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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 = "ensembl_cli"
description = """Ensembl cli tools"""
# remember to update cogent3/_version.py too!
version = "2023.7.9a1"
authors = [
{ name = "Gavin Huttley", email = "[email protected]"},
]
keywords = ["biology", "genomics", "evolution", "bioinformatics"]
readme = "README.md"
license = { file = "LICENSE" }
requires-python = ">=3.8,<3.12"
dependencies = ["click",
"scitrack",
"typing_extensions",
"cogent3 @ git+https://github.com/cogent3/cogent3.git@develop",
"pydantic",
"rich",
"numba",
"numpy",
"unsync",
"wakepy",
]
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 :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
]
[project.urls]
Documentation = "https://github.com/cogent3/ensembl_cli"
"Bug Tracker" = "https://github.com/cogent3/ensembl_cli/issues"
"Source Code" = "https://github.com/cogent3/ensembl_cli"
[project.scripts]
ensembl_cli = "ensembl_cli.cli:main"
[project.optional-dependencies]
test = [
"black==23.3.0",
"isort==5.12.0",
"click==8.1.3", # black needs this pinned
"pytest",
"pytest-cov",
"pytest-xdist",
"nox"]
doc = ["click==8.1.3",
"sphinx",
"sphinx-autobuild",
"sphinx>=1.6",
"sphinx_book_theme",
"sphinx_panels",
"sphinxcontrib-bibtex"]
dev = ["black==23.3.0",
"click==8.1.3",
"flit",
"ipykernel",
"ipython",
"ipywidgets",
"isort==5.12.0",
"jupyter-sphinx",
"jupyter_client",
"jupyterlab",
"jupytext",
"kaleido",
"nbconvert>5.4",
"nbformat",
"nbsphinx",
"nox",
"numpydoc",
"pandas",
"pillow",
"plotly",
"psutil",
"pytest",
"pytest-cov",
"pytest-xdist",
"scriv",
"sphinx",
"sphinx-autobuild",
"sphinx_book_theme",
"sphinx_panels",
"sphinxcontrib-bibtex"]
[tool.flit.sdist]
include = ["doc/", "requirements.txt", "src/*", "pyproject.toml"]
exclude = ["doc/*.html"]
[tool.pytest.ini_options]
markers = [
"slow: marks tests as slow (deselect with '-m \"not slow\"')",
]
addopts = ["--strict-config", "-ra"]
testpaths = "tests"
[tool.black]
line-length = 88
target-version = ["py38", "py39", "py310"]
exclude = '''
/(
\.eggs
| \.git
| \.hg
| \.mypy_cache
| \.nox
| \.venv
| _build
| build
| 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
src_paths = ["src", "tests","doc","noxfile.py"]
[tool.scriv]
format="md"
categories=["Contributors", "ENH", "BUG", "DOC", "Deprecations", "Discontinued"]
output_file="changelog.md"
version="literal: src/cogent3/__init__.py:__version__"
skip_fragments="README.*"
new_fragment_template="file: changelog.d/templates/new.md.j2"
entry_title_template="file: changelog.d/templates/title.md.j2"