pyproject.toml

[project]
name = "pybwa"
version = "2.3.0"
description = "Python bindings for BWA"
readme = "README.md"
authors = [{name = "Nils Homer", email = "nils@fulcrumgenomics.com"}]
license = "MIT"
homepage = "https://github.com/fulcrumgenomics/pybwa"
repository = "https://github.com/fulcrumgenomics/pybwa"
keywords = ["bioinformatics"]
packages = [{ include = "pybwa" }]
classifiers = [
	"Development Status :: 3 - Alpha",
	"Environment :: Console",
	"Intended Audience :: Developers",
	"Intended Audience :: Science/Research",
	"License :: OSI Approved :: MIT License",
	"Operating System :: OS Independent",
	"Programming Language :: Python :: 3",
	"Topic :: Scientific/Engineering :: Bio-Informatics",
	"Topic :: Software Development :: Documentation",
	"Topic :: Software Development :: Libraries :: Python Modules",
]
requires-python = ">=3.10.0,<4.0"
dependencies = [
	"fgpyo >=0.7.0",
	"pysam >=0.22.1",
	"typing_extensions >=3.7.4; python_version <'3.13'",
]

[tool.poetry]
include = [
    # pybwa
	{ path = "LICENSE", format = ["sdist", "wheel"] },
	{ path = "README.md", format = ["sdist", "wheel"] },
	{ path = "pybwa/libbwa*.so", format = "wheel" },
	{ path = "patches/*patch", format = ["sdist", "wheel"] },
	{ path = "tests", format = "sdist" },
	# bwa
	{ path = "bwa/*.h", format = ["sdist", "wheel"] },
	{ path = "bwa/*.c", format = ["sdist", "wheel"] },
	{ path = "bwa/Makefile", format = ["sdist", "wheel"] },
	{ path = "bwa/README.md", format = ["sdist", "wheel"] },
	# htslib
	{ path = "htslib/**/*.h", format = ["sdist", "wheel"] },
	{ path = "htslib/**/*.c", format = ["sdist", "wheel"] },
	{ path = "htslib/LICENSE", format = ["sdist", "wheel"] },
	{ path = "htslib/README", format = ["sdist", "wheel"] },
	{ path = "htslib/configure.ac", format = ["sdist", "wheel"] },
	{ path = "htslib/m4/*.m4", format = ["sdist", "wheel"] },
	{ path = "htslib/*.in", format = ["sdist", "wheel"] },
	{ path = "htslib/configure", format = ["sdist", "wheel"] },
	{ path = "htslib/config.guess", format = ["sdist", "wheel"] },
	{ path = "htslib/config.sub", format = ["sdist", "wheel"] },
	{ path = "htslib/version.sh", format = ["sdist", "wheel"] },
	{ path = "htslib/Makefile", format = ["sdist", "wheel"] },
	{ path = "htslib/*mk", format = ["sdist", "wheel"] },
]
exclude = [
	"pybwa/**/*.so",
	"**/*.so",
	"*.so",
	"htslib/*config*.h",
]
requires-poetry = ">=2.1"

[tool.poetry.build]
generate-setup-file = false
script = "build.py"

[tool.poetry.dependencies]

[tool.poetry.requires-plugins]
poethepoet = ">=0.29"

[tool.poetry.group.dev.dependencies]
# dependencies for linting, style checking, and unit testing
mypy = ">=1.13.0"
pytest = ">=8.3.3"
pytest-cov = ">=5.0.0"
ruff = ">=0.7.4"
setuptools = ">=68.0.0"
black = ">=24.8.0"  # for readthedocs
cython = ">=3.0.11"
coverage = {extras = ["toml"], version = ">=7.6.10"}
types-setuptools = "^78.1.0.20250329"

[tool.poetry.group.docs.dependencies]
# dependencies for building docs 
sphinx = { version = ">=7.0.0,<9"}
enum-tools = ">=0.12.0"
sphinx-toolbox = ">=3.8.1"
sphinx-jinja2-compat = ">=0.3.0"
sphinx-rtd-theme = ">=3.0.2"
sphinx-autodoc-typehints = "2"

[build-system]
requires = ["poetry-core>=2.1.1", "cython>=3.0.11", "setuptools>=75.1.0", "pysam >=0.22.1"]
build-backend = "poetry.core.masonry.api"

