pyproject.toml

[build-system]
build-backend = "setuptools.build_meta:__legacy__"
requires = ["setuptools>=42",
	    "setuptools_scm[toml]>=6.2",
	    "swig>=4.2.1,<=4.2.1.post0", # pin `swig` to 4.2.1 (swig 4.3.0 creates extensions that segfault)
	                                 # fallback to 4.2.1 if a 4.2.1.post0 compatible package not available
	    "tomli",
	    "cffconvert @ git+https://github.com/alexlancaster/cffconvert.git@combine_features#egg=cffconvert",
	    "importlib-metadata; python_version <= '3.8'"
	    ]
[project]
name = "pypop-genomics"
description = "PyPop: Python for Population Genomics"
license = { text = "GPL-2.0-or-later" }
authors = [{ name = "Alex Lancaster" }]
maintainers = [{ name = "PyPop team" }]
dynamic = ["readme", "version"]
keywords = [
    "bioinformatics",
    "population-genomics",
    "evolutionary-biology",
    "population-genetics"
]
classifiers = [
    "Programming Language :: Python :: 3",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Operating System :: MacOS :: MacOS X",
    "Operating System :: Microsoft :: Windows",
    "Operating System :: POSIX :: Linux"
]
dependencies = [
    "numpy <= 2.5.0",
    "lxml <= 6.1.1",
    "pooch <=1.9.0",
    "importlib-resources; python_version <= '3.8'",
    "importlib-metadata; python_version <= '3.8'"
]

[project.optional-dependencies]
test = [
  "pytest",
  "pytest-benchmark[histogram]",
  "pytest-doctestplus",
  'sphinx; platform_python_implementation != "PyPy"',
]
test-pval-benchmarking = ["scipy"]

[project.urls]
Homepage = "http://pypop.org/"
Documentation = "http://pypop.org/docs/"
Changelog = "https://github.com/alexlancaster/pypop/blob/main/NEWS.md"
Source = "https://github.com/alexlancaster/pypop/"
Tracker = "https://github.com/alexlancaster/pypop/issues"

[project.scripts]
pypop = "PyPop.pypop:main"
popmeta = "PyPop.popmeta:main"
pypop-interactive = "PyPop.pypop:main_interactive"

[tool.setuptools]

[tool.setuptools.packages.find]
where = ["src"]
include = ["PyPop", "PyPop.xslt"]

[tool.setuptools.package-data]
"PyPop" = ["citation/CITATION*"]

[tool.setuptools.dynamic]
readme = { file = "README.rst", content-type = "text/x-rst" }

[tool.setuptools_scm]
write_to = "src/PyPop/_version.py"
version_scheme = "post-release"

[tool.pytest.ini_options]
minversion = "6.0"
addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config", "--doctest-modules", "--doctest-glob=*.rst"]
xfail_strict = true
# convert warnings to errors, except for ImportWarnings in numpy (needed for pp38)
# FIXME: eventually we should be able to remove the numpy exception
filterwarnings = ["error", "default::ImportWarning", "ignore:.*Arlequin.*deprecated.*"]
log_cli_level = "INFO"
testpaths = [
  "website/docs",
  "tests",
]
norecursedirs = [
 "tests/data"
]

[tool.cibuildwheel]
enable = ["pypy"]             # explicitly enable, this will be required for cibuildwheel >= 3
skip = ["*-win32", "*_i686",  # skip 32-bit builds
     "pp37-*",             # skip certain PyPy configurations
     "pp*_aarch64 ",       # no numpy wheels for aarch64 on PyPy
     "pp311-*",            # no numpy wheels for PyPy 3.11
     "cp36-musllinux_*", "cp37-musllinux_*", "cp38-musllinux_*", # older musllinux missing numpy wheels
     "cp314t*"             # lxml not yet built
     ]
test-skip = ["*-win_arm64", "cp38-macosx_arm64"]
test-extras = ["test"]
test-command = ["sphinx-build -b doctest {package}/website/doctest _doctests",
	        "pytest -v --pyargs PyPop {package}/tests"]
# FIXME: can add "test-command" that would allow unit test output to be saved
# "pytest -v {package}/tests && echo {package} && ls && tar zcvf unit_tests_output.tar.gz run_test_* && cp unit_tests_output.tar.gz {package}/wheelhouse/"

