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[scverse hackathon] cloud future - #907

Closed
ap-- wants to merge 41 commits into
scverse:mainfrom
berombau:cloud-future
Closed

[scverse hackathon] cloud future#907
ap-- wants to merge 41 commits into
scverse:mainfrom
berombau:cloud-future

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@ap--

@ap--ap-- commented Mar 18, 2025•
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Draft PR so we can keep track of progress during the hackathon.

These changes would need to land on main, so we can start with the API refactor

Include:

#905
#904
#903
#902
#901

berombauand others added 30 commits January 24, 2025 10:34
@berombau
add basic support and remote SpatialData tests
5718cba
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
a8be620
for more information, see https://pre-commit.ci
@LucaMarconato
fix pre-commit
ce686e4
@LucaMarconato
Revert "Update pyproject.toml"
e7fa020
This reverts commit 1f8a01c.
@LucaMarconato
removed 3.13 from test ci
a9c0801
@LucaMarconato
Merge branch 'no_python_313' into remote2
5cfdaec
@LucaMarconato
fix
4fe6a47
@LucaMarconato
uploading sdata to local s3 storage
d97a1d2
@berombau
add _open_zarr_store
5e26b5e
@berombau@LucaMarconato
revert changing write function signature
5794871
Co-authored-by: LucaMarconato <LucaMarconato@users.noreply.github.com>
@berombau
update _open_zarr_store with StoreLike
0207ff7
@berombau
read image element from base store
7e497ff
@berombau
clean up remote mock tests, focus only on reading raster elements
c674281
@berombau
improve remote http test, add alternative
fb953a0
@berombau
add support for consolidated metadata store in util function, add _cr…
52bb5fc
…eate_upath function
@berombau
allow for groups as store input
ca82493
@berombau
handle consolidated metadata with upath
ecea0e6
@berombau
split remote reading tests between http and http with consolidated me…
734eb45
…tadata
@berombau
remove f_store_path, support remote raster types fully and keep local…
c0ffb1c
… support for other elements
@berombau
Fix metadata_key bug now that store is not always FSStore. Add extra …
d60bd85
…comments.
@berombau
add mypy fixes
c3fa8cf
@ap--
Merge branch 'main' into remote2
d16a638
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
23f4a89
for more information, see https://pre-commit.ci
@ap--
Fix linting errors
a80588c
@ap--
fixed majority of tests
020810b
@ap--
spatialdata._io._utils: _open_zarr_store has to set dimension_separat…
ba25564
…or to emulate previous ome_zarr.io.parse_url
@ap--
stay in sync with ome zarr format
b2ff8f8
@ap--
spatialdata._io.io_raster: support remote stores
70480ce
@ap--
prevent crashing tests on 3.10
10cef3f
@ap--
Merge branch 'spatial-data-crash310' into remote2
d9e4eac
@ap--ap-- changed the title Cloud future[scverse hackathon] cloud futureMar 18, 2025
@codecov

codecovBot commented Mar 18, 2025•
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Codecov Report

❌ Patch coverage is 91.60839% with 12 lines in your changes missing coverage. Please review.
✅ Project coverage is 92.08%. Comparing base (4021946) to head (e9e2c7b).
⚠️ Report is 24 commits behind head on main.

Files with missing linesPatch %Lines
src/spatialdata/_io/_utils.py87.87%4 Missing ⚠️
src/spatialdata/_io/io_raster.py84.00%4 Missing ⚠️
src/spatialdata/_io/io_zarr.py89.47%4 Missing ⚠️
Additional details and impacted files
@@ Coverage Diff @@## main #907 +/- ##
==========================================
- Coverage 92.11% 92.08% -0.03% 
==========================================
Files 48 48 Lines 7429 7493 +64 ==========================================
+ Hits 6843 6900 +57 - Misses 586 593 +7
Files with missing linesCoverage Δ
src/spatialdata/_core/spatialdata.py91.60% <100.00%> (+0.14%)⬆️
src/spatialdata/_io/format.py88.39% <100.00%> (+0.06%)⬆️
src/spatialdata/_io/io_points.py100.00% <100.00%> (ø)
src/spatialdata/_io/io_shapes.py95.16% <100.00%> (ø)
src/spatialdata/_io/io_table.py94.00% <100.00%> (-0.45%)⬇️
src/spatialdata/_types.py100.00% <100.00%> (ø)
src/spatialdata/_io/_utils.py88.26% <87.87%> (-0.19%)⬇️
src/spatialdata/_io/io_raster.py95.10% <84.00%> (-1.75%)⬇️
src/spatialdata/_io/io_zarr.py88.79% <89.47%> (+0.33%)⬆️
🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@berombauberombau mentioned this pull request Mar 18, 2025
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@berombauberombau mentioned this pull request Apr 4, 2025
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@melonora

melonora commented Aug 20, 2025

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Closing this in preference of merging smaller PRs one by one.

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4 participants

@ap--@melonora@berombau@LucaMarconato