Update to numpy v2 #317
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Update to numpy v2 #317
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…umpy-2-compatibility Ensure compatibility with NumPy 2
- Added optional development dependencies in `pyproject.toml`: `pytest`, `pytest-cov`, `flake8`, and `coveralls`. - Updated `README.md` to include installation instructions for development and detailed testing commands. - Removed `test.sh` script in favor of direct `pytest` commands in the workflow. - Updated GitHub Actions workflow to install dependencies in editable mode and run tests directly.
- Removed upper version constraint for `gtfparse`. - Added `pyarrow` with a minimum version of 16.0.0. - Added `pandas` with a minimum version of 2.0.0.
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This pull request introduces several significant updates to modernize the
pyensemblproject. Key changes include migrating the build system topyproject.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:
setup.pywithpyproject.tomlfor 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:
pip install -e ".[dev]") and replaced the test execution command withpytestfor 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))test.shscript in favor of directpytestcommands. ([test.shL1](https://github.com/openvax/pyensembl/pull/317/files#diff-3722d9ba8feb2d3feac8ce71a209a638d4b404e1c53f937188761181594023e2L1))Documentation Enhancements:
README.mdto 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))README.mdby adding a proper title and header formatting. ([README.mdL7-R8](https://github.com/openvax/pyensembl/pull/317/files#diff-b335630551682c19a781afebcf4d07bf978fb1f8ac04c6bf87428ed5106870f5L7-R8))Codebase Modernization:
numpy.typeDictto address its removal in recent NumPy versions. ([pyensembl/__init__.pyR13-R22](https://github.com/openvax/pyensembl/pull/317/files#diff-f73de41d4b9038f9a2c385bce083cc495653ba85a40666398cae6ab5e6892a20R13-R22))importlib.resourcesfor 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
gtfparse @ git+https://github.com/nick-youngblut/gtfparse.git@pyarrow_updatein thepyproject.toml