Remove backports.tempfile for Python compatibility and bump version
#134
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gwaybio
approved these changes
Oct 10, 2024
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Thanks @gwaybio for the review! Going to merge this in now and work towards a GitHub and PyPI release. |
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This PR updates
cytominer-databaseto remove thebackports.tempfiledependency which sometimes can cause issues with Python versions and/or various architectures (see here for a related error from a Pycytominer conda build). I've bumped the patch version as I feel we need to release this to PyPI and Conda-forge in order to work around any places wherebackports.tempfilemay be causing issues (like the Pycytominer build mentioned).Along the journey towards this PR I noticed that
csvkit>=2has an API change which appears to cause many failing tests. As a result I set a maximum range to avoid these errors. Additionally, the Pandas SQL API had changed so I needed to make adjustments to tests in order for them to pass.I ran tests with Python 3.8.19 to be cautious of any other remaining changes we might need to make for passing tests (given the deprecated status of this project). My steps for testing were the following (please let me know if I missed something):
pip install -e .pip install pytestpython -m pytestReferences conda-forge/pycytominer-feedstock#11