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156 lines (148 loc) · 5 KB
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[build-system]
requires = [
"maturin>=1.0,<2.0"
]
build-backend = "maturin"
[tool.maturin]
python-source = "pydeeptools"
exclude = ["pydeeptools/deeptools/test/**/*"]
module-name = "deeptools.hp"
bindings = "pyo3"
[project]
name = "deeptools"
version = "4.0.0"
authors = [
{name="Vivek Bhardwaj"},
{name="Ward Deboutte"},
{name="Lucille Delisle"},
{name="Sarah Diehl"},
{name="Galina Erikson"},
{name="Friederike Dündar"},
{name="Björn Grüning"},
{name="Steffen Heyne"},
{name="Fabian Kilpert"},
{name="Wolfgang Maier"},
{name="Thomas Manke"},
{name="Saim Momin"},
{name="Mohit Navander"},
{name="Juan Perez Caballero"},
{name="Fidel Ramirez"},
{name="Adrian Salatino"},
{name="Andreas S Richter"},
{name="Devon P Ryan"},
{name="Pavankumar Videm"},
{email="w@rddeboutte.com"}
]
requires-python = ">= 3.12"
dependencies = [
"numpy >= 2.0",
"scipy >= 1.13",
"matplotlib >= 3.10",
"pysam >= 0.23",
"pyBigWig >= 0.3",
"deeptoolsintervals >= 0.1",
"maturin"
]
description = "Useful tools for exploring deep sequencing data."
license = {file = "LICENSE.txt"}
classifiers = [
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Bio-Informatics",
# Supported Python versions:
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
"Programming Language :: Python :: 3.14"
]
readme = "README.md"
[project.optional-dependencies]
actions = [
"ruff",
"pytest",
"twine",
"build",
"planemo",
]
docs = [
"sphinx >= 7.2.6",
"mock >= 5.1.0",
"sphinx_rtd_theme >= 2.0.0",
"sphinx-argparse >= 0.4.0",
"myst-parser >= 3.0.0",
]
[project.urls]
homepage = "https://pypi.python.org/pypi/deepTools/"
documentation = "https://deeptools.readthedocs.io/en/latest/"
repository = "https://github.com/deeptools/deepTools"
[tool.setuptools]
packages = ["deeptools"]
[tool.ruff.lint]
ignore = [
"N999", #invalid module name
"BLE001", # bare excepts
]
[project.scripts]
bamPEFragmentSize = "deeptools.bamPEFragmentSize:main"
bigwigAverage = "deeptools.bigwigAverage:main"
bigwigCompare = "deeptools.bigwigCompare:main"
computeMatrixOperations = "deeptools.computeMatrixOperations:main"
deeptools = "deeptools.deeptools_list_tools:main"
estimateReadFiltering = "deeptools.estimateReadFiltering:main"
estimateScaleFactor = "deeptools.estimateScaleFactor:main"
multiBigwigSummary = "deeptools.multiBigwigSummary:main"
plotCorrelation = "deeptools.plotCorrelation:main"
plotCoverage = "deeptools.plotCoverage:main"
plotEnrichment = "deeptools.plotEnrichment:main"
plotFingerprint = "deeptools.plotFingerprint:main"
plotHeatmap = "deeptools.plotHeatmap:main"
plotPCA = "deeptools.plotPCA:main"
plotProfile = "deeptools.plotProfile:main"
bamCoverage = "deeptools.bamCoverage2:main"
bamCompare = "deeptools.bamCompare2:main"
computeMatrix = "deeptools.computeMatrix2:main"
alignmentSieve = "deeptools.alignmentSieve2:main"
multiBamSummary = "deeptools.multiBamSummary2:main"
[tool.pixi.workspace]
channels = ["conda-forge", "bioconda"]
platforms = ["linux-64", "osx-arm64", "osx-64"]
[tool.pixi.dependencies]
libclang = "<22"
clangdev = "<22"
htslib = "<=1.19"
zlib = "*"
# conda-forge's rust 1.98.0 build segfaults in LLVM target init on osx-arm64
# (reproducible even after a clean env reinstall); capped until that's fixed upstream.
rust = ">=1.87,<1.98"
maturin = ">=1.0,<2.0"
pip = "*"
openssl = "*"
pkg-config = "*"
py-spy = "*"
[tool.pixi.pypi-dependencies]
deeptools = { path = ".", editable = true, extras = ['actions', 'docs'] }
[tool.pixi.activation.env]
LIBCLANG_PATH = "$CONDA_PREFIX/lib"
OPENSSL_NO_VENDOR = "1"
OPENSSL_DIR = "$CONDA_PREFIX"
[tool.pixi.tasks]
build = "maturin develop --release"
test = "pytest pydeeptools/deeptools/test/"
docs = "sphinx-build -b html docs docs/_build/html -W --keep-going"
ruff = "ruff check pydeeptools/ scripts/"
planemo = "planemo test --no_dependency_resolution --galaxy_branch release_26.0 --install_galaxy galaxy/wrapper/alignmentSieve.xml galaxy/wrapper/bamCompare.xml galaxy/wrapper/bamCoverage.xml galaxy/wrapper/bamPEFragmentSize.xml galaxy/wrapper/bigwigCompare.xml galaxy/wrapper/bigwigAverage.xml galaxy/wrapper/computeMatrix.xml galaxy/wrapper/computeMatrixOperations.xml galaxy/wrapper/estimateReadFiltering.xml galaxy/wrapper/multiBamSummary.xml galaxy/wrapper/multiBigwigSummary.xml galaxy/wrapper/plotCorrelation.xml galaxy/wrapper/plotCoverage.xml galaxy/wrapper/plotEnrichment.xml galaxy/wrapper/plotFingerprint.xml galaxy/wrapper/plotHeatmap.xml galaxy/wrapper/plotPCA.xml galaxy/wrapper/plotProfiler.xml"
[tool.pixi.feature.py312.dependencies]
python = "3.12.*"
[tool.pixi.feature.py313.dependencies]
python = "3.13.*"
[tool.pixi.feature.py314.dependencies]
python = "3.14.*"
[tool.pixi.feature.ess]
platforms = ["linux-64"]
[tool.pixi.feature.ess.dependencies]
ucsc-facount = "*"
khmer = "*"
python = "3.*"
[tool.pixi.environments]
py312 = ["py312"]
py313 = ["py313"]
py314 = ["py314"]
ess = { features = ["ess"], no-default-feature = true }