pyproject.toml

[project]
name = "plenoptic"
dynamic = ["version"]
authors = [{name="Plenoptic authors"}]
description = "Python library for model-based stimulus synthesis."
readme = "README.md"
requires-python = ">=3.10"
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "License :: OSI Approved :: MIT License",
    "Intended Audience :: Science/Research",
]
keywords = ['neuroscience', 'pytorch', 'visual information processing', 'machine learning', 'explainability', 'computational models']

dependencies = [
    "numpy>=1.1",
    "torch>=1.8,!=1.12.0",
    "pyrtools>=1.0.11",
    "scipy>=1.0",
    "matplotlib>=3.3",
    "tqdm>=4.29",
    "imageio>=2.5",
    "scikit-image>=0.15.0",
    "einops>=0.3.0",
    "importlib-resources>=6.0",
    # for updated tarfile behavior, https://github.com/plenoptic-org/plenoptic/issues/336
    "pooch>=1.9.0",
    "lazy_loader",
]

[build-system]
requires = ["setuptools", "setuptools-scm[toml]"]
build-backend = "setuptools.build_meta"

[project.optional-dependencies]
docs = [
     'sphinx',
     'pydata-sphinx-theme',
     'sphinx-autodoc-typehints',
     'sphinx-copybutton',
     "myst-parser[linkify]",
     "sphinxcontrib-bibtex>=2.6.4",
     "sphinx-design",
     "myst-nb",
     "ipywidgets",
     "torchvision",
     "timm",
     "jupytext",
     "sphobjinv",
     "sphinx-togglebutton",
]

test = [
    # 9.1.0 unsupported because of https://github.com/pytest-dev/pytest/issues/14591
    "pytest>=5.1.2,!=9.1.0",
    'pytest-cov',
    'pytest-xdist',
    'pytest-order',
    "torchvision",
    "timm",
]

lint = [
    "ruff>=0.6.8",
    'numpydoc',
]

dev = ["plenoptic[test,lint]"]

nb = [
    "jupyter",
    "jupyterlab>=4.5",
    "jupyterlab_myst>=2.6",
    "ipywidgets",
    "nbclient>=0.5.5",
    "torchvision>=0.3",
    "jupytext",
    "myst-nb",
]

[project.urls]
"Homepage" = "https://github.com/plenoptic-org/plenoptic"
"Documentation" = "https://docs.plenoptic.org"
"Download" = "https://zenodo.org/doi/10.5281/zenodo.10151130"

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

[tool.setuptools_scm]
version_scheme = 'semver-pep440'
local_scheme = 'no-local-version'

[tool.pytest.ini_options]
addopts = "--cov=plenoptic --cov-append -n auto --cov-report term --dist worksteal"
testpaths = ["tests"]
doctest_optionflags = "NORMALIZE_WHITESPACE NUMBER ELLIPSIS"

# ignore a bunch of common plenoptic-generated warnings, and raise errors
# otherwise. this way we can actually stay on top of deprecations etc. Per docs
# (https://docs.pytest.org/en/stable/how-to/capture-warnings.html#controlling-warnings):
# "When a warning matches more than one option in the list, the action for the
# last matching option is performed."
filterwarnings = [
    "error",
    # seems to be necessary to solve https://github.com/pytest-dev/pytest-cov/issues/693
    "ignore:Failed to generate report:",
]

# seems to be necessary to solve https://github.com/pytest-dev/pytest-cov/issues/693
[tool.coverage.run]
disable_warnings = ["module-not-measured"]

[tool.ruff]
extend-include = ["*.ipynb"]
src = ["src", "tests", "examples"]
# Exclude a variety of commonly ignored directories.
exclude = []

# Set the maximum line length (same as Black)
line-length = 88

indent-width = 4 # same as Black

[tool.ruff.format]
# Like Black, use double quotes for strings.
quote-style = "double"

# Like Black, indent with spaces, rather than tabs.
indent-style = "space"

# Like Black, respect magic trailing commas.
skip-magic-trailing-comma = false

# Like Black, automatically detect the appropriate line ending.
line-ending = "auto"

docstring-code-format = true

[tool.ruff.lint]
select = [
    # pycodestyle
    "E",
    # Pyflakes: basic static analysis for common errors like undefined names
    # and missing imports.
    "F",
    # pyupgrade
    "UP",
    # flake8-simplify
    "SIM",
    # isort
    "I",
    # in particular, this looks for invalid escape sequences (has been an issue
    # for regex strings used in tests)
    "W",
    # docstrings, note that DOC rules (pydoclint) are all in preview, so have to be explicitly added
    "D", "DOC201", "DOC202", "DOC402", "DOC403", "DOC501",
    "ANN",
    # catch missing f-strings (this is in preview and so has to be explicitly added)
    "RUF027",
]
ignore = []

# allow preview rules, but require them to be explicitly added
preview = true
explicit-preview-rules = true

[tool.ruff.lint.flake8-annotations]
allow-star-arg-any = true
suppress-none-returning = true

[tool.ruff.lint.per-file-ignores]
# Ignore docstring rules everywhere except for the `src/` directory, from
# https://docs.astral.sh/ruff/settings/#lint_per-file-ignores.
"!src/**.py" = ["D", "DOC", "ANN"]
# this file has very long lines
"src/plenoptic/_api_change.py" = ["E501"]
# exercise notebooks sometimes will have undefined names in the skipped cells
"exercises*ipynb" = ["F821"]

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

[tool.numpydoc_validation]
checks = [
    "all",
    "SA01",
    # will remove this eventually
    "EX01",
    "PR04",
]

# don't report on objects that match any of these regex
exclude = [
    "__dir__",
    # init has no docstring, documented in the class docstring
    "__init__",
    "noxfile",
    "_api_change",
]

[tool.codespell]
# Ref: https://github.com/codespell-project/codespell#using-a-config-file
skip = '.git*,*.svg,*.css,*.pgm'
check-hidden = true
# ignore regex like [Tt]rue
ignore-regex = '\[[A-Z][a-z]\][a-z]+'
# ignore-words-list = ''
dictionary = "plenoptic-dict.txt,-"