openvax / pyensembl / 23928093620

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Modernize Python packaging: migrate from setup.py to pyproject.toml (#322)

* feat: add pyproject.toml configuration

Replaces setup.py with modern Python packaging configuration.
Includes all metadata, dependencies, and build system setup.

Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

* test: add build system and pyproject.toml verification tests

Adds comprehensive tests to verify:
- pyproject.toml exists and is valid TOML
- build-system uses setuptools.build_meta backend
- runtime dependencies match specification exactly
- pylint is not included in runtime dependencies

This fulfills the specification requirement to document and verify
that the build system is properly configured with pyproject.toml,
and that python -m build would fail without this file.

Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

* feat: replace pkg_resources with importlib.resources

Modernizes resource loading to use Python 3.9+ standard library
instead of deprecated pkg_resources.

* feat: modernize CI installation process

Updates GitHub Actions workflow to use pyproject.toml-based
installation with optional development dependencies.
Adds Python 3.12 to test matrix.

Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

* feat: remove legacy setup.py and requirements.txt

All configuration now consolidated in pyproject.toml.
Modern Python packaging no longer needs these files.

* Fix deprecated license configuration format

- Update license from deprecated format {text = "Apache-2.0"} to modern SPDX format "Apache-2.0"
- Remove duplicate license classifier which conflicts with new format
- Build now succeeds without deprecation warnings

Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>

* feat: complete Python packaging modernization

Successfully migrated from deprecated pkg_resources and setup.py
to modern pyproject.toml configuration with importlib.resources.

- Replaced pkg_resources with importlib.resources
- Consolidated all configurat... (continued)

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