pyproject.toml

[build-system]
build-backend = "setuptools.build_meta"
requires = [
  "setuptools >= 61.2.0",
  "setuptools-scm >= 6.3.2",
  "wheel >= 0.37.0",
]

[project]
name = "plasmapy"
description = "Python package for plasma science"
readme = "README.md"
keywords = [
  "astronomy",
  "fusion",
  "heliophysics",
  "plasma",
  "plasma physics",
  "science",
  "solar physics",
  "space plasmas",
]
license = {file = "LICENSE.md"}
# NumPy Enhancement Proposal 29 recommends that packages support minor
# releases of Python for 42 months after the initial release (see
# https://numpy.org/neps/nep-0029-deprecation_policy.html#support-table).
requires-python = ">=3.10"
classifiers = [
  "Development Status :: 4 - Beta",
  "Intended Audience :: Education",
  "Intended Audience :: Science/Research",
  "License :: OSI Approved :: BSD License",
  "Natural Language :: English",
  "Operating System :: OS Independent",
  "Programming Language :: Python :: 3",
  "Topic :: Scientific/Engineering :: Physics",
  "Topic :: Scientific/Engineering :: Astronomy",
]
dynamic = [
  "version",
]

# SPEC 0 recommends that support for core packages should generally be
# dropped two years after their initial release (see
# https://scientific-python.org/specs/spec-0000). Exceptions may include
# critical bugfixes or when making use of important new features. Any
# upper limits on package versions should be temporary because they can
# make it harder to resolve environments when PlasmaPy is installed
# alongside other packages, such as in the heliopythoniverse.

# When updating dependencies, run `tox -e requirements` to update the
# pinned requirements files. See `ci_requirements/README.txt` for
# details.

dependencies = [
  "astropy >= 5.1",
  "h5py >= 3.7.0",
  "ipykernel >= 6.8.0",
  "ipywidgets >= 7.7.0",
  "lmfit >= 1.1.0",
  "matplotlib >= 3.5.1",
  "mpmath >= 1.2.1",
  "numba >= 0.57.0",
  "numpy >= 1.23.0",
  "packaging >= 22.0",
  "pandas >= 1.4.0",
  "requests >= 2.28.0",
  "scipy >= 1.8.0",
  "setuptools >= 61.2.0",
  "tqdm >= 4.60.0",
  "voila >= 0.4.0",
  "wrapt >= 1.14.0",
  "xarray >= 2022.3.0",
]

[project.optional-dependencies]
# The documentation build occurs in an isolated environment that is not
# user-facing, so we can have stricter requirements.
docs = [
  "docutils >= 0.20.1",
  "jinja2 >= 3.1.3",
  "nbsphinx >= 0.9.3",
  "numpydoc >= 1.6.0",
  "pillow >= 10.2.0",
  "pygments >= 2.17.2",
  # install setuptools to get pkg_resources for doc build
  "setuptools; python_version >= '3.12'",
  # see issue 2497
  "sphinx >= 7.3.7",
  "sphinx-changelog >= 1.5.0",
  "sphinx-codeautolink >= 0.15.0",
  "sphinx-copybutton >= 0.5.2",
  "sphinx-gallery >= 0.15.0",
  "sphinx-hoverxref >= 1.3.0",
  "sphinx-issues >= 4.0.0",
  "sphinx-notfound-page >= 1.0.0",
  "sphinx-reredirects >= 0.1.3",
  "sphinx_rtd_theme >= 2.0.0",
  "sphinx_tabs >= 3.4.5",
  "sphinx_collapse >= 0.1.2",
  "sphinxcontrib-bibtex >= 2.6.2",
  "sphinxcontrib-globalsubs >= 0.1.1",
  "towncrier >= 23.11.0",
  "tox >= 4.12.1",
  "tox-uv >= 1.7.0",
  "unidecode >= 1.3.8",
]

# Test dependencies are not user-facing, so we can set stricter
# requirements to ensure that tests are run in consistent environments.
tests = [
  "hypothesis >= 6.97.4",
  "pre-commit >= 3.6.0",
  "pytest >= 8.0.2",
  "pytest-regressions >= 2.5.0",
  "pytest-rerunfailures >= 13.0",
  "pytest-xdist >= 3.5.0",
  "tomli >= 2.0.1",
  "tox >= 4.12.1",
  "tox-uv >= 1.7.0",
]

