff/rules/assert-raises-exception/
---------
Co-authored-by: Joe Hamman <joe@earthmover.io>
* Release notes for 2.18.0 (#1843)
* doc: cleanup release notes for 2.18.0
* Update release.rst (#1850)
* Group dependabot updates (#1854)
* chore: update pre-commit hooks (#1876)
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.3 → v0.4.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.3...v0.4.4)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix a regression with scalar indexing due to #1800 (#1875)
* release notes for 2.18.1 (#1885)
* reset release notes (#1886)
* Add zstd to old V3 supported codecs (#1914)
* add zstd to old V3 supported codecs
* get to full test coverage and add release note
* fix pre-commit
* doc: update release notes for 2.18.2 (#1915)
* Drop support for Python 3.9
* Revert "Drop support for Python 3.9"
This reverts commit a054afbbdaf7c8560d0ce5df77af969bc863e335.
* Update TEAM.md (#2071)
* [v2] Fix doctests with numpy 2.0 (#2073)
* Fix version number in built docs (#2044)
* Fix orthogonal indexing with scalar. (#1947)
Co-authored-by: David Stansby <dstansby@gmail.com>
* Bump the requirements group across 1 directory with 7 updates (#2092)
Bumps the requirements group with 7 updates in the / directory:
| Package | From | To |
| --- | --- | --- |
| [numpy](https://github.com/numpy/numpy) | `1.26.4` | `2.0.1` |
| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) | `8.1.2` | `8.1.3` |
| [setuptools-scm](https://github.com/pypa/setuptools_scm) | `8.0.4` | `8.1.0` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.1.1` | `8.3.2` |
| [lmdb](https://github.com/jnwatson/py-lmdb) | `1.4.1` | `1.5.1` |
| [redis](https://github.com/redis/redis-py) | `5.0.4` | `5.0.8` |
| [pymongo](https://github.com/mongodb/mongo-python-driver) | `4.6.3` | `4.8.0` |
Updates `numpy` from 1.26.4 to 2.0.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.4...v2.0.1)
Updates `ipywidgets` from 8.1.2 to 8.1.3
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.2...8.1.3)
Updates `setuptools-scm` from 8.0.4 to 8.1.0
- [Release notes](https://github.com/pypa/setuptools_scm/releases)
- [Changelog](https://github.com/pypa/setuptools_scm/blob/main/CHANGELOG.md)
- [Commits](https://github.com/pypa/setuptools_scm/compare/v8.0.4...v8.1.0)
Updates `pytest` from 8.1.1 to 8.3.2
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.1.1...8.3.2)
Updates `lmdb` from 1.4.1 to 1.5.1
- [Changelog](https://github.com/jnwatson/py-lmdb/blob/master/ChangeLog)
- [Commits](https://github.com/jnwatson/py-lmdb/compare/py-lmdb_1.4.1...py-lmdb_1.5.1)
Updates `redis` from 5.0.4 to 5.0.8
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.4...v5.0.8)
Updates `pymongo` from 4.6.3 to 4.8.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.6.3...4.8.0)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-major
dependency-group: requirements
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: setuptools-scm
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: pytest
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: lmdb
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump the actions group with 2 updates (#2087)
Bumps the actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `actions/setup-python` from 5.1.0 to 5.1.1
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.1.0...v5.1.1)
Updates `pypa/gh-action-pypi-publish` from 1.8.14 to 1.9.0
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.14...v1.9.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* [v2] Drop support for Python 3.9 (#2074)
* Drop support for Python 3.9
* Ignore B905 ruff rule
* Fix release notes
* Fix Array.__array__ for numpy 2.1 (#2106)
* Fix Array.__array__ for numpy 2.1
* Add changelog
* Depend on np.array for array coercions
* Bump test version of numcodecs (#2114)
* Bump test version of numcodecs
* Fix test for numcodecs 0.13
* fix: numpy 1.24 compat for Array.__array__ (#2123)
* Deprecate N5Store (#2103)
* deprecate(n5): add deprecation warning to N5Store
* also deprecate N5FSStore
* docs
* fix doc
* Run tests on numpy 1.23 (#2124)
* Bump the requirements group across 1 directory with 3 updates (#2129)
Bumps the requirements group with 3 updates in the / directory: [numpy](https://github.com/numpy/numpy), [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) and [azure-storage-blob](https://github.com/Azure/azure-sdk-for-python).
