pyproject.toml

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

[project]
name = "flowsom"
version = "0.0.1"
description = "The complete FlowSOM package known from R, now available in Python!"
readme = "README.md"
requires-python = ">=3.9"
license = { file = "LICENSE" }
authors = [
    { name = "Artuur Couckuyt", email = "Artuur.Couckuyt@ugent.be" },
    { name = "Benjamin Rombaut", email = "Benjamin.Rombaut@ugent.be" },
    { name = "Yvan Saeys", email = "Yvan.Saeys@UGent.be" },
    { name = "Sofie Van Gassen", email = "Sofie.VanGassen@UGent.be" },
]
maintainers = [
    { name = "Artuur Couckuyt", email = "Artuur.Couckuyt@ugent.be" },
    { name = "Benjamin Rombaut", email = "Benjamin.Rombaut@ugent.be" },
    { name = "Yvan Saeys", email = "Yvan.Saeys@UGent.be" },
    { name = "Sofie Van Gassen", email = "Sofie.VanGassen@UGent.be" },
]
urls.Documentation = "https://flowsom.readthedocs.io/en/latest/"
urls.Source = "https://github.com/saeyslab/FlowSOM_Python"
urls.Home-page = "https://github.com/saeyslab/FlowSOM_Python"
dependencies = [
    "mudata<=0.2.4",
    "numpy",
    "matplotlib",
    "pandas",
    "scipy",
    "readfcs",
    "scikit-learn",
    "igraph",
    "session-info",
    "numba",
    "scanpy",
    "seaborn",
    "anndata<=0.10.8",
    "loguru",
]


[project.optional-dependencies]
dev = ["pre-commit", "twine>=4.0.2"]
doc = [
    "docutils>=0.8,!=0.18.*,!=0.19.*",
    "sphinx>=4",
    "sphinx-book-theme>=1.0.0",
    "myst-nb",
    "sphinxcontrib-bibtex>=1.0.0",
    "sphinx-autodoc-typehints",
    "sphinxext-opengraph",
    # For notebooks
    "ipykernel",
    "ipython",
    "sphinx-copybutton",
    # For example notebooks
    "pytometry>=0.1.5",
]
test = ["pytest", "coverage"]

[tool.hatch.build.targets.wheel]
packages = ['src/flowsom']

[tool.coverage.run]
source = ["flowsom"]
omit = ["**/test_*.py"]

[tool.pytest.ini_options]
testpaths = ["tests"]
xfail_strict = true
addopts = [
    "--import-mode=importlib", # allow using test files with same name
]

[tool.fawltydeps]
code = ["src"]                  # Only search for imports under ./src
deps = ["pyproject.toml"]       # Only look for declared dependencies here
ignore_undeclared = ["flowsom"]

[tool.ruff]
line-length = 120
src = ["src"]
extend-include = ["*.ipynb"]

[tool.ruff.format]
docstring-code-format = true

[tool.ruff.lint]
select = [
    "F",      # Errors detected by Pyflakes
    "E",      # Error detected by Pycodestyle
    "W",      # Warning detected by Pycodestyle
    "I",      # isort
    "D",      # pydocstyle
    "B",      # flake8-bugbear
    "TID",    # flake8-tidy-imports
    "C4",     # flake8-comprehensions
    "BLE",    # flake8-blind-except
    "UP",     # pyupgrade
    "RUF100", # Report unused noqa directives
]
ignore = [
    # line too long -> we accept long comment lines; formatter gets rid of long code lines
    "E501",
    # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
    "E731",
    # allow I, O, l as variable names -> I is the identity matrix
    "E741",
    # Missing docstring in public package
    "D104",
    # Missing docstring in public module
    "D100",
    # Missing docstring in __init__
    "D107",
    # Errors from function calls in argument defaults. These are fine when the result is immutable.
    "B008",
    # __magic__ methods are are often self-explanatory, allow missing docstrings
    "D105",
    # first line should end with a period [Bug: doesn't work with single-line docstrings]    "D400",
    # First line should be in imperative mood; try rephrasing
    "D401",
    ## Disable one in each pair of mutually incompatible rules
    # We don’t want a blank line before a class docstring
    "D203",
    # We want docstrings to start immediately after the opening triple quote
    "D213",
]

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

[tool.ruff.lint.per-file-ignores]
"docs/*" = ["I"]
"tests/*" = ["D"]
"*/__init__.py" = ["F401"]

[tool.cruft]
skip = [
    "tests",
    "src/**/__init__.py",
    "src/**/basic.py",
    "docs/api.md",
    "docs/changelog.md",
    "docs/references.bib",
    "docs/references.md",
    "docs/notebooks/example.ipynb",
]