# don't try and install pypi packages that need build from source
# this is mainly import during the testing phase
environment = { PIP_ONLY_BINARY=":all:", PIP_VERBOSE="0", PYPOP_DOCS_MODE="installed" }

# use pip and override the PIP_ONLY_BINARY=:all: during wheel generation
# so that certain source-only build deps (like cffconvert) install
build-frontend = { name = "pip", args = ["--only-binary=:none:"] }

[tool.cibuildwheel.linux]
# add aarch64 to default ("auto") architectures
archs = ["auto", "aarch64"]
# default linux wheels use CentOS-based runners, local cibuildwheel docker
before-all = ["yum install -y gsl-devel"]
# force use of newer `manylinux_2_28`: in cibuildwheel >= 3.0 it will be the default
manylinux-x86_64-image = "manylinux_2_28"
manylinux-pypy_x86_64-image = "manylinux_2_28"
manylinux-aarch64-image = "manylinux_2_28"
manylinux-pypy_aarch64-image = "manylinux_2_28"

[[tool.cibuildwheel.overrides]]
# run the benchmarking only on cp314
select = "cp314-manylinux_x86_64"
inherit.test-extras = "append"
test-extras = ["test-pval-benchmarking"]
inherit.environment = "append"
environment = { PYTEST_OPTIONS="--runslow --pval-benchmarking" }

[[tool.cibuildwheel.overrides]]
# skip sphinx doctest on PyPy: can't install sphinx
select = "pp*"
test-command = ["pytest -v --pyargs PyPop {package}/tests"]

[[tool.cibuildwheel.overrides]]
# musl uses apk/apt
select = "*musllinux*"
before-all = ["apk add gsl-dev"]
# FIXME: if we want to run the full tests, need to enable the below to force
# musllinux_1_1 image for the time being on x86_64 (musllinux_1_2 segfaults on
# any test involving emhaplofreq)
# musllinux-x86_64-image="musllinux_1_1"

[tool.cibuildwheel.macos]
# use oras to get archived 2.7.1 bottles of `gsl` that has 10.15 (on x86) / 11.0 (on arm64) builds
before-all = ["brew install --quiet oras",
	     "oras pull ghcr.io/homebrew/core/gsl:2.7.1"]
archs = ["arm64", "x86_64"]  # don't enable "universal2" binary

[[tool.cibuildwheel.overrides]]
select = "*-macosx_*"
inherit.environment="append"
environment = { CPATH="/opt/homebrew/include", LIBRARY_PATH="/opt/homebrew/lib", PYTHONFAULTHANDLER="1", HOMEBREW_DEVELOPER="1", HOMEBREW_GREP_WARNINGS="-e 'is available and more recent than version' -e 'Cannot verify the integrity of'" }

[[tool.cibuildwheel.overrides]]
select = "*-macosx_x86_64"
inherit.environment="append"
environment = { MACOSX_DEPLOYMENT_TARGET="10.15" } # target 10.15/Catalina
inherit.before-all="append"
# install the Catalina version of `gsl` to match
before-all = ["brew install --quiet ./gsl--2.7.1.catalina.bottle.tar.gz"]

[[tool.cibuildwheel.overrides]]
select = "*-macosx_arm64"
inherit.environment="append"
environment = { MACOSX_DEPLOYMENT_TARGET="11.0" } # target for 11.0/Big Sur
inherit.before-all="append"
# install the Big Sur version of `gsl` to match
before-all = ["brew install --quiet ./gsl--2.7.1.arm64_big_sur.bottle.tar.gz"]

[tool.cibuildwheel.windows]
archs = ["auto", "ARM64"]

[[tool.cibuildwheel.overrides]]
# overrides for X86
select ="*-win_amd64*"
# use nuget to install gsl on Windows, and manually supply paths
before-all = "nuget install gsl-msvc14-x64 -Version 2.3.0.2779"
inherit.environment="append"
environment = { CPATH="gsl-msvc14-x64.2.3.0.2779\\\\build\\\\native", LIBRARY_PATH="gsl-msvc14-x64.2.3.0.2779\\\\build\\\\native\\\\static" }

