[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="bioinfo-core@ie-freiburg.mpg.de"}
]
requires-python = ">= 3.12"
dependencies = [
    "numpy >= 2.0",
    "scipy >= 1.13",
    "matplotlib >= 3.10",
    "pysam >= 0.23",
    "pyBigWig >= 0.3",
    "py2bit >= 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"
]
readme = "README.md"
[project.optional-dependencies]
actions = [
    "flake8",
    "pytest",
    "twine",
    "build",
    "planemo",
]
docs = [
    "sphinx >= 7.2.6",
    "mock >= 5.1.0",
    "sphinx_rtd_theme >= 2.0.0",
    "sphinx-argparse >= 0.4.0",
]
[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"]

[project.scripts]
alignmentSieve_old = "deeptools.alignmentSieve:main"
bamCompare_old = "deeptools.bamCompare:main"
bamCoverage_old = "deeptools.bamCoverage:main"
bamPEFragmentSize = "deeptools.bamPEFragmentSize:main"
bigwigAverage = "deeptools.bigwigAverage:main"
bigwigCompare = "deeptools.bigwigCompare:main"
computeGCBias = "deeptools.computeGCBias:main"
computeMatrix_old = "deeptools.computeMatrix:main"
computeMatrixOperations = "deeptools.computeMatrixOperations:main"
correctGCBias = "deeptools.correctGCBias:main"
deeptools = "deeptools.deeptools_list_tools:main"
estimateReadFiltering = "deeptools.estimateReadFiltering:main"
estimateScaleFactor = "deeptools.estimateScaleFactor:main"
multiBamSummary_old = "deeptools.multiBamSummary: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"

[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.environments]
py312 = ["py312"]
py313 = ["py313"]
py314 = ["py314"]