pyproject.toml

[tool.poetry]
name = "gentropy"
# !! version is managed by semantic_release
version = "0.0.0"
description = "Open Targets python framework for post-GWAS analysis"
authors = ["Open Targets core team"]
license = "Apache-2.0"
readme = "README.md"
documentation = "https://opentargets.github.io/gentropy/"
repository = "https://github.com/opentargets/gentropy"
packages = [{ include = "gentropy", from = "src" }]

[tool.poetry.urls]
"Bug Tracker" = "http://github.com/opentargets/issues"
"Funding" = "https://www.opentargets.org"
"Documentation" = "https://opentargets.github.io/gentropy/"

[tool.poetry.scripts]
gentropy = "gentropy.cli:main"

[tool.poetry.dependencies]
python = "^3.10, <3.11"
pyspark = "3.3.4"
scipy = "^1.11.4"
hydra-core = "^1.3.2"
pyliftover = "^0.4"
numpy = "^1.26.2"
hail = "0.2.127"
wandb = ">=0.16.2,<0.19.0"
google = "^3.0.0"
omegaconf = "^2.3.0"
typing-extensions = "^4.9.0"
scikit-learn = "^1.3.2"
pandas = { extras = ["gcp", "parquet"], version = "^2.2.2" }
skops = ">=0.9,<0.11"
google-cloud-secret-manager = "^2.20.0"
shap = "^0.46.0"
matplotlib = "3.7.3"

[tool.poetry.dev-dependencies]
pre-commit = "^4.0.0"
mypy = "^1.13"
pep8-naming = "^0.14.1"
interrogate = "^1.7.0"
isort = "^5.13.2"
darglint = "^1.8.1"
ruff = "^0.7.0"

[tool.poetry.group.docs.dependencies]
mkdocs = "^1.5.3"
mkdocstrings-python = "^1.8.0"
mkdocs-material = "*"
mkdocs-section-index = "^0.3.4"
mkdocs-git-revision-date-localized-plugin = "^1.2.2"
mkdocs-autolinks-plugin = "^0.7.1"
mkdocs-awesome-pages-plugin = "^2.9.2"
mkdocs-exclude = "^1.0.2"
mkdocs-git-committers-plugin-2 = "^2.2.3"
lxml = "^5.1.0"
pymdown-extensions = "^10.7"


[tool.poetry.group.tests.dependencies]
pytest-cov = ">=4.1,<6.0"
pytest-sugar = ">=0.9.5,<1.1.0"
dbldatagen = ">=0.3.1,<0.5.0"
pyparsing = "^3.1.1"
pytest = ">=7.4.4,<9.0.0"
pytest-xdist = "^3.5.0"


[tool.poetry.group.dev.dependencies]
ipython = "^8.19.0"
ipykernel = "^6.28.0"
google-cloud-dataproc = "^5.8.0"
pydoclint = ">=0.3.8,<0.6.0"
prettier = "^0.0.7"
deptry = ">=0.12,<0.21"
yamllint = "^1.33.0"

[tool.semantic_release]
logging_use_named_masks = true
build_command = "pip install poetry && poetry build"
assets = []
version_toml = ["pyproject.toml:tool.poetry.version"]
upload_to_pypi = false
upload_to_release = true

[tool.semantic_release.branches.main]
match = "(main|master)"
prerelease = false

[tool.semantic_release.branches."release"]
match = "release/*"
prerelease = true
prerelease_token = "rc"

[tool.semantic_release.publish]
dist_glob_patterns = ["dist/*"]
upload_to_vcs_release = true

[tool.semantic_release.changelog]
changelog_file = "CHANGELOG.md"
exclude_commit_patterns = ["chore\\(release\\):"]

[tool.semantic_release.branches."step"]
match = "(build|chore|ci|docs|feat|fix|perf|style|refactor|test)"
prerelease = true
prerelease_token = "alpha"

[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"

[tool.deptry]
extend_exclude = ["src/conftest.py", "src/utils"]

[tool.deptry.per_rule_ignores]
DEP001 = ["gentropy"]
DEP003 = ["gentropy"]

[tool.interrogate]
fail-under = 95
color = true
exclude = ["dist"]

[tool.pytest.ini_options]
addopts = "-n auto --doctest-modules --cov=src/ --cov-report=xml"
pythonpath = ["."]
testpaths = ["tests/gentropy", "src/gentropy"]
markers = ["step_test"]

# Semi-strict mode for mypy
[tool.mypy]
check_untyped_defs = true
disallow_any_generics = true
disallow_incomplete_defs = true
no_implicit_optional = true
no_implicit_reexport = true
strict_equality = true
warn_redundant_casts = true
warn_unused_ignores = true
disallow_untyped_defs = true

[[tool.mypy.overrides]]
module = [
  "google.cloud",
  "yaml",
  "hail",
  "pyliftover",
  "dbldatagen",
  "scipy",
  "scipy.stats",
  "chardet",
  "omegaconf",
  "xgboost",
  "sklearn",
]
ignore_missing_imports = true


