pyproject.toml

[build-system]
build-backend = "flit_core.buildapi"

requires = [ "flit-core>=3.4,<4" ]

[project]
name = "pyclustree"
version = "0.3.2"
description = "Visualize cluster assignments at different resolutions"
readme = "README.md"
license = { file = "LICENSE" }
maintainers = [
  { name = "Malte Hellmig", email = "harryhaller001@gmail.com" },
  { name = "Malte Kuehl", email = "malte.kuehl@clin.au.dk" },
]
authors = [ { name = "Malte Hellmig" }, { name = "Malte Kuehl" } ]
requires-python = ">=3.9"
classifiers = [
  "Development Status :: 3 - Alpha",
  "Intended Audience :: Healthcare Industry",
  "Intended Audience :: Science/Research",
  "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
  "Natural Language :: English",
  "Operating System :: OS Independent",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.9",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Typing :: Typed",
]
dependencies = [
  "anndata",
  "matplotlib",
  "networkx",
  "numpy",
  "pandas",
  "seaborn",
  # for debug logging (referenced from the issue template)
  "session-info",
]

optional-dependencies.dev = [
  "coverage",
  "docutils>=0.8,!=0.18.*,!=0.19.*",
  "flit",
  "furo",
  "ipykernel",
  "ipython",
  "myst-parser",
  "nbsphinx",
  "pandas",
  "pandoc",
  "pre-commit",
  "pytest",
  "python-igraph",
  "scanpy",
  # Until pybtex >0.23.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
  "setuptools",
  "sphinx>=4",
  "sphinx-autoapi",
  "sphinx-autodoc-typehints",
  "sphinx-book-theme>=1",
  "sphinx-copybutton",
  "sphinx-design",
  "sphinx-rtd-theme",
  "sphinx-tabs",
  "sphinxcontrib-bibtex>=1",
  "sphinxext-opengraph",
  "twine>=4.0.2",
]
# https://docs.pypi.org/project_metadata/#project-urls
urls.Documentation = "https://pyclustree.readthedocs.io/"
urls.Homepage = "https://github.com/complextissue/pyclustree"
urls.Source = "https://github.com/complextissue/pyclustree"

[tool.flit.sdist]
exclude = [ "docs/*", "test/*" ]

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

format.docstring-code-format = true

lint.select = [
  "B",      # flake8-bugbear
  "BLE",    # flake8-blind-except
  "C4",     # flake8-comprehensions
  "D",      # pydocstyle
  "E",      # Error detected by Pycodestyle
  "F",      # Errors detected by Pyflakes
  "I",      # isort
  "RUF100", # Report unused noqa directives
  "TID",    # flake8-tidy-imports
  "UP",     # pyupgrade
  "W",      # Warning detected by Pycodestyle
]
lint.ignore = [
  "B008", # Errors from function calls in argument defaults. These are fine when the result is immutable.
  "D100", # Missing docstring in public module
  "D104", # Missing docstring in public package
  "D105", # __magic__ methods are often self-explanatory, allow missing docstrings
  "D107", # Missing docstring in __init__
  # Disable one in each pair of mutually incompatible rules
  "D203", # We don’t want a blank line before a class docstring
  "D213", # <> We want docstrings to start immediately after the opening triple quote
  "D400", # first line should end with a period [Bug: doesn’t work with single-line docstrings]
  "D401", # First line should be in imperative mood; try rephrasing
  "E501", # line too long -> we accept long comment lines; formatter gets rid of long code lines
  "E731", # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
  "E741", # allow I, O, l as variable names -> I is the identity matrix
]
lint.per-file-ignores."*/__init__.py" = [ "F401" ]
lint.per-file-ignores."docs/*" = [ "I" ]
lint.per-file-ignores."tests/*" = [ "D" ]
lint.pydocstyle.convention = "google"

[tool.pytest.ini_options]
log_format = "%(asctime)s %(levelname)s %(message)s"
log_date_format = "%Y-%m-%d %H:%M:%S"
log_level = "WARN"
log_cli = "true"
testpaths = [ "tests" ]
xfail_strict = true
addopts = [
  "--import-mode=importlib", # allow using test files with same name
]

[tool.coverage.run]
source = [ "pyclustree" ]
omit = [ "*/test/*" ]

[tool.coverage.report]
exclude_lines = [
  "if __name__ == __main__:",
  "raise",
  "except",
  "warning",
  "def __repr__",
  "def __str__",
  "file_path = Path",
  "return None",
] # don't complain if non-runnable code isn't run:
ignore_errors = true

[tool.coverage.html]
directory = "docs/coverage_report"