Python packaging, testing suite, and general improvements#18
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vinisalazar wants to merge 6 commits intoKoslickiLab:mainfrom
Open
Python packaging, testing suite, and general improvements#18vinisalazar wants to merge 6 commits intoKoslickiLab:mainfrom
vinisalazar wants to merge 6 commits intoKoslickiLab:mainfrom
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- Move funcprofiler.py and funcprofiler_many.py into fmh_funprofiler/ package - Add fmh_funprofiler/__init__.py with version string - Add pyproject.toml with build config, dependencies, and CLI entry points - Update .gitignore with Python build artifact patterns
53 tests covering: - Package import and version string - CLI --help flags for both entry points - check_args validation for funcprofiler and funcprofiler_many (file existence, ksize, scaled, threshold_bp) - parse_args / parse_arguments positional and optional arguments Also registers pytest testpaths and dev extras in pyproject.toml.
- Update README.md install instructions
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Hi @dkoslicki,
Thank you for providing fmh-funprofiler. We (@nickp60 and I) are hoping to use it for a new nf-core pipeline, funcprofiler. For that, it would be great if the code was packaged as a Python package (as proposed in #15), and ideally as a Bioconda package (happy to tackle this after this one is merged).
This PR converts the repository into an installable Python package
fmhfunprofiler.Installable package structure: source files are now organized under
fmhfunprofiler/, with apyproject.tomldefining build metadata. Users get access to thefuncprofiler.pyandfuncprofiler-many.pyscripts in the PATH after install.Direct install from GitHub: it can be installed with a single pip command straight from the repository, without requiring a PyPI release:
pip install git+https://github.com/KoslickiLab/funprofiler.gitAn
environment.yamlis also provided for users who prefer to set up the full conda environment (including sourmash and biom-format) in one step.Pytest test suite: added tests covering argument validation, argument parsing, package imports, version string, and CLI --help flags for both entry points. Tests can be run with pytest from the repo root.
Summary of changes:
fmhfunprofiler/— Python package directory (scripts moved from repo root)pyproject.toml— build config, dependencies, CLI entry points, dev extrasenvironment.yaml— conda environment definitiontests/— pytest suite (test_package.py, test_funcprofiler.py, test_funcprofiler_many.py)README.md— updated installation instructions1.1.0