Updates `numpy` from 2.0.1 to 2.1.0
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.0.1...v2.1.0)
Updates `ipywidgets` from 8.1.3 to 8.1.5
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.3...8.1.5)
Updates `azure-storage-blob` from 12.16.0 to 12.21.0
- [Release notes](https://github.com/Azure/azure-sdk-for-python/releases)
- [Changelog](https://github.com/Azure/azure-sdk-for-python/blob/main/doc/esrp_release.md)
- [Commits](https://github.com/Azure/azure-sdk-for-python/compare/azure-storage-blob_12.16.0...azure-storage-blob_12.21.0)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: ipywidgets
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: azure-storage-blob
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore: bump minimum numpy version to 1.24 (#2127)
* chore: bump minimum version to 1.24
* Update .github/workflows/python-package.yml
* Remove un-needed package installs in CI (#2095)
* Bump the actions group with 2 updates (#2146)
Bumps the actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `actions/setup-python` from 5.1.1 to 5.2.0
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.1.1...v5.2.0)
Updates `pypa/gh-action-pypi-publish` from 1.9.0 to 1.10.0
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.9.0...v1.10.0)
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-minor
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump numpy from 2.1.0 to 2.1.1 in the requirements group (#2151)
Bumps the requirements group with 1 update: [numpy](https://github.com/numpy/numpy).
Updates `numpy` from 2.1.0 to 2.1.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.0...v2.1.1)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* chore(docs): update release notes ahead of 2.18.4 (#2152)
* Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1 in the actions group (#2161)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.0 to 1.10.1
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.0...v1.10.1)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
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* [docs] remove primary sidebar from tutorial (#2142)
* remove primary sidebar from tutorial
* lint
* Bump pytest from 8.3.2 to 8.3.3 in the requirements group (#2172)
Bumps the requirements group with 1 update: [pytest](https://github.com/pytest-dev/pytest).
Updates `pytest` from 8.3.2 to 8.3.3
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.3.2...8.3.3)
---
updated-dependencies:
- dependency-name: pytest
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump pypa/gh-action-pypi-publish in the actions group (#2220)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.1 to 1.10.2
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.1...v1.10.2)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
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* Update TEAM.md (#2227)
* Bump the requirements group across 1 directory with 3 updates (#2284)
Bumps the requirements group with 3 updates in the / directory: [redis](https://github.com/redis/redis-py), [pymongo](https://github.com/mongodb/mongo-python-driver) and [h5py](https://github.com/h5py/h5py).
Updates `redis` from 5.0.8 to 5.1.0
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.8...v5.1.0)
Updates `pymongo` from 4.8.0 to 4.10.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.8.0...4.10.0)
Updates `h5py` from 3.11.0 to 3.12.1
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](https://github.com/h5py/h5py/compare/3.11.0...3.12.1)
---
updated-dependencies:
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
- dependency-name: h5py
dependency-type: direct:development
update-type: version-update:semver-minor
dependency-group: requirements
...
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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump pymongo from 4.10.0 to 4.10.1 in the requirements group (#2288)
Bumps the requirements group with 1 update: [pymongo](https://github.com/mongodb/mongo-python-driver).
Updates `pymongo` from 4.10.0 to 4.10.1
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.10.0...4.10.1)
---
updated-dependencies:
- dependency-name: pymongo
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Fix low contrast box titles (#2287) (#2292)
* Bump pypa/gh-action-pypi-publish in the actions group (#2304)
Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).
Updates `pypa/gh-action-pypi-publish` from 1.10.2 to 1.10.3
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.2...v1.10.3)
---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
dependency-type: direct:production
update-type: version-update:semver-patch
dependency-group: actions
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump the requirements group with 2 updates (#2303)
Bumps the requirements group with 2 updates: [numpy](https://github.com/numpy/numpy) and [redis](https://github.com/redis/redis-py).
Updates `numpy` from 2.1.1 to 2.1.2
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.1...v2.1.2)
Updates `redis` from 5.1.0 to 5.1.1
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.1.0...v5.1.1)
---
updated-dependencies:
- dependency-name: numpy
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
- dependency-name: redis
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump numcodecs from 0.13.0 to 0.13.1 in the requirements group (#2326)
Bumps the requirements group with 1 update: [numcodecs](https://github.com/zarr-developers/numcodecs).
Updates `numcodecs` from 0.13.0 to 0.13.1
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.rst)
- [Commits](https://github.com/zarr-developers/numcodecs/compare/v0.13.0...v0.13.1)
---
updated-dependencies:
- dependency-name: numcodecs
dependency-type: direct:development
update-type: version-update:semver-patch
dependency-group: requirements
...
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* remove zarr.types from v2
---------
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Co-authored-by: Janick Martinez Esturo <janick@jme.pub>
Co-authored-by: David Stansby <dstansby@gmail.com>
Co-authored-by: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com>
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: jakirkham <jakirkham@gmail.com>
Co-authored-by: Jeff Peck <jeffrey.peck@10xgenomics.com>
Co-authored-by: Norman Rzepka <code@normanrz.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
Co-authored-by: Hood Chatham <roberthoodchatham@gmail.com>
Co-authored-by: Wei Ouyang <oeway007@gmail.com>
Co-authored-by: Daniel Jahn (dahn) <dahnjahn@gmail.com>
Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com>
Co-authored-by: Ian Carroll <carroll.ian@gmail.com>
Co-authored-by: Martin Durant <martin.durant@alumni.utoronto.ca>
Co-authored-by: Ryan Abernathey <ryan.abernathey@gmail.com>
Co-authored-by: Jonny Saunders <sneakers-the-rat@protonmail.com>
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