[tool.poe]
poetry_command = "task"

[tool.poe.tasks]
fix-format = "ruff format pybwa tests build.py"
fix-lint   = "ruff check --fix pybwa tests build.py"

fix-all.ignore_fail = "return_non_zero"
fix-all.sequence    = [
    "fix-format",
    "fix-lint"
]

check-lock   = "poetry check --lock"
check-format = "ruff format --check --diff pybwa tests build.py"
check-lint   = "ruff check pybwa tests build.py"
check-tests  = "pytest"
check-typing = "mypy build.py pybwa tests --config=pyproject.toml"

check-all.ignore_fail = "return_non_zero"
check-all.sequence    = [
    "check-lock",
    "check-format",
    "check-lint",
    "check-tests",
    "check-typing",
	"build-docs"
]

fix-and-check-all.ignore_fail = "return_non_zero"
fix-and-check-all.sequence    = [
    "fix-all",
    "check-all"
]

build-docs.cwd = "docs"
build-docs.cmd = "make html"

[tool.ruff]
line-length    = 100
target-version = "py310"
output-format  = "full"
preview        = true

[tool.ruff.lint]
select    = [
    "ARG",    # Unused arguments
    "C901",   # McCabe complexity
    "B",      # bugbear
    "D",      # pydocstyle (docstrings. We have the "google" convention enabled)
    "D204",   # Blank line between class docstring and first (__init__) method
    "D213",   # Summary line should be located on the line after opening quotes
    "E",      # pycodestyle errors
    "LOG",    # flake8-logging
    "LOG015", # (preview rule) Prohibit calls to the root logger
    "F",      # pyflakes
    "I",      # isort
    "N",      # PEP8 naming
    "W",      # pycodestyle warnings
    "Q",      # flake8-quotes
]
ignore    = [
    "E203",
    "E701",
    "D212",  # summary line should be located on the same line as opening quotes
    "D100",  # missing docstring in public module
    "D104",  # missing docstring in public package
]
unfixable = ["B"]
# NB: only preview rules explicitly selected above (e.g. LOG015) will be enforced
preview = true
explicit-preview-rules = true

[tool.ruff.lint.isort]
force-single-line = true

[tool.ruff.lint.pydocstyle]
convention = "google"

[tool.ruff.lint.per-file-ignores]
"tests/*" = ["D103"] # missing docstring in public function

[tool.mypy]
strict_optional             = true
strict_equality             = true
check_untyped_defs          = true
disallow_incomplete_defs    = true
disallow_untyped_calls      = true
disallow_untyped_decorators = true
disallow_untyped_defs       = true
no_implicit_optional        = true
warn_no_return              = true
warn_redundant_casts        = true
warn_return_any             = true
warn_unreachable            = true
warn_unused_configs         = true
warn_unused_ignores         = true
enable_error_code           = [
    "ignore-without-code",
    "possibly-undefined",
]
exclude                     = [
    "docs/",
    "site/",
]

[[tool.mypy.overrides]]
module = ["pyximport.*", "_test_libbwaindex", "Cython.Distutils.build_ext", "Cython.Build"]
ignore_missing_imports = true

[tool.coverage.run]
plugins = ["Cython.Coverage"]
branch = true

[tool.git-cliff.changelog]
header = ""
trim = true
body = """
{% for group, commits in commits | group_by(attribute="group") %}
    ## {{ group | upper_first }}
    {% for commit in commits %}
        - {{ commit.message | upper_first }} ({{ commit.id | truncate(length=8, end="") }})\
    {% endfor %}
{% endfor %}\n
"""

[tool.git-cliff.git]
conventional_commits = true
commit_parsers = [
    { message = "^.+!:*", group = "Breaking"},
    { message = "^feat*", group = "Features"},
    { message = "^fix*", group = "Bug Fixes"},
    { message = "^docs*", group = "Documentation"},
    { message = "^perf*", group = "Performance"},
    { message = "^refactor*", group = "Refactor"},
    { message = "^style*", group = "Styling"},
    { message = "^test*", group = "Testing"},
    { message = "^chore\\(release\\):*", skip = true},
    { message = "^chore*", group = "Miscellaneous Tasks"},
    { body = ".*security", group = "Security"}
]
filter_commits = false