pyproject.toml

# Copyright (C) 2023 Roberto Rossini <roberros@uio.no>
#
# SPDX-License-Identifier: MIT

[build-system]
requires = [
  "conan>=2.0.5",
  "nanobind>=2", # This is required in order to run stubgen
  "numpy>=2",
  "scikit-build-core>=0.10",
  "typing_extensions",
]

build-backend = "scikit_build_core.build"

[project]
name = "hictkpy"
dynamic = ["version"]
description = "Python bindings for hictk: read and write .cool and .hic files directly from Python"
readme = "README.md"
authors = [
  {name = "Roberto Rossini", email = "roberros@uio.no"}
]
requires-python = ">=3.9"
classifiers = [
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.9",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
  "License :: OSI Approved :: MIT License"
]

dependencies = []

optional-dependencies.numpy = [
  "numpy",
]

optional-dependencies.pandas = [
  "hictkpy[pyarrow]",
  "pandas>=2.1.0,!=2.2.0",
]

optional-dependencies.pyarrow = [
  "pyarrow>=16",
]

optional-dependencies.scipy = [
  "scipy",
]

optional-dependencies.all = [
  "hictkpy[numpy,pandas,pyarrow,scipy]",
]

optional-dependencies.test = [
  "pytest>=8.0",
]

optional-dependencies.dev = [
  "hictkpy[all,test]",
  "black>=24.10",
  "clang-format>=19.1",
  "isort>=5.13",
  "gersemi>=0.15",
]

[tool.scikit-build]
minimum-version = "0.10"
build-dir = "build/{wheel_tag}"
metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
sdist.include = ["src/_version.py"]
wheel.expand-macos-universal-tags = true
cmake.build-type = "Release"

[tool.scikit-build.cmake.define]
BUILD_SHARED_LIBS = "OFF"
CMAKE_OSX_DEPLOYMENT_TARGET = "10.15"
CMAKE_PROJECT_TOP_LEVEL_INCLUDES = { env="HICTKPY_PROJECT_TOP_LEVEL_INCLUDES", default="cmake/conan_provider.cmake" }
CONAN_INSTALL_ARGS = { env="HICTKPY_CONAN_INSTALL_ARGS", default="--settings=compiler.cppstd=17;--settings=build_type=Release;--build=missing;--update;--options=*/*:shared=False" }
HICTK_BUILD_BENCHMARKS = "OFF"
HICTK_BUILD_EXAMPLES = "OFF"
HICTK_BUILD_TOOLS = "OFF"
HICTK_ENABLE_FUZZY_TESTING = "OFF"
HICTK_ENABLE_GIT_VERSION_TRACKING = "OFF"
HICTK_ENABLE_TESTING = "OFF"
HICTK_WITH_ARROW = "ON"
HICTK_WITH_EIGEN = "ON"

[tool.setuptools_scm]
write_to = "src/_version.py"

[tool.pytest.ini_options]
minversion = "8.0"
addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
xfail_strict = true
filterwarnings = [
  "error",
  "ignore:(ast.Str|Attribute s|ast.NameConstant|ast.Num) is deprecated:DeprecationWarning:_pytest",
  "ignore:datetime\\.datetime\\.utcfromtimestamp\\(\\)*:DeprecationWarning",  # https://github.com/pytest-dev/pytest/issues/11528
]
python_files = [
  "test/test*.py"
]
testpaths = [
  "test/"
]

[tool.cibuildwheel]
build-frontend = "build"
manylinux-x86_64-image = "quay.io/pypa/manylinux_2_28_x86_64:2024.11.09-1"
manylinux-i686-image = "quay.io/pypa/manylinux_2_28_i686:2024.11.09-1"
manylinux-aarch64-image = "quay.io/pypa/manylinux_2_28_aarch64:2024.11.09-1"
manylinux-ppc64le-image = "quay.io/pypa/manylinux_2_28_ppc64le:2024.11.09-1"
manylinux-s390x-image = "quay.io/pypa/manylinux_2_28_s390x:2024.11.09-1"
manylinux-pypy_x86_64-image = "quay.io/pypa/manylinux_2_28_x86_64:2024.11.09-1"
manylinux-pypy_i686-image = "quay.io/pypa/manylinux_2_28_i686:2024.11.09-1"
manylinux-pypy_aarch64-image = "quay.io/pypa/manylinux_2_28_aarch64:2024.11.09-1"

skip = ["cp314*", "*musllinux*", "pp*"]
test-command = "python -m pytest {project}/test"
test-extras = ["test", "numpy", "pandas", "pyarrow", "scipy"]
test-skip = ["cp314*", "*universal2", "pp*"]

# Setuptools bug causes collision between pypy and cpython artifacts
before-build = [
  "rm -rf '{project}/build'",
]

# We are using static linking, thus repairing wheels should not be necessary.
# Exception being when building portable Linux wheels.
# See https://github.com/scikit-build/scikit-build-core/pull/698#issuecomment-2082991257
[tool.cibuildwheel.macos]
repair-wheel-command = ""

[tool.cibuildwheel.windows]
repair-wheel-command = ""

[tool.ruff]
extend-select = [
  "B", # flake8-bugbear
  "B904",
  "I", # isort
  "PGH", # pygrep-hooks
  "RUF", # Ruff-specific
  "UP", # pyupgrade
]
extend-ignore = [
  "E501", # Line too long
]
target-version = "py39"

[tool.black]
line-length = 120
target-version = ["py39"]

[tool.isort]
profile = "black"