scanpy v1.9.4

[regro-cf-autotick-bot]

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• Dependencies have been updated if changed: see upstream
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Dependency Analysis

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Analysis by source code inspection shows a discrepancy between it and the the package's stated requirements in the meta.yaml.

Packages found by source code inspection but not in the meta.yaml:

• cycler

Packages found in the meta.yaml but not found by source code inspection:

• importlib_metadata

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[conda-forge-webservices]

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

[jdblischak]

The package was built but then the test failed to run import scanpy:

import: 'scanpy'
+ scanpy
Traceback (most recent call last):
  File "/home/conda/feedstock_root/build_artifacts/scanpy_1692902435179/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/python3.11/site-packages/scanpy/cli.py", line 47, in __getitem__
    return self.parser_map[k]
           ~~~~~~~~~~~~~~~^^^
KeyError: 'settings'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
    raise ArgumentError(
argparse.ArgumentError: No command settings. Choose from set()
Tests failed for scanpy-1.9.4-pyhd8ed1ab_0.conda - moving package to /home/conda/feedstock_root/build_artifacts/broken

[jdblischak]

Looking at all the file changes between 1.9.3 and 1.9.4, the file cli.py wasn't updated

[flying-sheep]

deps didn’t change much: scverse/scanpy@1.9.3...1.9.4#diff-50c86b7ed8

[flying-sheep]

the test failed to run

seems like we didn’t backport this one: https://github.com/scverse/scanpy/pull/2596/files

the CLI is broken with Python 3.11, but IDK how many people use it (nobody complained about that). so I guess we can just deactivate the commands: [scanpy] test until the next minor version.

[jdblischak]

the CLI is broken with Python 3.11, but IDK how many people use it (nobody complained about that). so I guess we can just deactivate the commands: [scanpy] test until the next minor version.

That makes me hesitatant, but I see that you are a maintainer, so I trust your judgement

[jdblischak]

Ah, I just remembered why I was watching the releases on this feedstock. scanpy 1.9.4 dropped support for Python 3.7. Thus the recipe needs to change python >= 3.7 to python >= 3.8. Otherwise it will get installed into Python 3.7 envs and break

[jdblischak]

Essentially, I want to avoid the situation we had with anndata, where I had to send a repodata patch to prevent it from installing in Python 3.7 envs after Python 3.7 support was dropped (conda-forge/anndata-feedstock#28, conda-forge/conda-forge-repodata-patches-feedstock#433)

[jdblischak]

Bump Python minimum version to 3.8 in both the host and run requirements: python >= 3.8

https://github.com/scverse/scanpy/blob/1.9.4/pyproject.toml#L13

scverse/scanpy#2447

[jdblischak]

Also, just like in conda-forge/anndata-feedstock#28, you can remove the manually packaged LICENSE file in this recipe. It is bundled in the PyPI tarball. This has the added benefit of ensuring the license file is always kept up-to-date

wget https://files.pythonhosted.org/packages/77/ea/b2f7d61a41fc979676e226a628ff38ad86d6c66c7a2794833eeb775ce1b6/scanpy-1.9.4.tar.gz
tar --list -f scanpy-1.9.4.tar.gz | grep LICENSE
## scanpy-1.9.4/LICENSE

[flying-sheep]

all great points, I think it should be fine now!