Adopt the scverse cookiecutter template

.codecov.yaml

@@ -0,0 +1,17 @@
+# Based on pydata/xarray
+codecov:
+ require_ci_to_pass: no
+
+coverage:
+ status:
+ project:
+ default:
+ # Require 1% coverage, i.e., always succeed
+ target: 1
+ patch: false
+ changes: false
+
+comment:
+ layout: diff, flags, files
+ behavior: once
+ require_base: no

.cruft.json

@@ -0,0 +1,44 @@
+{
+ "template": "https://github.com/scverse/cookiecutter-scverse",
+ "commit": "eb4523fde2e18bcfc121ff2cd722c9037ff8b910",
+ "checkout": null,
+ "context": {
+ "cookiecutter": {
+ "project_name": "spatialdata",
+ "package_name": "spatialdata",
+ "project_description": "Spatial data format.",
+ "author_full_name": "scverse",
+ "author_email": "giov.pll@gmail.com",
+ "github_user": "scverse",
+ "github_repo": "spatialdata",
+ "license": "BSD 3-Clause License",
+ "ide_integration": true,
+ "issue_categorization": "labels",
+ "_copy_without_render": [
+ ".github/workflows/build.yaml",
+ ".github/workflows/test.yaml",
+ "docs/_templates/autosummary/**.rst"
+ ],
+ "_exclude_on_template_update": [
+ "CHANGELOG.md",
+ "LICENSE",
+ "README.md",
+ "docs/api.md",
+ "docs/index.md",
+ "docs/notebooks/example.ipynb",
+ "docs/references.bib",
+ "docs/references.md",
+ "src/**",
+ "tests/**"
+ ],
+ "_render_devdocs": false,
+ "_jinja2_env_vars": {
+ "lstrip_blocks": true,
+ "trim_blocks": true
+ },
+ "_template": "https://github.com/scverse/cookiecutter-scverse",
+ "_commit": "eb4523fde2e18bcfc121ff2cd722c9037ff8b910"
+ }
+ },
+ "directory": null
+}

.editorconfig

@@ -9,5 +9,8 @@ trim_trailing_whitespace = true
 insert_final_newline = true
 line_length = 120
 
+[{*.{yml,yaml,toml},.cruft.json}]
+indent_size = 2
+
 [Makefile]
 indent_style = tab

