pyproject.toml

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

[tool.poetry]
name = "simicpipeline"
version = "0.1.0"
description = "simicpipeline is the user-friendly package to run SimiC a single-cell gene regulatory inference framework that overcomes this limitation by jointly inferring distinct, but related, gene regulatory dynamics per phenotype."
authors = ["Irene Marín-Goñi <imarin.4@alumni.unav.es>"]
license = "LICENSE"
readme = "README.md"
homepage = "https://github.com/irenemaring/SimiCPipeline"
repository = "https://github.com/irenemaring/SimiCPipeline"
packages = [{include = "simicpipeline", from = "src"}]

[tool.poetry.scripts]
jupyter-simic = "simicpipeline._jupyter:jupyter"

[tool.poetry.dependencies]
python = "^3.10"
numpy = "^1.24.0"
pandas = "^2.0.3"
scikit-learn = "^1.7.2"
scipy = "^1.15"
scprep = "1.2.3"
anndata = "^0.11.4"
magic-impute = "3.0.0"
matplotlib = "^3.7.0"
seaborn = "^0.13.0"
scanpy = "^1.11.5"

[tool.poetry.group.dev.dependencies]
pytest = "^7.4.0"
pytest-cov = "^4.1.0"
ruff = "^0.8.0"
mypy = "^1.5.0"
ipython = "^8.12.0"
jupyter = "^1.0.0"

[tool.poetry.group.docs]
optional = true

[tool.poetry.group.docs.dependencies]
sphinx = "^7.0.0"
sphinx-rtd-theme = "^1.3.0"

# Ruff configuration
[tool.ruff]
# Same as Black.
line-length = 88
indent-width = 4

# Assume Python 3.10
target-version = "py310"

# Exclude common directories
exclude = [
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".git-rewrite",
    ".hg",
    ".ipynb_checkpoints",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".pyenv",
    ".pytest_cache",
    ".pytype",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    ".vscode",
    "__pypackages__",
    "_build",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "site-packages",
    "venv",
]

[tool.ruff.lint]
# Enable pycodestyle (`E`) and Pyflakes (`F`) codes by default.
# Add additional rules: isort (I), pydocstyle (D), pyupgrade (UP), etc.
select = [
    "E",     # pycodestyle errors
    "W",     # pycodestyle warnings
    "F",     # Pyflakes
    "I",     # isort
    "N",     # pep8-naming
    "UP",    # pyupgrade
    "B",     # flake8-bugbear
    "C4",    # flake8-comprehensions
    "SIM",   # flake8-simplify
    "TCH",   # flake8-type-checking
]

# Allow fix for all enabled rules (when `--fix` is provided).
fixable = ["ALL"]
unfixable = []

# Allow unused variables when underscore-prefixed.
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"

ignore = [
    "E501",  # Line too long (handled by formatter)
    "D100",  # Missing docstring in public module
    "D101",  # Missing docstring in public class
    "D102",  # Missing docstring in public method
    "D103",  # Missing docstring in public function
    "D104",  # Missing docstring in public package
]

[tool.ruff.format]
# Use double quotes for strings.
quote-style = "double"

# Indent with spaces, rather than tabs.
indent-style = "space"

# Respect magic trailing commas.
skip-magic-trailing-comma = false

# Automatically detect the appropriate line ending.
line-ending = "auto"

[tool.ruff.lint.isort]
known-first-party = ["simicpipeline"]

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

# Mypy configuration
[tool.mypy]
python_version = "3.10"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = false
disallow_incomplete_defs = false
check_untyped_defs = true
no_implicit_optional = true
warn_redundant_casts = true
warn_unused_ignores = true
warn_no_return = true
strict_equality = true

[[tool.mypy.overrides]]
module = [
    "magic.*",
    "scprep.*",
    "anndata.*",
]
ignore_missing_imports = true

# Pytest configuration
[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py", "*_test.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = [
    "--verbose",
    "--cov=simicpipeline",
    "--cov-report=term-missing",
    "--cov-report=html",
]

# Coverage configuration
[tool.coverage.run]
source = ["src/simicpipeline"]
omit = [
    "*/tests/*",
    "*/test_*.py",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "raise AssertionError",
    "raise NotImplementedError",
    "if __name__ == .__main__.:",
    "if TYPE_CHECKING:",
    "@abstractmethod",
]