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Bump existing package versions and add tests. - #223

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sdhutchins merged 20 commits into
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Jul 14, 2026
Merged

Bump existing package versions and add tests.#223
sdhutchins merged 20 commits into
mainfrom
dev

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@sdhutchins sdhutchins commented Jul 14, 2026

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sdhutchins and others added 20 commits December 2, 2025 16:13
Updated author information and added email addresses. Changed version to 1.0.0b2 and added repository code and license details.
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>
* 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.
@sdhutchins sdhutchins self-assigned this Jul 14, 2026
@sdhutchins sdhutchins changed the title Dev Bump existing package versions and add tests. Jul 14, 2026
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codecov Bot commented Jul 14, 2026

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Codecov Report

❌ Patch coverage is 92.45283% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 37.90%. Comparing base (5215bc4) to head (5914295).
✅ All tests successful. No failed tests found.

Files with missing lines Patch % Lines
OrthoEvol/Tools/sge/sgejob.py 0.00% 2 Missing ⚠️
OrthoEvol/Manager/biosql/biosql.py 80.00% 1 Missing ⚠️
OrthoEvol/Manager/database_management.py 50.00% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #223      +/-   ##
==========================================
+ Coverage   32.49%   37.90%   +5.40%     
==========================================
  Files          69       70       +1     
  Lines        4345     4327      -18     
==========================================
+ Hits         1412     1640     +228     
+ Misses       2933     2687     -246     

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@sdhutchins
sdhutchins merged commit c83c4e8 into main Jul 14, 2026
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