Modernize dependencies, tests, and Python support. - #221
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…rs to 'main' and 'dev'.
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## dev #221 +/- ##
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This will have to stay open a bit as mygene's dealing with a proxy issue for their API. |
…to restrict support to Python 3.11 and 3.12.
…sts for resource consumers.
sdhutchins
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Jul 14, 2026
* Fixes to readme. * Add tests for Genbank. * Add align tests. * Convert README to md. * Tweaks to readme formatting. * Add MIT license. * Add pyproject.toml. * Fixing manifest and setup files. * Fix docs ci. * Fix cookiecutter classifier. * Update CITATION.cff with author and version info. Updated author information and added email addresses. Changed version to 1.0.0b2 and added repository code and license details. * Bump werkzeug (#218) Bumps [werkzeug](https://github.com/pallets/werkzeug) from 0.15.3 to 3.1.5. - [Release notes](https://github.com/pallets/werkzeug/releases) - [Changelog](https://github.com/pallets/werkzeug/blob/main/CHANGES.rst) - [Commits](pallets/werkzeug@0.15.3...3.1.5) --- updated-dependencies: - dependency-name: werkzeug dependency-version: 3.1.5 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add tests for Genbank. * Add align tests. * Convert README to md. * Tweaks to readme formatting. * Fixing manifest and setup files. * Modernize dependencies, tests, and Python support. (#221) * Refactor post-installation script permissions handling in setup.py. * Make the Cookiecutter Flask stack compatible with Flask 3.1.3 and Python 3.11+. * Deprecate pkg_resources. * Update CI workflow to limit branches for push and pull request triggers to 'main' and 'dev'. * Update PackageVersion test to use 'OrthoEvol' as the package name. * Update Python version requirements in pyproject.toml and CI workflow to restrict support to Python 3.11 and 3.12. * Refactor data management to use updated config import and add unit tests for resource consumers. --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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Changes proposed in this pull request:
addCleanup.pkg_resourcesusage withimportlib.metadata.Python compatibility
OrthoEvolution now requires:
Python 3.13 and 3.14 are excluded because ETE3 imports the removed standard-library
cgimodule. The latest ETE3 release has the same incompatibility, so upgradingETE3 alone does not resolve the collection failure.