pyproject.toml

[build-system]
# CI installs setuptools-scm with the same bound to compute the version of
# images (`.github/workflows/ci.yml`)
requires = ["setuptools>=77", "setuptools-scm>=8"]
build-backend = "setuptools.build_meta"

[tool.ruff]
line-length = 88
target-version = "py313"

[tool.ruff.lint]
# The rule set shared by FOCA and FOCA apps: FOCA's rules plus `G` and `S`;
# unlike in FOCA, `D` applies everywhere, also to the tests and docs hooks
select = [
    "B",    # flake8-bugbear
    "C4",   # flake8-comprehensions
    "D",    # pydocstyle (docstrings)
    "E",    # pycodestyle errors
    "F",    # Pyflakes
    "G",    # flake8-logging-format
    "I",    # isort
    "PL",   # Pylint
    "RUF",  # Ruff-specific rules
    "S",    # flake8-bandit (security)
    "SIM",  # flake8-simplify
    "UP",   # pyupgrade
    "W",    # pycodestyle warnings
]
ignore = [
    # Complexity limits, as in FOCA: some functions mirror the API's
    # operations or take many test fixtures, and splitting them would obscure
    # them
    "PLR0912",  # too-many-branches
    "PLR0913",  # too-many-arguments
    "PLR0915",  # too-many-statements
    "PLR0917",  # too-many-positional-arguments
    # Flags HTTP status codes and other literals (e.g., lengths), which are
    # clear as is
    "PLR2004",  # magic-value-comparison
]

[tool.ruff.lint.isort]
force-sort-within-sections = true
known-first-party = ["pro_tes", "tests"]

[tool.ruff.lint.per-file-ignores]
# pytest checks with `assert`
"tests/**" = ["S101"]

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

[tool.mypy]
files = ["pro_tes", "docs/hooks.py", "scripts", "tests"]
python_version = "3.13"
# Complete type hints: all functions annotated, generic types parametrized
# (instead of ruff's `ANN` rules, which report missing hints only, without
# checking them)
disallow_untyped_defs = true
disallow_any_generics = true
warn_unused_ignores = true

# Connexion 2 ships no type information
[[tool.mypy.overrides]]
module = ["connexion", "connexion.*"]
ignore_missing_imports = true

# geopy ships no type information (distance-based middleware)
[[tool.mypy.overrides]]
module = ["geopy", "geopy.*"]
ignore_missing_imports = true

# py-tes ships no type information
[[tool.mypy.overrides]]
module = ["tes", "tes.*"]
ignore_missing_imports = true

# Gunicorn ships no type information (used by the tests only)
[[tool.mypy.overrides]]
module = ["gunicorn", "gunicorn.*"]
ignore_missing_imports = true

[tool.coverage.run]
source = ["pro_tes", "scripts"]

[tool.coverage.report]
exclude_also = ['if __name__ == "__main__":']
# `coverage report` and `coverage xml` (CI) fail below 100%; Codecov's
# targets are the same (`codecov.yml`)
fail_under = 100

[project]
name = "pro-tes"
authors = [
    {name = "ELIXIR On-Cloud", email = "cloud-service@elixir-europe.org"},
    {name = "Alexander Kanitz"},
]
keywords = [
    "ga4gh", "tes", "proxy", "gateway", "elixir", "cloud", "rest", "restful",
    "api", "app", "server", "openapi", "swagger", "mongodb", "python", "flask"
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Natural Language :: English",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.13",
]
# The Python version of the base image in the `Dockerfile`, the only one the
# app is tested with
requires-python = ">=3.13"
description = "Proxy for GA4GH Task Execution Service (TES) instances by ELIXIR On-Cloud"
license = "Apache-2.0"
dynamic = ["version"]
dependencies = [
    "connexion>=2.15.1,<3.0.0",
    # FOCA minors are bumped by hand, together with the base image in the
    # `Dockerfile` (`.github/dependabot.yml`).
    "foca>=0.17.0,<0.18",
    "geopy>=2.2.0,<3",
    "gunicorn>=26.2.0,<27",
    "py-tes>=1.1,<2",
    # Used directly (TES backends, geolocation services); 2.33.0 fixes
    # CVE-2026-25645
    "requests>=2.33.0,<3",
    # Used directly (errors that show whether requests to TES backends were
    # sent)
    "urllib3>=2,<3",
]

[project.optional-dependencies]
# Local hooks of `.pre-commit-config.yaml` use these too
dev = [
    "ast-grep-cli>=0.51",
    "build>=1.6",
    "celery-types>=0.20.0",
    "coverage>=7.16",
    "mongomock>=4.3",
    "mypy>=2.4",
    "packaging>=26.3",
    "pre-commit>=4.6",
    "pytest>=9.1",
    # Used by the tests; builds use `build-system.requires`
    "setuptools-scm>=10.3",
    "types-PyYAML>=6.0.12",
    "types-requests>=2.28.5",
]
# Documentation (`mkdocs.yml`), built by Read the Docs (`.readthedocs.yaml`)
# and in CI. The packages that add warnings, which fail the strict build, are
# listed too, to bound their major versions (new warnings of minor releases
# still fail it)
docs = [
    "griffelib>=2.4,<3",
    "mkdocs>=1.6.1,<2",
    "mkdocs-autorefs>=1.4.4,<2",
    "mkdocs-material>=9.7.7,<10",
    # 1.0.6 and earlier fail with pymdown-extensions 12
    "mkdocstrings>=1.0.8,<2",
    "mkdocstrings-python>=2.0.10,<3",
    "pymdown-extensions>=12.3,<13",
]

[project.readme]
file = "README.md"
content-type = "text/markdown"

[project.urls]
homepage = "https://github.com/elixir-cloud-aai/proTES"
Tracker = "https://github.com/elixir-cloud-aai/proTES/issues"
Documentation = "https://protes.readthedocs.io"

[tool.setuptools_scm]
# Version from Git tags (`vX.Y.Z`), the only place it is stored; builds
# without Git metadata (e.g., Docker builds, which get no `.git`) report the
# fallback unless `SETUPTOOLS_SCM_PRETEND_VERSION` is set
fallback_version = "0.0.0.dev0"

[tool.setuptools.packages.find]
include = ["pro_tes*"]

[tool.setuptools.package-data]
pro_tes = ["config.yaml", "api/*.yaml", "access_control/*.conf"]