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@ivirshup ivirshup commented Jun 6, 2024

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: single-cell-data/TileDB-SOMA#1926

@ivirshup ivirshup marked this pull request as draft June 6, 2024 18:14
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johnkerl commented Jun 6, 2024

Not positive it's entirely related but we had a hard fail on MacOS, beyond our control:
single-cell-data/TileDB-SOMA#1926 (comment)

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codecov bot commented Jun 7, 2024

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 ⚠️
.../cellxgene_census/experimental/util/_eager_iter.py 75.00% 1 Missing ⚠️
Additional details and impacted files
@@            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 Coverage Δ
unittests 91.21% <97.64%> (+0.02%) ⬆️

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ivirshup commented Jul 2, 2024

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 ivirshup changed the title Update min python version, allow python 3.12 [python] Follow spec-0 Jul 2, 2024
@ivirshup ivirshup marked this pull request as ready for review July 3, 2024 18:21
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ivirshup commented Jul 3, 2024

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.

@ivirshup ivirshup requested review from ebezzi and pablo-gar July 3, 2024 18:22
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github-actions bot commented Aug 6, 2024

This PR has not seen any activity in the past 4 weeks; if no one comments or reviews it in the next 3 days, this PR will be closed.

@github-actions github-actions bot added the Stale label Aug 6, 2024
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ivirshup commented Aug 7, 2024

no

@github-actions github-actions bot removed the Stale label Aug 8, 2024
@ivirshup ivirshup mentioned this pull request Sep 4, 2024
@ivirshup ivirshup merged commit fc7aefe into main Sep 5, 2024
@ivirshup ivirshup deleted the spec-0 branch September 5, 2024 20:21
ryan-williams added a commit to ryan-williams/cellxgene-census that referenced this pull request Sep 10, 2024
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Follow SPEC-0 for minimum supported versions of dependencies

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