pyproject.toml

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name='clinvarbitration'
description='CPG ClinVar Re-interpretation'
readme = "README.md"
version="2.2.11"
requires-python = ">=3.10,<3.12"
license={ "file" = "LICENSE" }
classifiers=[
    'Environment :: Console',
    'Intended Audience :: Science/Research',
    'License :: OSI Approved :: MIT License',
    'Natural Language :: English',
    'Operating System :: MacOS :: MacOS X',
    'Operating System :: POSIX',
    'Operating System :: Unix',
    'Programming Language :: Python',
    'Topic :: Scientific/Engineering',
    'Topic :: Scientific/Engineering :: Bio-Informatics',
]

dependencies=[
    'cpg-flow~=1.3',
    'pyspark==3.5.3',
    'requests'
]

[project.urls]
Repository = "https://github.com/populationgenomics/ClinvArbitration"

[project.optional-dependencies]
test = [
    'bump-my-version',
    'pre-commit',
    'pytest',
    'pytest-xdist>=3.6.0',
]
cpg = [
    'google-cloud-secret-manager',  # used to pull secrets for the zenodo publish workflow
]

[project.scripts]
# sets off the whole workflow in cpg-flow orchestrated Stages
run_workflow = 'clinvarbitration.run_workflow:cli_main'
run_nextflow = 'clinvarbitration.stages.nextflow_stages:cli_main'

[tool.hatch.build.targets.wheel]
packages = ["src/clinvarbitration"]
exclude = [
  "data/*.gz",
]

[tool.hatch.build.targets.sdist]
exclude = [
  "/data/*.gz",
]

[tool.hatch.build.targets.wheel.sources]
"src" = ""

[options]
include_package_data = true

[options.package_data]
'clinvarbitration'=  ['config_template.toml']

[tool.mypy]
ignore_missing_imports = true

[tool.pytest.ini_options]
testpaths = ['test']

[tool.ruff]
line-length = 120
extend-exclude = ["venv", ".mypy_cache", ".venv", "build", "dist"]

[tool.ruff.format]
indent-style = 'space'
quote-style = "single"

[tool.ruff.lint]
select = ["A", "B", "C", "E", "E501", "F", "G", "I", "N", "Q", "S", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "ERA", "EXE", "ICN", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "UP", "YTT"]

fixable = ["A", "B", "C", "D", "E", "E501", "F", "G", "I", "N", "Q", "S", "T", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "ERA", "EXE", "FBT", "ICN", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "UP", "YTT"]

ignore = [
    "ANN201", # Missing return type annotation for public function
    "ANN204", # Missing type annotation for special method `__init__`
    "Q000", # Single quotes found but double quotes preferred
    "PLR0912", # Too many branches (> 12)
    "PLR0913", # Too many arguments in function (> 5)
    "COM819",  # Trailing comma prohibited
    "C901", # method is too complex (> 10 conditions)
]

[tool.ruff.lint.isort]
section-order = ["future", "standard-library", "third-party", "hail", "cpg", "first-party", "local-folder"]

[tool.ruff.lint.isort.sections]
cpg = ["cpg_flow", "cpg_utils"]
hail = ["hail", "hailtop"]

[tool.ruff.lint.per-file-ignores]
# suppress the ARG002 "Unused method argument" warning in the stages.py file
## - we don't need any generic cpg-flow arguments, but need to fit the required method signature
"src/clinvarbitration/stages.py" = ["ARG002"]
"src/clinvarbitration/nextflow_stages.py" = ["ARG002"]
"test/**" = ["S101"]

[tool.bumpversion]
current_version = "2.2.11"
parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
serialize = ["{major}.{minor}.{patch}"]
commit = true
message = "Bump version: {current_version} → {new_version}"
commit_args = ""

[[tool.bumpversion.files]]
filename = "pyproject.toml"
search = "version=\"{current_version}\""
replace = "version=\"{new_version}\""

[[tool.bumpversion.files]]
filename = "src/clinvarbitration/__init__.py"
search = "{current_version}"
replace = "{new_version}"

[[tool.bumpversion.files]]
filename = "Dockerfile"
search = "{current_version}"
replace = "{new_version}"

[[tool.bumpversion.files]]
filename = "src/clinvarbitration/cpg_internal/Dockerfile"
search = "{current_version}"
replace = "{new_version}"