pyproject.toml

[tool.poetry]
name = "bedspec"
version = "0.5.0"
description = "An HTS-specs compliant BED toolkit."
authors = ["Clint Valentine <valentine.clint@gmail.com>"]
license = "MIT"
readme = "README.md"
homepage = "https://github.com/clintval/bedspec"
repository = "https://github.com/clintval/bedspec"
keywords = ["bioinformatics", "BED", "NGS", "HTS", "interval"]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Environment :: Console",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Natural Language :: English",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: File Formats",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Software Development :: Documentation",
    "Topic :: Software Development :: Libraries :: Python Modules",
    "Typing :: Typed",
]
include = ["CONTRIBUTING.md", "LICENSE"]
packages = [{ include = "bedspec" }, { include = "cgranges" }]

[tool.poetry.dependencies]
python = "^3.10.0,<4.0.0"
typeline = "^0.6"
typing-extensions = "^4.12"

[tool.poetry.dev-dependencies]
basedpyright = "^1.21"
mypy = "^1.13"
pytest = "^8.3"
pytest-cov = "^5.0"
pytest-doctestplus = "^1.2"
ruff = "^0.7"

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

[build-system]
requires = ["poetry-core>=1.8", "setuptools>=70.1.1", "Cython>=3.0.10"]
build-backend = "poetry.core.masonry.api"

[tool.poe]
poetry_command = "task"

[tool.poe.tasks]
fix-format = "ruff format"
fix-lint   = "ruff check --fix"

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

check-lock   = "poetry check --lock"
check-format = "ruff format --check --diff"
check-lint   = "ruff check"
check-tests  = "pytest --doctest-glob='*.md'"

_check-mypy    = "mypy"
_check-pyright = "basedpyright"
check-typing.sequence = [
    "_check-mypy",
    "_check-pyright"
]

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

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

[tool.coverage.run]
omit = ["cgranges/*"]

[[tool.mypy.overrides]]
module = "Cython.Build"
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = "setuptools"
ignore_missing_imports = true

[tool.pytest.ini_options]
minversion = "7.4"
addopts    = [
    "--color=yes",
    "--cov-fail-under=80",
    "--cov-report=term-missing",
    "--cov",
    "--cov=typeline",
    "--doctest-modules",
    "--doctest-plus",
    "--import-mode=importlib",
    "--ignore=build.py",
    "--ignore=cgranges/",
]
doctest_plus = "enabled"
doctest_optionflags = [
    "ELLIPSIS",
    "IGNORE_EXCEPTION_DETAIL",
    "NORMALIZE_WHITESPACE",
]

[tool.mypy]
files                       = ["build.py", "bedspec/", "tests/"]
strict_optional             = false
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"

[tool.pyright]
include = ["bedspec/"]
reportAny = false
pythonVersion = "3.10"

[tool.ruff]
include        = ["build.py", "bedspec/**", "tests/**"]
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
    "D212",  # summary line should be located on the same line as opening quotes
    "E",     # pycodestyle errors
    "F",     # pyflakes
    "I",     # isort
    "N",     # PEP8 naming
    "W",     # pycodestyle warnings
    "Q"      # flake8-quotes
]
ignore    = [
    "E203",
    "E701",
    "D213",  # Summary line should be located on the line after opening quote
    "D100",  # missing docstring in public module
    "D104",  # missing docstring in public package
]
unfixable = ["B"]

[tool.ruff.lint.mccabe]
max-complexity = 13

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

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

[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 = "^security*", group = "Security"},
    { 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