pyproject.toml

[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"

[project]
name = "sekupy"
description = "Detergent for your dirty neuroimaging pipelines"
version = "0.0.1"
authors = [
    { name = "Roberto Guidotti", email = "roberto.guidotti@unich.it" },
]
license = {file = "LICENSE"}
readme = "README.md"
requires-python = ">=3.9"
keywords = [
    "neuroscience",
    "neuroimaging",
    "MEG",
    "EEG",
    "MVPA",
    "fMRI",
    "brain",
    "machine learning"
]
classifiers = [
    "Intended Audience :: Science/Research",
    "Intended Audience :: Developers",
    "License :: OSI Approved",
    "Programming Language :: Python",
    "Topic :: Software Development",
    "Topic :: Scientific/Engineering",
    "Operating System :: Microsoft :: Windows",
    "Operating System :: POSIX",
    "Operating System :: Unix",
    "Operating System :: MacOS",
    "Programming Language :: Python :: 3",
]

dependencies = [
    "numpy",
    "scipy",
    "matplotlib",
    "tqdm",
    "scikit-learn",
    "nibabel",
    "pandas",
    "seaborn",
    "imbalanced-learn",
    "mne",
    "lazy_loader",
    "statsmodels",
    "pybids",
    "nilearn",
    "pymatreader",
    "h5py"
]

[project.optional-dependencies]
# Variants with dependencies that will get installed on top of those listed unter
# project.dependencies

# Leave this one here for backward-compat
data = []

# Dependencies for running the test infrastructure
test = [
    "pytest>=8.0.0rc2",
    "pytest-cov",
    "pytest-timeout",
    "pytest-harvest",
    "pytest-qt",
    "ruff",
    "numpydoc",
    "codespell",
    "tomli; python_version<'3.11'",
    "twine",
    "wheel",
    "pre-commit",
    "mypy",
]

# Dependencies for building the documentation
doc = [
    "sphinx>=6",
    "numpydoc",
    "pydata_sphinx_theme==0.13.3",
    "sphinx-gallery",
    "sphinxcontrib-bibtex>=2.5",
    "sphinxcontrib-towncrier",
    "memory_profiler",
    "neo",
    "seaborn!=0.11.2",
    "sphinx_copybutton",
    "sphinx-design",
    "sphinxcontrib-youtube",
    "mne-bids",
    "pyxdf",
    "mne-connectivity",
    "mne-gui-addons",
    "pygments>=2.13",
    "pytest",
    "graphviz",
    "pyzmq!=24.0.0",
    "ipython!=8.7.0",
    "selenium",
]

[project.urls]
Homepage = "https://github.com/robbisg/sekupy"
"Bug Tracker" = "https://github.com/robbisg/sekupy/issues/"
Documentation = "https://sekupy.readthedocs.io/"
"Source Code" = "https://github.com/robbisg/sekupy"

[tool.hatch.build]
exclude = [
    "/.*",
    "/*.yml",
    "/*.yaml",
    "/*.toml",
    "/*.txt",
    "/sekupy/**/tests",
    "/dist",
    "/doc",
    "/sekupy/io/data/*",
    "/joss",
    "/examples",
    "/Dockerfile"
] # tracked by git, but we don't want to ship those files

[tool.hatch.version]
source = "vcs"
raw-options = { version_scheme = "release-branch-semver" }

[tool.codespell]
ignore-words = "ignore_words.txt"
builtin = "clear,rare,informal,names,usage"
skip = "doc/references.bib"

[tool.ruff]
select = ["A", "B006", "D", "E", "F", "I", "W", "UP"]
exclude = ["__init__.py", "constants.py", "resources.py"]
ignore = [
    "D100", # Missing docstring in public module
    "D104", # Missing docstring in public package
    "D413", # Missing blank line after last section
    "UP031", # Use format specifiers instead of percent format
]

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



[tool.bandit.assert_used]
skips = ["*/test_*.py"] # assert statements are good practice with pytest

[tool.rstcheck]
report_level = "WARNING"
ignore_roles = [
    "attr",
    "class",
    "doc",
    "eq",
    "exc",
    "file",
    "footcite",
    "footcite:t",
    "func",
    "gh",
    "kbd",
    "meth",
    "mod",
    "newcontrib",
    "py:mod",
    "ref",
    "samp",
    "term",
]

ignore_directives = [
    "autoclass",
    "autofunction",
    "automodule",
    "autosummary",
    "bibliography",
    "cssclass",
    "currentmodule",
    "dropdown",
    "footbibliography",
    "glossary",
    "graphviz",
    "grid",
    "highlight",
    "minigallery",
    "tabularcolumns",
    "toctree",
    "rst-class",
    "tab-set",
    "towncrier-draft-entries",
]

ignore_messages = "^.*(Unknown target name|Undefined substitution referenced)[^`]*$"