[[tool.cibuildwheel.overrides]]
# overrides for ARM64
select ="*-win_arm64*"
before-all = 'nuget install gsl-msvc14-arm64 -Source "%CD%\\vendor-binaries"'
# use local nuget package to install gsl on Windows ARM64, and manually supply paths
inherit.environment = "append"
environment = { CPATH="gsl-msvc14-arm64.2.3.0.2779\\\\build\\\\native\\\\include", LIBRARY_PATH="gsl-msvc14-arm64.2.3.0.2779\\\\build\\\\native\\\\lib" }

[tool.ruff]
target-version = "py37"

[tool.ruff.lint]
extend-select = [
  "ARG",      # flake8-unused-arguments
  "B",        # flake8-bugbear
  "C4",       # flake8-comprehensions
  # "C90",    # mccabe complexity
  "D",        # all pydocstyle/PEP 257 checks
  "DTZ",      # good datetime practices
  "EM",       # flake8-errmsg
  # "ERA",    # erdicate useless code
  "EXE",      # flake8-executable
  "FA",       # flake8-future-annotations
  "FURB",     # refurb
  "G",        # flake8-logging-format
  "I",        # isort
  "ICN",      # flake8-import-conventions
  "LOG",      # logger
  "N",        # pep8 naming
  "NPY",      # NumPy specific rules
  "PD",       # pandas-vet
  "PGH",      # pygrep-hooks
  "PIE",      # flake8-pie
  "PL",       # pylint
  "PT",       # flake8-pytest-style
  "PTH",      # flake8-use-pathlib
  "PYI",      # flake8-pyi
  #  "Q",     # flake8-quotes
  "RET",      # flake8-return
  "RUF",      # Ruff-specific
  #  "S",     # flake8-bandit (security testing)
  "SIM",      # flake8-simplify
  "T20",      # flake8-print
  #  "TD",    # flake8-todos
  "TID",      # tidy imports
  "TRY",      # try.ceratptops exception handling
  "UP",       # pyupgrade
  "YTT",      # flake8-2020
]
ignore = [
  "T201",     # allow `print()`
  "PTH107",   # allow .`os.remove` until `Path.unlink` works on later Pythons
  "PTH123",   # allow `open()`
  "ISC001",   # Conflicts with formatter
  "PLR09",    # Too many <...>
  "PLR2004",  # Magic value used in comparison
  "D107",  # Skip "missing docstring in __init__" if you merge class+init docstrings
  "D102",  # missing docstring in method -- FIXME disable currently
  "N802",  # we don't currently require functions to be lowercase
  "N803",  # we don't currently require methods to be lowercase
  "N806",  # we don't currently require methods to be lowercase
  "N815",  # mixed case OK in class scope
  "N816",  # mixed case OK in global scope
  "S101",  # allow assert
]

typing-modules = ["mypackage._compat.typing"]
# this won't work for Python 3.6, disable
#isort.required-imports = ["from __future__ import annotations"]

[tool.ruff.lint.pydocstyle]
convention = "google"  # also "numpy" or "pep257"

[tool.ruff.lint.per-file-ignores]
"tests/**" = ["T20", "D100", "D103"]  # don't need docs on every unit test function

[tool.codespell]
skip = '*tests/data/*,.data/*,src/obsolete/*,src/slatkin-exact/README,src/pval/*,src/PyPop/xslt/xsl.dtd,src/haplo-stats/haplo_em_pin.c,website/requirements-docs.txt'
count = true
quiet-level = 3
ignore-words-list = 'nd,Fallin,commmon'

[tool.mdformat]
number = true
#exclude = [
#	"NEWS.md",
#	"website/**"
#	]

[tool.repo-review.ignore]
PY004 = "docs in website not `docs` folder"
PC111 = "doesn't use blacken directly (uses ruff)"
PC140 = "doesn't use typechecker"
MY = "no typechecker"
RTD = "doesn't use read the docs"

[tool.pydoclint]
style = "google"                        # Google style
# require-return = true                 # Require documenting returns
check-param-types = true              # Ensure param types are provided
check-return-types = false              # Disable return type checking
arg-type-hints-in-signature = false     # We don't use type hints in signature
should-document-star-arguments = false  # don't require document **kwargs
allow-init-docstring = true             # allow docstrin in init.py