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,116 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+ - type: markdown
+ attributes:
+ value: |
+ **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+ detailing how to provide the necessary information for us to reproduce your bug. In brief:
+ * Please provide exact steps how to reproduce the bug in a clean Python environment.
+ * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
+ * Replicate problems on public datasets or share data subsets when full sharing isn't possible.
+
+ Generally, the easier it is for us to reproduce the issue, the faster we can work on it. If you can, please:
+
+ 1. Reproduce using the [`blobs` dataset](https://spatialdata.scverse.org/en/stable/api/datasets.html#spatialdata.datasets.blobs):
+
+ ```python
+ from spatialdata.datasets import blobs
+
+ sdata = blobs()
+ ```
+
+ You can also use [`blobs_annotating_element`](https://spatialdata.scverse.org/en/stable/api/datasets.html#spatialdata.datasets.blobs_annotating_element) for more control:
+
+ ```python
+ from spatialdata.datasets import blobs_annotating_element
+
+ sdata = blobs_annotating_element("blobs_labels")
+ ```
+
+ 2. If the above is not possible, reproduce using a public dataset and explain how we can download the data.
+ 3. If the data is private, consider sharing an anonymized version/subset via a [Zulip private message](https://scverse.zulipchat.com/#user/480560), or provide screenshots/GIFs showing the behavior.
+
+ Please report only one bug per issue.
+
+ - type: textarea
+ id: report
+ attributes:
+ label: Report
+ description: A clear and concise description of what the bug is.
+ validations:
+ required: true
+
+ - type: textarea
+ id: versions
+ attributes:
+ label: Versions
+ description: |
+ Which version of packages.
+
+ Please install `session-info2`, run the following command in a notebook,
+ click the “Copy as Markdown” button, then paste the results into the text box below.
+
+ ```python
+ In[1]: import session_info2; session_info2.session_info(dependencies=True)
+ ```
+
+ Alternatively, run this in a console:
+
+ ```python
+ >>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
+ ```
+ render: python
+ placeholder: |
+ anndata	0.11.3
+ ----	----
+ charset-normalizer	3.4.1
+ coverage	7.7.0
+ psutil	7.0.0
+ dask	2024.7.1
+ jaraco.context	5.3.0
+ numcodecs	0.15.1
+ jaraco.functools	4.0.1
+ Jinja2	3.1.6
+ sphinxcontrib-jsmath	1.0.1
+ sphinxcontrib-htmlhelp	2.1.0
+ toolz	1.0.0
+ session-info2	0.1.2
+ PyYAML	6.0.2
+ llvmlite	0.44.0
+ scipy	1.15.2
+ pandas	2.2.3
+ sphinxcontrib-devhelp	2.0.0
+ h5py	3.13.0
+ tblib	3.0.0
+ setuptools-scm	8.2.0
+ more-itertools	10.3.0
+ msgpack	1.1.0
+ sparse	0.15.5
+ wrapt	1.17.2
+ jaraco.collections	5.1.0
+ numba	0.61.0
+ pyarrow	19.0.1
+ pytz	2025.1
+ MarkupSafe	3.0.2
+ crc32c	2.7.1
+ sphinxcontrib-qthelp	2.0.0
+ sphinxcontrib-serializinghtml	2.0.0
+ zarr	2.18.4
+ asciitree	0.3.3
+ six	1.17.0
+ sphinxcontrib-applehelp	2.0.0
+ numpy	2.1.3
+ cloudpickle	3.1.1
+ sphinxcontrib-bibtex	2.6.3
+ natsort	8.4.0
+ jaraco.text	3.12.1
+ setuptools	76.1.0
+ Deprecated	1.2.18
+ packaging	24.2
+ python-dateutil	2.9.0.post0
+ ----	----
+ Python	3.13.2 | packaged by conda-forge | (main, Feb 17 2025, 14:10:22) [GCC 13.3.0]
+ OS	Linux-6.11.0-109019-tuxedo-x86_64-with-glibc2.39
+ Updated	2025-03-18 15:47

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+ - name: Scverse Community Forum
+url: https://discourse.scverse.org/
+about: If you have questions about “How to do X”, please ask them here.

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for spatialdata
+labels: enhancement
+body:
+ - type: textarea
+ id: description
+ attributes:
+ label: Description of feature
+ description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+ validations:
+ required: true

.github/dependabot.yml

@@ -0,0 +1,21 @@
+version: 2
+updates:
+ - package-ecosystem: pre-commit
+ directory: /
+ schedule:
+ interval: weekly
+ cooldown:
+ default-days: 7
+ groups:
+ pre-commit:
+ patterns: ["*"]
+ - package-ecosystem: github-actions
+ directory: /
+ schedule:
+ interval: weekly
+ cooldown:
+ default-days: 7
+ groups:
+ actions-deps:
+ patterns:
+ - "*"

.github/release.yml

@@ -1,29 +1,29 @@
 changelog:
-exclude:
-labels:
-- release-ignore
-authors:
-- pre-commit-ci
-- pre-commit-ci[bot]
-categories:
-- title: Added
-labels:
-- "release-added"
-- title: Changed
-labels:
-- "release-changed"
-- title: Deprecated
-labels:
-- "release-deprecated"
-- title: Removed
-labels:
-- "release-removed"
-- title: Fixed
-labels:
-- "release-fixed"
-- title: Security
-labels:
-- "release-security"
-- title: Other Changes
-labels:
-- "*"
+ exclude:
+ labels:
+ - release-ignore
+ authors:
+ - pre-commit-ci
+ - pre-commit-ci[bot]
+ categories:
+ - title: Added
+ labels:
+ - "release-added"
+ - title: Changed
+ labels:
+ - "release-changed"
+ - title: Deprecated
+ labels:
+ - "release-deprecated"
+ - title: Removed
+ labels:
+ - "release-removed"
+ - title: Fixed
+ labels:
+ - "release-fixed"
+ - title: Security
+ labels:
+ - "release-security"
+ - title: Other Changes
+ labels:
+ - "*"