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Update docs build #253

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merged 23 commits into from
Jul 6, 2024
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catanzaromj
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The documentation and build process use outdated github actions. This PR updates these and adds a dependabot to ensure they remain up-to-date moving forward.

There were changes on master that never made it into a release because these procedures were out of date. Therefore, this PR may also fix some other lingering issues as well.

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codecov bot commented Mar 16, 2024

Codecov Report

Attention: Patch coverage is 50.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 80.34%. Comparing base (ece5d47) to head (ec4aaaa).

Current head ec4aaaa differs from pull request most recent head 2c9c1c8

Please upload reports for the commit 2c9c1c8 to get more accurate results.

Files Patch % Lines
kmapper/visuals.py 50.00% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master     #253      +/-   ##
==========================================
+ Coverage   80.32%   80.34%   +0.02%     
==========================================
  Files          11       11              
  Lines         864      865       +1     
  Branches      189      203      +14     
==========================================
+ Hits          694      695       +1     
+ Misses        138      137       -1     
- Partials       32       33       +1     

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@catanzaromj
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I had to drop python 3.7 compatibility due to the way sparse matrices/arrays are handled in newer versions of scipy and numpy. Newer versions of numpy (and therefore scikit-learn) raise an error on sparse scipy matrices, in favor of sparse scipy arrays. These were not introduced until scipy 1.8.0, which requires python3.8+.

This arose from me unpnning the dependencies and updating things. Rather than keeping the dependencies pinned, I'm in favor of dropping python3.7 support (its EoL anyways). I think unpinned dependencies is better moving forward so that we stay up to date with the packages we rely on. The built and published wheels can be used for backwards compatibility.

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We're planning on making one larger release once several other PRs get merged in. I think this is good to go for now.

@catanzaromj catanzaromj marked this pull request as ready for review June 29, 2024 14:53
@catanzaromj catanzaromj self-assigned this Jun 29, 2024
@catanzaromj catanzaromj added bug docs Documentation related issues labels Jun 29, 2024
This was linked to issues Jun 29, 2024
@catanzaromj
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@deargle @ctralie @sauln Please review this PR if you have any bandwidth to do so. Originally I intended this PR to be small to fix only the docs, but so much was deprecated that had to be updated. I fixed the github actions so the releases should work moving forward (there were several changes to master that were never released) along with updating the release process on PyPI, fixed the docs to use a modern readthedocs config, updated the runners to use current versions of python, and fixed some failing tests.

@catanzaromj catanzaromj merged commit e7db6e7 into scikit-tda:master Jul 6, 2024
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Issue with generating visuals in mapper plotlyviz error
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