Migrate to the scverse cookiecutter template #106
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Codecov Report❌ Patch coverage is
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## main #106 +/- ##
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- Coverage 96.78% 67.30% -29.48%
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Files 13 12 -1
Lines 872 1918 +1046
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+ Hits 844 1291 +447
- Misses 28 627 +599
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ilia-kats
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They don't work on Github and may not work on readthedocs in the future, since we don't keep old versions of the documentation around.
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adapt current version of hatch-vcs-footgun-example
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I love it - thank you @ilia-kats ! |
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Re: pandas 3, we are releasing now a version of anndata 0.12 to upper bound + give future looking I would have a look at scverse/anndata#2250 and scverse/anndata#2133 for what we are doing specifically. In general, we are actively making a decision for 0.13 to make breaking changes while keeping 0.12 behavior as-is (as to your columns question). Not sure about Hence the delay on reviewing this, looking now. |
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Some bigger points - is there anything specific to look at? There are a lot of small changes that are just linting so it's hard to parse what is a "big" change. Some of this stuff is unrelated to this PR but I'm noticing it now
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| # https://docs.readthedocs.io/en/stable/config-file/v2.html | |||
| version: 2 | |||
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Do you guys have a deployment set up? I don't see anything in your CI. This could make reviewing easier
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I think we do, but readthedocs doesn't use github actions, I think they have their own hooks that get triggered. But I don't have access to our readthedocs setup, so I'm also not sure if we build on PRs or not.
| license = { file = "LICENSE" } | ||
| maintainers = [ | ||
| { name = "Danila Bredikhin", email = "danila@stanford.edu" }, | ||
| { name = "Danila Bredikhin", email = "danila@stanford.edu" }, |
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I think you can add yourself now :)
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In a separate PR/commit, if @gtca doesn't object.
| optional-dependencies.test = [ | ||
| "coverage>=7.10", | ||
| "pytest", | ||
| "zarr<3", |
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That got moved from somewhere else in this file. But good point, we should remove the bound for 0.4. But that's a separate PR/commit, I think.
I think the only really big changes are this commit and the rephrasing of the changelog to conform to keepachangelog. The rest ist just moving things around and linting. |
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Thanks @ilia-kats let's try to get the docs sorted out and then everything else should be ok |
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Closes #42, closes #84, closes #10.
The tests on
-preare failing due to Pandas 3.0 RC being pulled in. On that I would like some advice: Should we allow people to mix Pandas 3.0 with AnnData 0.12, and if so, what would be the best approach here? ConvertingStringDTypecolumns toobjectcolumns manually if an older AnnData version is detected? Settinganndata.settings.allow_write_nullable_strings=Trueautomatically and emitting a warning?@gtca has indicated to me that he wants to release 0.3.3 with the fixes to
updateandpush_attr/pull_attrrather quickly, so ideally this should go in after 0.3.3 as preparation for 0.4.