recount3/pyproject.toml at main · MoseleyBioinformaticsLab/recount3 · GitHub

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[build-system]
requires = ["setuptools>=68"]
build-backend = "setuptools.build_meta"

[project]
name = "recount3"
dynamic = ["version"]
description = "API and CLI to discover, download, and assemble recount3 resources."
dependencies = [
  "numpy>=2.0,<3.0",
  "pandas>=2.2,<3.0",
  "scipy>=1.13,<2.0",
]
readme = { file = "README.rst", content-type = "text/x-rst" }
requires-python = ">=3.10"
license = "BSD-3-Clause-Clear"
license-files = ["LICENSE"]
authors = [
  { name = "Alexander A. Alsalihi" },
  { name = "Robert M. Flight" },
  { name = "Hunter N.B. Moseley" }
]
maintainers = [
  { name = "Moseley Bioinformatics Lab" }
]
keywords = [
  "bioinformatics",
  "genomics",
  "recount3",
  "RNA-seq",
  "CLI",
  "data-pipelines",
  "manifests",
]
classifiers = [
  "Development Status :: 5 - Production/Stable",
  "Intended Audience :: Science/Research",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
  "Programming Language :: Python",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Programming Language :: Python :: 3.14",
  "Typing :: Typed",
]

# Console entry point: `recount3`
[project.scripts]
recount3 = "recount3.cli:main"

[project.urls]
Homepage = "https://github.com/MoseleyBioinformaticsLab/recount3"
Repository = "https://github.com/MoseleyBioinformaticsLab/recount3"
Issues = "https://github.com/MoseleyBioinformaticsLab/recount3/issues"
Documentation = "https://moseleybioinformaticslab.github.io/recount3/"
Changelog = "https://github.com/MoseleyBioinformaticsLab/recount3/blob/main/CHANGELOG.rst"

[tool.setuptools]
package-dir = {"" = "src"}
include-package-data = true

[tool.setuptools.packages.find]
where = ["src"]
include = ["recount3*"]

[tool.setuptools.package-data]
recount3 = ["py.typed"]

[tool.setuptools.dynamic]
version = { attr = "recount3.version.__version__" }

[project.optional-dependencies]
bigwig = [
  "pybigwig>=0.3.18",
]
biocpy = [
  "biocframe>=0.7",
  "genomicranges>=0.8",
  "summarizedexperiment>=0.6",
]
docs = [
  "sphinx>=7",
  "sphinx-rtd-theme>=2",
]
dev = [
  "pytest>=8,<9",
  "pytest-cov>=5,<6",
  "pytest-mock>=3.12,<4",
  "pytest-xdist>=3,<4",
  "pylint>=3.2,<4",
  "build>=1.2",
  "twine>=5",
]

all = [
  "recount3[bigwig,biocpy,docs,dev]"
]

[tool.black]
line-length = 80

[tool.pytest.ini_options]
minversion = "8.0"
addopts = "-ra"
testpaths = ["tests"]
pythonpath = ["src"]

[tool.coverage.run]
branch = true
source = ["src"]

[tool.coverage.report]
show_missing = true
skip_covered = true
exclude_lines = [
  "pragma: no cover",
  "if __name__ == .__main__.:",
]