[build-system] requires = ["poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api" [tool.poetry] name = "core" version = "0.0.0" description = "The Gymrek Lab's core python library" authors = ["Gymrek Lab"] license = "MIT" repository = "https://github.com/gymrek-lab/core" homepage = "https://github.com/gymrek-lab/core" documentation = "https://core.readthedocs.io" readme = "README.md" [tool.poetry.dependencies] python = ">=3.7,<4.0" numpy = ">=1.20.0" click = ">=8.0.3" pysam = ">=0.19.0" cyvcf2 = ">=0.30.14" matplotlib = ">=3.5.1" Pgenlib = ">=0.90.1" [tool.poetry.group.docs.dependencies] Sphinx = ">=4.3.2" sphinx-autodoc-typehints = ">=1.12.0" sphinx-rtd-theme = ">=1.0.0" numpydoc = ">=1.1.0" sphinx-click = ">=3.0.2" [tool.poetry.group.tests.dependencies] pytest = ">=7.4.3" pytest-cov = ">=3.0.0" black = ">=23.3.0" ipython = ">=7.34.0" coverage = {extras = ["toml"], version = ">=7.2.7"} filprofiler = ">=2023.3.1" [tool.poetry.scripts] core = 'core.__main__:main' [tool.black] line-length = 88 preview = true [tool.pytest.ini_options] log_cli_level = "DEBUG" log_cli_format = "%(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s)" log_cli_date_format = "%Y-%m-%d %H:%M:%S" addopts = """ --ignore noxfile.py """ [tool.coverage.run] omit = [ ".nox/*", "noxfile.py", "core/__init__.py", "core/tr_harmonizer.py", ] [tool.coverage.report] exclude_lines = [ "pragma: no cover", ]