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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"
[project]
name = "pyitab"
description = "MVPA Pipelines at ITAB"
dynamic = ["version"]
authors = [
{ name = "Roberto Guidotti", email = "roberto.guidotti@unich.it" },
]
license = { text = "BSD-3-Clause" }
readme = { file = "README.md", content-type = "text/x-rst" }
requires-python = ">=3.7"
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",
]
scripts = { mne = "mne.commands.utils:main" }
dependencies = [
"numpy>=1.21.2",
"scipy>=1.7.1",
"matplotlib>=3.5.0",
"tqdm",
"scikit-learn",
"nibabel",
"pandas",
"seaborn",
"imbalanced-learn",
"pymvpa2",
"mne",
"lazy_loader>=0.3",
"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 docuemntation
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/pyitab"
"Bug Tracker" = "https://github.com/robbisg/pyitab/issues/"
Documentation = "https://pyitab.readthedocs.io/"
"Source Code" = "https://github.com/robbisg/pyitab"
[tool.hatch.build]
exclude = [
"/.*",
"/*.yml",
"/*.yaml",
"/*.toml",
"/*.txt",
"/pyitab/**/tests",
"/dist",
"/doc",
"/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.ruff.per-file-ignores]
"tutorials/time-freq/10_spectrum_class.py" = [
"E501", # line too long
]
"mne/datasets/*/*.py" = [
"D103", # Missing docstring in public function
]
"mne/utils/tests/test_docs.py" = [
"D101", # Missing docstring in public class
"D410", # Missing blank line after section
"D411", # Missing blank line before section
"D414", # Section has no content
]
"examples/*/*.py" = [
"D205", # 1 blank line required between summary line and description
]
[tool.pytest.ini_options]
# -r f (failed), E (error), s (skipped), x (xfail), X (xpassed), w (warnings)
# don't put in xfail for pytest 8.0+ because then it prints the tracebacks,
# which look like real errors
addopts = """--durations=20 --doctest-modules -rfEXs --cov-report= --tb=short \
--cov-branch --doctest-ignore-import-errors --junit-xml=junit-results.xml \
--color=yes --capture=sys"""
junit_family = "xunit2"
[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)[^`]*$"