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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["flit_core >=3.2,<4"]
build-backend = "flit_core.buildapi"
[project]
name = "cogent3"
description = """COmparative GENomics Toolkit 3: genomic sequence analysis within notebooks or on compute systems with 1000s of CPUs."""
dynamic = ["version"]
authors = [
{ name = "Gavin Huttley", email = "[email protected]"},
]
keywords = ["biology", "genomics", "statistics", "phylogeny", "evolution", "bioinformatics"]
readme = "README.md"
license = { file = "LICENSE" }
requires-python = ">=3.7,<3.11"
dependencies = ["chardet",
"numpy",
"numba>0.48.0;python_version<'3.9'",
"numba>0.53; python_version>='3.9'",
"numba>0.54; python_version>='3.10'",
"scitrack",
"tqdm",
"tinydb"]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: BSD License",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Software Development :: Libraries :: Python Modules",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
]
[project.urls]
Documentation = "https://www.cogent3.org/"
"Bug Tracker" = "https://github.com/cogent3/cogent3/issues"
"Source Code" = "https://github.com/cogent3/cogent3"
Changelog = "https://github.com/cogent3/cogent3/blob/develop/changelog.md"
[project.optional-dependencies]
test = [
"black",
"isort",
"pytest",
"pytest-cov",
"pytest-xdist",
"nox"]
doc = ["click",
"ipykernel",
"ipython",
"ipywidgets",
"jupyter-sphinx",
"jupyter_client",
"jupyterlab",
"jupytext",
"kaleido",
"matplotlib",
"nbconvert>5.4",
"nbformat",
"nbsphinx",
"numpydoc",
"pillow",
"plotly",
"psutil",
"sphinx",
"sphinx-autobuild",
"sphinx-gallery",
"sphinx>=1.6",
"sphinx_bootstrap_theme",
"sphinx_panels",
"sphinxcontrib-bibtex"]
extra = ["pandas", "plotly", "psutil", "kaleido"]
dev = ["black",
"click",
"flit",
"ipykernel",
"ipython",
"ipywidgets",
"isort",
"jupyter-sphinx",
"jupyter_client",
"jupyterlab",
"jupytext",
"kaleido",
"matplotlib",
"nbconvert>5.4",
"nbformat",
"nbsphinx",
"nox",
"numpydoc",
"pandas",
"pillow",
"plotly",
"psutil",
"pytest",
"pytest-cov",
"pytest-xdist",
"sphinx",
"sphinx-autobuild",
"sphinx-gallery",
"sphinx_bootstrap_theme",
"sphinx_panels",
"sphinxcontrib-bibtex"]
[tool.flit.sdist]
include = ["doc/", "requirements.txt", "src/*", "pyproject.toml"]
exclude = ["doc/*.html"]
[tool.pytest.ini_options]
addopts = ["--strict-config", "-ra"]
testpaths = "tests"
filterwarnings = [
'ignore:FORCED EXIT from optimiser',
'ignore:Motif probs overspecified',
'ignore:Model not reversible',
]
[tool.black]
line-length = 88
target-version = ["py37", "py38", "py39", "py310"]
exclude = '''
/(
\.eggs
| \.git
| \.hg
| \.mypy_cache
| \.nox
| \.venv
| _build
| build
| doc
| dist
| tests/data
)/
'''
[tool.isort]
atomic=true
force_grid_wrap=0
include_trailing_comma=true
lines_after_imports=2
lines_between_types=1
multi_line_output=3
use_parentheses=true