pyproject.toml

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

[project]
name = "mne-bids-pipeline"
# Keep in sync with README.md:
description = "A full-flegded processing pipeline for your MEG and EEG data"
readme = "README.md"
requires-python = ">=3.10"
license = { file = "LICENSE.txt" }
keywords = ["science", "neuroscience", "psychology"]
authors = [
  { name = "Eric Larson" },
  { name = "Alexandre Gramfort" },
  { name = "Mainak Jas" },
  { name = "Richard Höchenberger", email = "richard.hoechenberger@gmail.com" },
]
classifiers = [
  "Intended Audience :: Science/Research",
  "Programming Language :: Python",
]
dependencies = [
  "psutil",               # for joblib
  "packaging",
  "numpy",
  "scipy",
  "matplotlib",
  "nibabel",
  "joblib >= 0.14",
  "threadpoolctl",
  "dask[distributed]",
  "bokeh",            # for distributed dashboard
  "jupyter-server-proxy", # to have dask and jupyter working together
  "scikit-learn",
  "pandas",
  "pyarrow",              # from pandas
  "seaborn",
  "json_tricks",
  "pydantic >= 2.0.0",
  "annotated-types",
  "rich",
  "python-picard",
  "qtpy",
  "pyvista",
  "pyvistaqt",
  "openpyxl",
  "autoreject",
  "mne[hdf5] >=1.7",
  "mne-bids[full]",
  "filelock",
]
dynamic = ["version"]

[project.optional-dependencies]
tests = [
  "pytest",
  "pytest-cov",
  "pooch",
  "psutil",
  "ruff",
  "jinja2",
  "openneuro-py >= 2022.2.0",
  "httpx >= 0.20",
  "tqdm",
  "Pygments",
  "pyyaml",
]
docs = [
  "mkdocs",
  "mkdocs-material >= 9.0.4",
  "mkdocs-material-extensions",
  "mkdocs-macros-plugin",
  "mkdocs-include-markdown-plugin",
  "mkdocs-exclude",
  "mkdocstrings-python",
  "mike",
  "livereload",
  "black",                          # docstring reformatting
]

[project.scripts]
mne_bids_pipeline = "mne_bids_pipeline._main:main"

[project.urls]
homepage = "https://mne.tools/mne-bids-pipeline"
repository = "https://github.com/mne-tools/mne-bids-pipeline"
changelog = "http://mne.tools/mne-bids-pipeline/changes.html"

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

[tool.hatch.build]
exclude = [
  "/.*",
  "/codecov.yml",
  "**/tests",
  "/docs",
  "/docs/source/examples/gen_examples.py", # specify explicitly because its exclusion is negated in .gitignore
  "/Makefile",
  "/CONTRIBUTING.md",
  "ignore_words.txt",
]

[tool.codespell]
skip = "docs/site/*,*.html,steps/freesurfer/contrib/*"
ignore-words = "ignore_words.txt"
builtin = "clear,rare,informal,names,usage"
quiet-level = 3
interactive = 3
enable-colors = ""
count = ""

[tool.pytest.ini_options]
addopts = "-ra -vv --tb=short --cov=mne_bids_pipeline --cov-report= --junit-xml=junit-results.xml --durations=10"
testpaths = ["mne_bids_pipeline"]
junit_family = "xunit2"

[tool.ruff]
exclude = ["**/freesurfer/contrib", "dist/", "build/", "**/.*cache"]

[tool.ruff.lint]
select = ["A", "B006", "D", "E", "F", "I", "W", "UP", "TID252"]
ignore = [
  "D104", # Missing docstring in public package
]

[tool.ruff.per-file-ignores]
"mne_bids_pipeline/typing.py" = ["A005"]

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

[tool.mypy]
ignore_errors = false
scripts_are_modules = true
disable_error_code = [
  # For libraries like matplotlib that we don't have types for
  "import-not-found",
  "import-untyped",
]
strict = true
modules = ["mne_bids_pipeline", "docs.source"]

[[tool.mypy.overrides]]
module = ["mne_bids_pipeline.steps.freesurfer.contrib.*"]
ignore_errors = true  # not our code, don't validate

[[tool.mypy.overrides]]
module = ["mne_bids_pipeline.tests.*"]
disable_error_code = [
  "misc",  # Untyped decorator makes function "test_all_functions_return" untyped
]

[[tool.mypy.overrides]]
module = ['mne_bids_pipeline.tests.configs.*']
disable_error_code = [
  "assignment",  # Incompatible types in assignment
  "var-annotated",  # Need type annotation for "plot_psd_for_runs"
]