pyproject.toml

[project]
name = "snake-fmri"  # Required
# corresponds to the "Summary" metadata field:
description = "A simulator and validator of fMRI reconstruction methods."
# This field corresponds to the "Description" metadata field:
readme = "README.md" # Optional

requires-python = ">=3.10"
dynamic = ["version"]

license = {file = "LICENSE.txt"}

keywords = ["simulation", "fMRI"]

authors = [
  {name = "Pierre-Antoine Comby", email = "pierre-antoine.comby@cea.fr" } # Optional
]

# Classifiers help users find your project by categorizing it.
#
# For a list of valid classifiers, see https://pypi.org/classifiers/
classifiers = [  # Optional
  # How mature is this project? Common values are
  #   3 - Alpha
  #   4 - Beta
  #   5 - Production/Stable
  "Development Status :: 3 - Alpha",

  # Indicate who your project is intended for
  "Intended Audience :: Developers",
  "License :: OSI Approved :: MIT License",

  # Specify the Python versions you support here. In particular, ensure
  # that you indicate you support Python 3. These classifiers are *not*
  # checked by "pip install". See instead "python_requires" below.
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
]

dependencies = [ # Optional
  "numpy",
  "scipy",
  "nilearn",
  "pandas",
  "scikit-image",
  "brainweb-dl",
  "mri-nufft",
  "ismrmrd",
  "hydra-core",
  "hydra-callbacks",
  "hydra-colorlog",
]

[project.optional-dependencies] # Optional
dev = ["black", "ruff", "isort"]
test = ["pytest", "pytest-cov", "pytest-sugar", "pytest-xdist"]
doc = ["myst-parser", "sphinx-copybutton","sphinx-gallery","sphinx-book-theme","matplotlib", "pysap-fmri", "ipywidgets"]
toolkit = [ "matplotlib", "pysap-fmri"]
# List URLs that are relevant to your project
# This field corresponds to the "Project-URL" and "Home-Page" metadata fields:
[project.urls]  # Optional
"Homepage" = "https://github.com/paquiteau/simfmri"
"Bug Reports" = "https://github.com/paquiteau/simfmri/issues"
"Source" = "https://github.com/paquiteau/simfmri"

[project.scripts]
snake-acq = "snake.toolkit.cli.acquisition:acquisition_cli"
snake-rec = "snake.toolkit.cli.reconstruction:reconstruction_cli"
snake-main = "snake.toolkit.cli.main:main_cli"

[build-system]
# These are the assumed default build requirements from pip:
# https://pip.pypa.io/en/stable/reference/pip/#pep-517-and-518-support
requires = ["setuptools>=43.0.0", "setuptools_scm[toml]>=6.2", "wheel"]
build-backend = "setuptools.build_meta"

[tool.setuptools.packages.find]
where = ["src"]

[tool.setuptools_scm]
write_to = "src/snake/_version.py"
version_scheme = "python-simplified-semver"
local_scheme="no-local-version"
fallback_version="v99-dev"

[tool.coverage.report]
precision = 2
exclude_lines = ["pragma: no cover", "raise NotImplementedError"]

# Formatting using black.
[tool.black]

[tool.isort]
profile="black"

[tool.pytest.ini_options]
minversion = "6.0"
addopts = [
    "--cov=snake",
    "--cov-report=term-missing",
    "--cov-report=xml"
]


[tool.ruff]
include = ["src/**/*.py", "tests/**/*.py", "examples/*.py"]

[tool.ruff.lint]
select = ["E", "F", "B", "Q", "D", "UP", "ANN"]
ignore = [
    "ANN101", # missing type annotation for self
    "ANN102", # missing type annotation for cls in classmethod.
    "ANN204", # missing return type for __init__
    "ANN401",
    "D105", # missing docstring in magic method
    "D404", # Imperative mode is not necessary everywhere, trust me.
]

[tool.ruff.lint.pydocstyle]
convention = "numpy"
[tool.ruff.lint.per-file-ignores]
# relax code quality for tests and examples.
"examples/conftest.py" = ["ANN"]
"examples/*.py" = ["D",
"ANN", # no annotation in examples
"E402", # import in the middle of the file
"B018", # allow for useless expression (prints)
"B905"
]
"tests/test_*.py" = ["D", "ANN"]


[tool.pylsp-mypy]
enabled = true
live_mode = true
strict = true
#overrides = ["--ignore-missing-imports"]

[tool.mypy]
ignore_missing_imports=true
exclude = ["examples/"]
#overrides = ["--ignore-missing-imports"]

[tool.codespell]
ignore-words-list = ["TE","fpr"]
skip = ["docs/generated", "*.ipynb"]