pyproject.toml

# Check this for proper formatting: https://packaging.python.org/en/latest/specifications/declaring-project-metadata/#declaring-project-metadata
[project]
name = "vr2f"
version = "1.0.0"
description = "EEG-decodability of facial expressions and their stereoscopic depth cues in immersive virtual reality."
readme = "README.md"
requires-python = ">=3.10"
license = { file = "LICENSE" }
authors = [
    { name = "Felix Klotzsche", email = "klotzsche@cbs.mpg.de" },
]
maintainers = [
    { name = "Felix Klotzsche", email = "klotzsche@cbs.mpg.de" },
]
keywords = ["virtual reality", "EEG", "face processing", "stereoscopic depth"]
# Check for classifiers: https://pypi.org/classifiers/
classifiers = [
    "Development Status :: 1 - Planning",
    "Intended Audience :: Science/Research",
    "Natural Language :: English",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
]

# Similar to a requirements.txt file, fill in the dependencies your project requires
# Install the project code as Python module with `pip install -e .`
dependencies = [
    "ipykernel==6.29.5",
    "toml==0.10.2",
    "mne==1.2.3",
    "autoreject==0.4.3",
    "ipython==8.12.3",
    "matplotlib==3.10.5",
    "numpy==2.3.2",
    "pandas==1.4.3",
    "scikit_learn==1.7.1",
    "scipy==1.16.1",
    "seaborn==0.13.2",
    "setuptools==71.0.4",
    "statsmodels==0.14.2",
    "tqdm==4.66.4",
]

# Following can be co-installed with `pip install -e .[develop]`
[project.optional-dependencies]
develop = [
    "black[jupyter]>=24.2.0",
    "ruff>=0.3.1",
    "tox>=4.12.1",
    "pytest>=8.0.0",
    "pytest-cov>=4.1.0",
]

[project.urls]
repository = "https://github.com/eioe/vr2f" 
data = "https://doi.org/10.17617/3.CQ2VXX"

# Entry points for the project
# For a command line interface (CLI) [uncomment and/or adopt the following if needed]
# [project.scripts]
# vr2f = "vr2f.main:main"

[tool.setuptools]
platforms = [
    "unix",
    "linux",
    "osx",
    "cygwin",
    "win32",
] # TODO: keep only intended platforms
zip-safe = false

# To automatically find the package(s) (Beta feature (Oct, 2022)):
[tool.setuptools.packages.find]
where = ["code"]
include = [
    "vr2f",
    "vr2f.*",
]
exclude = ["tests", "notebooks", "configs"]

# Include non-python files in the package (uncomment if needed)
# [options.package_data]
# vr2f = ["*.txt", "*.rst"]

# Exclude specific non-python files in the package (uncomment if needed)
# [tool.setuptools.exclude-package-data]
# vr2f = [".gitattributes"]

# ALL ABOVE IS AN ADAPTATION OF THE FORMER setup.cfg
# ALL BELOW WAS ALREADY PART OF pyproject.toml [Oct, 2022]

[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[tool.pytest.ini_options]
#addopts = "--cov=vr2f"
testpaths = ["code/tests"]

[tool.mypy]
mypy_path = "code"
check_untyped_defs = true
disallow_any_generics = true
ignore_missing_imports = true
no_implicit_optional = true
show_error_codes = true
strict_equality = true
warn_redundant_casts = true
warn_return_any = true
warn_unreachable = true
warn_unused_configs = true
no_implicit_reexport = true

[tool.coverage.run] # https://coverage.readthedocs.io/en/latest/config.html
data_file = "code/tests/.coverage"

[tool.coverage.report]
exclude_lines = ["if __name__ == .__main__.:", "if TYPE_CHECKING:", "@abstract"]

[tool.coverage.html]
directory = "code/tests/coverage_html_report"

[tool.ruff]
# Select rules / linters to apply
lint.select = [ # add /comment-out rules (list below does not contain all rules)
    # "ALL",  # all rules
    "D",   # pydocstyle
    "E",   # pycodestyle [default]
    "F",   # Pyflakes [default]
    "I",   # isort imports
    "RUF", # ruff specific
    "UP",  # pyupgrade [default]
    "W",   # pycodestyle: warning
    "C90", # mccabe
    "N",   # pep8-naming
    # "ANN", # flake8-annotations (toggle on if you intend to work with type annotations)
    "S",   # flake8-bandit
    "BLE", # flake8-blind-except
    "B",   # flake8-bugbear
    "A",   # flake8-builtins
    "COM", # flake8-commas
    "C4",  # flake8-comprehensions
    # "EM", # flake8-errmsg
    # "FA", # flake8-future-annotations (see ANN above)
    "ISC", # flake8-implicit-str-concat
    # "ICN", # flake8-import-conventions
    "G",   # flake8-logging-format
    "INP", # flake8-no-pep420
    "PT",  # flake8-pytest-style
    "Q",   # flake8-quotes
    "RET", # flake8-return
    "SIM", # flake8-simplify
    "TCH", # flake8-type-checking
    "ARG", # flake8-unused-arguments
    "PTH", # flake8-use-pathlib
    "TD",  # flake8-todos
    "FIX", # flake8-fixme
    "ERA", # eradicate
    "PD",  # pandas-vet
    "PL",  # Pylint
    "NPY", # NumPy-specific rules
] # run `ruff linter` to see all rules; ; run e.g., `ruff rule ERA001` to see specs of specific rule

