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pyproject.toml
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[build-system]
requires = ["hatchling", "setuptools"]
build-backend = "hatchling.build"
[project]
name = "open-variant"
version = "1.0.1"
description = "OpenVariant provides different functionalities to read, parse and operate different multiple input file formats, being able to customize the output."
authors = [
{ name = "BBGLab (Barcelona Biomedical Genomics Lab)", email = "[email protected]" }
]
dependencies = [
"pyyaml==6.0.1",
"tqdm==4.66.3",
"click==8.1.3",
"pyliftover==0.4.1",
"appdirs==1.4.4",
]
readme = "README.md"
requires-python = ">=3.10"
license = { file = "LICENSE" }
keywords = ["bioinformatics", "openvariant", "openvar", "bbglab"]
[project.urls]
Homepage = "https://github.com/bbglab/openvariant"
Documentation = "https://openvariant.readthedocs.io/"
Repository = "https://github.com/bbglab/openvariant"
Issues = "https://github.com/bbglab/openvariant/issues"
[project.scripts]
"openvar" = "openvariant.commands.openvar:openvar"
[project.optional-dependencies]
docs = [
"alabaster==0.7.12",
"asttokens==2.0.5",
"attrs==22.1.0",
"babel==2.10.3",
"backcall==0.2.0",
"beautifulsoup4==4.11.1",
"bleach==5.0.1",
"charset-normalizer==2.1.0",
"click==8.1.3",
"decorator==5.1.1",
"defusedxml==0.7.1",
"docutils==0.17.1",
"entrypoints==0.4",
"executing==0.9.1",
"fastjsonschema==2.16.1",
"idna==3.7",
"imagesize==1.4.1",
"jedi==0.18.1",
"jinja2==3.1.4",
"jsonschema==4.8.0",
"jupyter-client==7.3.4",
"jupyter-core==4.11.2",
"jupyterlab-pygments==0.2.2",
"markupsafe==2.1.1",
"matplotlib-inline==0.1.3",
"nbclient==0.6.6",
"nbformat==5.4.0",
"nbsphinx==0.8.9",
"nest-asyncio==1.5.5",
"open-variant==1.0.0",
"packaging==21.3",
"pandocfilters==1.5.0",
"parso==0.8.3",
"pexpect==4.8.0",
"pickleshare==0.7.5",
"prompt-toolkit==3.0.30",
"ptyprocess==0.7.0",
"pure-eval==0.2.2",
"pydata-sphinx-theme==0.8.1",
"pygments==2.15.0",
"pyparsing==3.0.9",
"pyrsistent==0.18.1",
"python-dateutil==2.8.2",
"pytz==2022.1",
"pyyaml==6.0.1",
"pyzmq==26.2.0",
"requests==2.32.2",
"ruamel-yaml==0.16.13",
"six==1.16.0",
"snowballstemmer==2.2.0",
"soupsieve==2.3.2.post1",
"sphinx-copybutton==0.5.0",
"sphinx==4.5.0",
"sphinx-gallery==0.10.1",
"sphinx-panels==0.6.0",
"sphinxcontrib-applehelp==1.0.2",
"sphinxcontrib-autoyaml==1.0.0",
"sphinxcontrib-devhelp==1.0.2",
"sphinxcontrib-htmlhelp==2.0.0",
"sphinxcontrib-jsmath==1.0.1",
"sphinxcontrib-qthelp==1.0.3",
"sphinxcontrib-serializinghtml==1.1.5",
"stack-data==0.3.0",
"tinycss2==1.1.1",
"tornado==6.4.2",
"tqdm==4.66.3",
"traitlets==5.3.0",
"urllib3==1.26.19",
"wcwidth==0.2.5",
"webencodings==0.5.1",
"ipython>=8.18.0",
"nbconvert==7.0.0rc0",
"mistune==2.0.3",
"sphinxcontrib-bibtex==2.6.3",
"setuptools>=58.2.0",
]
linting = [
"flake8>=7.1.1",
"ruff>=0.8.3",
]
tests = [
"coverage>=7.6.9",
"pytest-cov>=6.0.0",
"pytest>=8.3.4",
]
[tool.hatch.metadata]
allow-direct-references = true
[tool.hatch.build.targets.wheel]
packages = ["openvariant"]
[tool.uv.sources]
open-variant = { workspace = true }
[tool.ruff.lint]
select = ["F"]
ignore = ["F401"]
[tool.ruff]
line-length = 127
[tool.ruff.format]
quote-style = "single"
indent-style = "space"
docstring-code-format = true