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chanzuckerberg / cellxgene-census

CZ CELLxGENE Discover Census
https://chanzuckerberg.github.io/cellxgene-census/
MIT License
72 stars 18 forks source link

[python] Follow spec-0 #1189

Open ivirshup opened 4 weeks ago

ivirshup commented 4 weeks ago

Fixes #1177

This PR implements adoption SPEC-0 for support windows of dependencies.

I'm going to hold off on running formatting for all files until I'm done with the manual changes to make this readable.

Blocked by tiledbsoma's pinning of pyarrow to v12 (current release is v16). It looks like it's difficult to install pyarrow~=12.0 on python 3.12 since there haven't been any wheel releases. See: https://github.com/single-cell-data/TileDB-SOMA/issues/1926

johnkerl commented 4 weeks ago

Not positive it's entirely related but we had a hard fail on MacOS, beyond our control: https://github.com/single-cell-data/TileDB-SOMA/issues/1926#issuecomment-1834695149

codecov[bot] commented 3 weeks ago

Codecov Report

Attention: Patch coverage is 97.64706% with 2 lines in your changes missing coverage. Please review.

Project coverage is 91.21%. Comparing base (f775282) to head (dcf94bd). Report is 1 commits behind head on main.

Files Patch % Lines
...us/src/cellxgene_census/experimental/_embedding.py 75.00% 1 Missing :warning:
.../cellxgene_census/experimental/util/_eager_iter.py 75.00% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #1189 +/- ## ========================================== + Coverage 91.19% 91.21% +0.02% ========================================== Files 77 79 +2 Lines 5971 6146 +175 ========================================== + Hits 5445 5606 +161 - Misses 526 540 +14 ``` | [Flag](https://app.codecov.io/gh/chanzuckerberg/cellxgene-census/pull/1189/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=chanzuckerberg) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/chanzuckerberg/cellxgene-census/pull/1189/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=chanzuckerberg) | `91.21% <97.64%> (+0.02%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=chanzuckerberg#carryforward-flags-in-the-pull-request-comment) to find out more.

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ivirshup commented 2 days ago

I've gone ahead and made a few changes here.

Right now I've followed spec-0, but since we can't do 3.12 while tiledbsoma pins it I've just left off support there.

My last commit is just letting the formatter run + a couple manual fixes. I can revert it if other changes are needed.

ivirshup commented 1 day ago

This is ready for review. I think the main question is whether we want to drop support for python 3.8 and 3.9 if we can't support 3.12 while tiledbsoma pins it.