(chore): adopt scientific python deprecation schedule #1768
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1768 +/- ##
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- Coverage 86.13% 83.54% -2.59%
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Files 41 40 -1
Lines 6277 6231 -46
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- Hits 5407 5206 -201
- Misses 870 1025 +155
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ilan-gold
commented
Jan 29, 2025
| @@ -57,7 +57,7 @@ jobs: | |||
| set -e | |||
| uv pip install --system --compile tomli packaging | |||
| deps=`python3 ci/scripts/min-deps.py pyproject.toml --extra dev test` | |||
| uv pip install --system --compile $deps pytest-cov "anndata @ ." | |||
| uv pip install --system --compile $deps pytest-cov "anndata[test,dev] @ ." | |||
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@flying-sheep I think this is a bug, no? The min-deps are created without respect for upper bounds so the constraints can end up not including the upper bounds because the min-deps script doesn't care about it? I think this is the correct fix given the fact that the script is called "min-deps" and not "min-deps-with-upper-bound" but maybe I'm off
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This PR forces us to adopt the scientific python deprecation schedule as much as possible. It also cleans up our use of spmatrix/sparray because of the bumping of
scipy.sparseso that handlingsparrayis always done via a concrete classspmatrixandsparray#1649