Update to numpy v2

[nick-youngblut]

This pull request introduces several significant updates to modernize the pyensembl project. Key changes include migrating the build system to pyproject.toml, improving the development workflow, and updating the codebase for compatibility with modern Python and NumPy versions. Additionally, the documentation has been expanded to include development and testing instructions.

Build and Dependency Management:

• Replaced setup.py with pyproject.toml for build system configuration, specifying dependencies, optional development dependencies, and package metadata. ([[1]](https://github.com/openvax/pyensembl/pull/317/files#diff-50c86b7ed8ac2cf95bd48334961bf0530cdc77b5a56f852c5c61b89d735fd711R1-R50), [[2]](https://github.com/openvax/pyensembl/pull/317/files#diff-60f61ab7a8d1910d86d9fda2261620314edcae5894d5aaa236b821c7256badd7L1-L74))

Development Workflow Improvements:

• Updated the GitHub Actions workflow to install dependencies in editable mode with development extras (pip install -e ".[dev]") and replaced the test execution command with pytest for better coverage reporting. ([[1]](https://github.com/openvax/pyensembl/pull/317/files#diff-1db27d93186e46d3b441ece35801b244db8ee144ff1405ca27a163bfe878957fL31-R31), [[2]](https://github.com/openvax/pyensembl/pull/317/files#diff-1db27d93186e46d3b441ece35801b244db8ee144ff1405ca27a163bfe878957fL52-R50))
• Removed the obsolete test.sh script in favor of direct pytest commands. ([test.shL1](https://github.com/openvax/pyensembl/pull/317/files#diff-3722d9ba8feb2d3feac8ce71a209a638d4b404e1c53f937188761181594023e2L1))

Documentation Enhancements:

• Updated README.md to include a new "Development and Testing" section with detailed instructions on installing the project in development mode, running tests, and generating coverage reports. ([README.mdR142-R195](https://github.com/openvax/pyensembl/pull/317/files#diff-b335630551682c19a781afebcf4d07bf978fb1f8ac04c6bf87428ed5106870f5R142-R195))
• Improved the visual structure of the README.md by adding a proper title and header formatting. ([README.mdL7-R8](https://github.com/openvax/pyensembl/pull/317/files#diff-b335630551682c19a781afebcf4d07bf978fb1f8ac04c6bf87428ed5106870f5L7-R8))

Codebase Modernization:

• Added a compatibility shim for numpy.typeDict to address its removal in recent NumPy versions. ([pyensembl/__init__.pyR13-R22](https://github.com/openvax/pyensembl/pull/317/files#diff-f73de41d4b9038f9a2c385bce083cc495653ba85a40666398cae6ab5e6892a20R13-R22))
• Updated logging configuration to use importlib.resources for compatibility with Python 3.9+ and fallback support for older versions. ([[1]](https://github.com/openvax/pyensembl/pull/317/files#diff-c3dc15650bad87614d5861ce25700b34aeeb863ac948461a2cbdba096198534bL43-R46), [[2]](https://github.com/openvax/pyensembl/pull/317/files#diff-c3dc15650bad87614d5861ce25700b34aeeb863ac948461a2cbdba096198534bL52-R57))

Notes

• Currently using gtfparse @ git+https://github.com/nick-youngblut/gtfparse.git@pyarrow_update in the pyproject.toml

[iskandr]

This will probably break many other OpenVax tools but it's probably time to pull off the bandaid.

The only change I object to is getting rid of test.sh, otherwise I'd merge this PR. I can't imagine a rationale for preferring making someone remember pytest --cov=pyensembl/ --cov-report=term-missing tests/ over ./test.sh.

[iskandr]

Closing — the pyproject.toml migration and importlib.resources changes were covered by #322. The numpy 2 upgrade is a separate effort that can be tackled independently. Thanks for the contribution!