Initial implementation of bwapy

[nh13]

The goal of this PR is to get a minimal example working for running bwa aln. The motivation is to replace the usage of https://github.com/fulcrumgenomics/bwa-aln-interactive in https://github.com/fulcrumgenomics/prymer and elsewhere. We can then use bwapy along with latest supported release of bwa.

Documentation, including examples and verbose docstrings, as well as improved test coverage, are planned to be added at a later date.

Todo:

• run large scale tests, especially for bwa mem given all the custom code ported over

[codecov]

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[msto]

I don’t know if it’s codified, I learned it through experience.

…

On Tue, Dec 17, 2024 at 9:13 PM Tim Fennell ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In pyproject.toml <#1 (comment)>: > +[tool.poetry] +name = "bwapy" +version = "0.0.1-dev" +description = "Python bindings for BWA" +authors = ["Nils Homer"] +license = "MIT" +readme = "README.md" +homepage = "https://github.com/fulcrumgenomics/bwapy" +repository = "https://github.com/fulcrumgenomics/bwapy" +keywords = ["bioinformatics"] +packages = [{ include = "bwapy" }] +classifiers = [ + "Development Status :: 3 - Alpha", + "Environment :: Console", + "Intended Audience :: Developers", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "Topic :: Scientific/Engineering :: Bio-Informatics", + "Topic :: Software Development :: Documentation", + "Topic :: Software Development :: Libraries :: Python Modules", +] +include = [ + "LICENSE", + { path = "bwapy/**/*.so", format = "wheel" }, + { path = "**/*.so", format = "wheel" }, + { path = "*.so", format = "wheel" }, + #{ path = "*.so", format = "wheel" } +] + +[tool.poetry.build] +generate-setup-file = false +script = "build.py" + +[tool.poetry.dependencies] +python = ">=3.9.0,<4.0" +pysam = ">=0.22.1" +typing_extensions = { version = ">=3.7.4", python = "<3.12" } + +[tool.poetry.group.dev.dependencies] +# dependencies for linting, style checking, and unit testing +mypy = ">=1.7.0" +pytest = ">=7.4.0" +pytest-cov = ">=2.8.1" +ruff = "0.4.8" +setuptools = ">=68.0.0" Is this a policy written down somewhere or an emergent policy? — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAANOFO66NYWKYDWMYHO4TT2GDK4ZAVCNFSM6AAAAABTSJJNSCVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZDKMJQGYYTGMJZHA> . You are receiving this because you commented.Message ID: ***@***.***>