[tool.ruff.lint]
select = [
  "B002",    # Python does not support the unary prefix increment
  "B007",    # Loop control variable {name} not used within loop body
  "B014",    # Exception handler with duplicate exception
  "B023",    # Function definition does not bind loop variable {name}
  "B026",    # Star-arg unpacking after a keyword argument is strongly discouraged
  "B904",    # Checks for raise statements in exception handlers that lack a from clause
  "C",       # complexity
  "COM818",  # Trailing comma on bare tuple prohibited
  "D",       # docstrings
  "DTZ003",  # Use datetime.now(tz=) instead of datetime.utcnow()
  "DTZ004",  # Use datetime.fromtimestamp(ts, tz=) instead of datetime.utcfromtimestamp(ts)
  "E",       # pycodestyle
  "F",       # pyflakes/autoflake
  "G",       # flake8-logging-format
  "I",       # isort
  "ICN001",  # import concentions; {name} should be imported as {asname}
  "ISC001",  # Implicitly concatenated string literals on one line
  "N804",    # First argument of a class method should be named cls
  "N805",    # First argument of a method should be named self
  "N815",    # Variable {name} in class scope should not be mixedCase
  "PGH004",  # Use specific rule codes when using noqa
  "PLC0414", # Useless import alias. Import alias does not rename original package.
  "PLC",     # pylint
  "PLE",     # pylint
  "PLR",     # pylint
  "PLW",     # pylint
  "Q000",    # Double quotes found but single quotes preferred
  "RUF006",  # Store a reference to the return value of asyncio.create_task
  "S102",    # Use of exec detected
  "S103",    # bad-file-permissions
  "S108",    # hardcoded-temp-file
  "S306",    # suspicious-mktemp-usage
  "S307",    # suspicious-eval-usage
  "S313",    # suspicious-xmlc-element-tree-usage
  "S314",    # suspicious-xml-element-tree-usage
  "S315",    # suspicious-xml-expat-reader-usage
  "S316",    # suspicious-xml-expat-builder-usage
  "S317",    # suspicious-xml-sax-usage
  "S318",    # suspicious-xml-mini-dom-usage
  "S319",    # suspicious-xml-pull-dom-usage
  "S320",    # suspicious-xmle-tree-usage
  "S601",    # paramiko-call
  "S602",    # subprocess-popen-with-shell-equals-true
  "S604",    # call-with-shell-equals-true
  "S608",    # hardcoded-sql-expression
  "S609",    # unix-command-wildcard-injection
  "SIM105",  # Use contextlib.suppress({exception}) instead of try-except-pass
  "SIM117",  # Merge with-statements that use the same scope
  "SIM118",  # Use {key} in {dict} instead of {key} in {dict}.keys()
  "SIM201",  # Use {left} != {right} instead of not {left} == {right}
  "SIM208",  # Use {expr} instead of not (not {expr})
  "SIM212",  # Use {a} if {a} else {b} instead of {b} if not {a} else {a}
  "SIM300",  # Yoda conditions. Use 'age == 42' instead of '42 == age'.
  "SIM401",  # Use get from dict with default instead of an if block
  "T100",    # Trace found: {name} used
  "T20",     # flake8-print
  "TID251",  # Banned imports
  "TRY004",  # Prefer TypeError exception for invalid type
  "TRY302",  # Remove exception handler; error is immediately re-raised
  "UP",      # pyupgrade
  "W",       # pycodestyle
]

ignore = [
  "E501", # line too long
  "E731", # do not assign a lambda expression, use a def

  # Ignore ignored, as the rule is now back in preview/nursery, which cannot
  # be ignored anymore without warnings.
  # https://github.com/astral-sh/ruff/issues/7491
  # "PLC1901", # Lots of false positives

  # False positives https://github.com/astral-sh/ruff/issues/5386
  "PLC0208", # Use a sequence type instead of a `set` when iterating over values
  "PLR0911", # Too many return statements ({returns} > {max_returns})
  "PLR0912", # Too many branches ({branches} > {max_branches})
  "PLR0913", # Too many arguments to function call ({c_args} > {max_args})
  "PLR0915", # Too many statements ({statements} > {max_statements})
  "PLR2004", # Magic value used in comparison, consider replacing {value} with a constant variable
  "PLW2901", # Outer {outer_kind} variable {name} overwritten by inner {inner_kind} target
  "UP006",   # keep type annotation style as is
  "UP007",   # keep type annotation style as is
  # Ignored due to performance: https://github.com/charliermarsh/ruff/issues/2923
  "UP038", # Use `X | Y` in `isinstance` call instead of `(X, Y)`

]

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["E402"]
"path/to/file.py" = ["E402"]
"**/{tests,docs,tools}/*" = ["E402"]

[tool.ruff.lint.flake8-quotes]
docstring-quotes = "double"

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

[tool.pydoclint]
style = 'google'
exclude = '\.git|\.venv|__init__.py|tests|docs'
require-return-section-when-returning-nothing = false
check-return-types = true
allow-init-docstring = true
arg-type-hints-in-docstring = true
skip-checking-short-docstrings = false
check-class-attributes = false