fix = false # true: Ruff will try to fix certain errors automatically

# List of rules to consider non-autofix-able.
lint.unfixable = [ # either with fix = true or when `ruff . --fix` is executed
    "ERA001", # found commented-out code
    "F401",   # unused imports
    "RUF100", # `noqa` directives that are no longer applicable
]

# Ignore specific rules (e.g., "ANN102") or the whole set of a rule (e.g., "ANN")
lint.ignore = [
    "ANN101", # flake8-annotations: Missing type annotation for self in method
    "ANN102", # flake8-annotations: Missing type annotation for cls in classmethod
    "ANN401", # flake8-annotations: Any
    "COM812", # Trailing comma missing
    "D203",   # 1 blank line required before class docstring: incompatible with D211 (=no blank line required)
    "D212",   # multi-line-summary-first-line incompatible with D213 (=should start at second line)
    "DTZ005", # timezone-naive datetime
    "E402",   # Module level import not at top of file (covert by ISORT)
    # "E501",  # Ignore line-length since we use 119
    # "ERA001",  # Found commented-out code
    "ISC001",  # single-line-implicit-string-concatenation [toogle if you use `ruff format`]
    "S301",   # suspicious-pickle-usage
    "TD002",  # Missing author in To-Do
    "TD003",  # Missing issue link on the line following a To-Do
    "RET504", # Unnecessary variable assignments preceding a return
]

lint.ignore-init-module-imports = true # void automatically removing unused imports in __init__.py
respect-gitignore = true          # files & folder ignored in gitignore are ignored by ruff as well [default: true]

src = ["code/vr2f", "code/notebooks", "code/tests"]
include = ["*.py", "*.pyi", "**/pyproject.toml", "*.ipynb"]

# Exclude a variety of commonly ignored directories:
extend-exclude = [
    "code/configs",
    "data",
    "literature",
    "organisation",
    "publications",
    "results",
]

line-length = 119 # same as flake8 & black
target-version = "py311" # assume Python 3.11
# output-format = "grouped"  # default : "text"
# preview = true  # true: Ruff will use unstable rules and fixes; default: false

# Ignore specific rules in specific files
[tool.ruff.lint.extend-per-file-ignores]
"__init__.py" = ["F401", "D104"]
"*.ipynb" = ["D100"]                            # ignore docsstring in notebooks
"code/tests/*.py" = ["S101", "PLC2701", "N802"] # ignore assert statements in tests, private name imports, & lowercase (tearDown, setUp)

[tool.ruff.format]
# Check: https://docs.astral.sh/ruff/settings/#format
# quote-style = "single"  # default: "double"
# indent-style = "tab"  # Use tabs instead of 4 space indentation.
# skip-magic-trailing-comma = true  # default: false
docstring-code-format = true # default: false
# docstring-code-line-length = 80
# preview = true  # true: Ruff will use unstable rules for formatting; default: false

# Configure specific linters
[tool.ruff.lint.flake8-annotations]
allow-star-arg-any = true
ignore-fully-untyped = true
suppress-none-returning = true

[tool.ruff.lint.flake8-comprehensions]
allow-dict-calls-with-keyword-arguments = true

[tool.ruff.lint.flake8-type-checking]
# quote-annotations = true # default: false

[tool.ruff.lint.isort]
known-local-folder = ["code/vr2f"]
# known-first-party = ...

[tool.ruff.lint.mccabe]
# Flag errors (`C901`) whenever the complexity level exceeds x.
max-complexity = 10 # default x: 10

[tool.ruff.lint.pep8-naming]
ignore-names = ["X"] # fill with specific class, function, variable names

[tool.ruff.lint.pydocstyle]
# convention = "numpy" # "google"  # , "pep257"

[tool.ruff.lint.pylint]
max-args = 10          # default: 5
max-branches = 12     # default: 12
max-locals = 15       # default: 15
max-returns = 6       # default: 6
max-statements = 100   # default: 50
max-nested-blocks = 5 # default: 5
# allow-magic-value-types = ["int"]

[tool.black]
line-length = 119
target-version = ["py311"]
src = ["code/vr2f", "code/notebooks", "code/tests"]
include = '(\.pyi?|\.ipynb)$'
exclude = '''  # A regex preceded with ^/ will apply only to files and directories in the root of the project.
(
  ^/code/configs
  | ^/data
  | ^/literature
  | ^/organisation
  | ^/publications
  | ^/results
  | /*/\..*  # ignore (hidden) files in hidden directories
)
'''
# preview = true  # include unstable / upcoming black features