[project.urls]
Changelog = "https://docs.plasmapy.org/en/stable/whatsnew/index.html"
Chat = "https://plasmapy.org/chat"
Documentation = "https://docs.plasmapy.org/"
Issues = "https://github.com/PlasmaPy/plasmapy/issues/"
Source = "https://github.com/PlasmaPy/plasmapy"
website = "https://www.plasmapy.org"

[project.scripts]
plasma-calculator = "plasmapy.utils.calculator:main"

[tool.setuptools]
include-package-data = true

[tool.setuptools.package-data]
"plasmapy.particles.data" = ["*"]
"plasmapy.tests" = ["coveragerc"]
"plasmapy.utils.calculator" = ["*"]

[tool.setuptools.packages.find]
where = ["src"]
exclude = ["docs/automodapi", "src/plasmapy/_dev"]
namespaces = false

[tool.setuptools_scm]
write_to = "src/plasmapy/_version.py"

[tool.pytest.ini_options]
testpaths = ['.']
xfail_strict = true
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
]
doctest_optionflags = """
NORMALIZE_WHITESPACE
ELLIPSIS
NUMBER
IGNORE_EXCEPTION_DETAIL"""
filterwarnings = [
  "ignore:.*deprecated in traitlets 4.2.*:DeprecationWarning",
  "ignore:.*MultiIndex.*:DeprecationWarning",  # https://github.com/PlasmaPy/PlasmaPy/issues/2319
]
norecursedirs = [
  '*egg-info*',
  '.*cache*',
  '.*env',
  '.[tn]ox',
  '.cov*',
  '.git*',
  '.hypothesis',
  '.idea',
  '.jupyter',
  '.vscode',
  '__pycache__',
  '_dev',
  'binder',
  'build',
  'changelog',
  'dist',
  'docs',
  'licenses',
  'node_modules',
  'venv',
  '.venv',
]


[tool.coverage.report]
exclude_lines = [
  "if TYPE_CHECKING",
  "if typing.TYPE_CHECKING",
  "coverage: ignore",
  "ImportError",
  "ModuleNotFoundError",
  "raise NotImplementedError",
  "@vectorize",
  "@numba.vectorize",
  "@numba.jit",
  "@jit",
  "@numba.njit",
  "@njit",
  "@abstractmethod",
]

[tool.coverage.run]
branch = true
source = ["src"]
omit = [
  "*/plasmapy/utils/calculator/*",
  "*/plasmapy/tests/*",
  "*/plasmapy/*version.py",
  "*/plasmapy/_dev/*",
]

[tool.build_docs]
source-dir = "docs"
build-dir = "docs/_build"
all_files = "1"

[tool.codespell]
skip = "*.png,*cache*,*egg*,.git,.hypothesis,.idea,.tox,_build,*charged_particle*.ipynb,venv"
# Add false positives found by codespell to ignore-words-list
ignore-words-list = """
aas,
aci,
afe,
ans,
ba,
bale,
bu,
circularly,
ded,
dne,
ect,
explin,
fo,
fof,
gud,
hax,
hist,
hve,
nd,
noo,
nwo,
ot,
recuse,
ro,
te,
ue,
ue,
windo"""

[tool.gilesbot]

[tool.gilesbot.pull_requests]
enabled = true

[tool.gilesbot.towncrier_changelog]
enabled = true
changelog_skip_label = "no changelog entry needed"
help_url = "https://docs.plasmapy.org/en/latest/contributing/changelog_guide.html#adding-a-changelog-entry"
changelog_missing = "Missing changelog entry (see `changelog/README.rst`)"
changelog_missing_long = "Please add a changelog entry at `changelog/NUMBER.TYPE.rst`, where `NUMBER` is the pull request number and `TYPE` is one of `feature`, `trivial`, `doc`, `internal`, `bugfix`, `breaking`, or `removal`.\n\nMinor pull requests, such as typo fixes and hyperlink updates, do not need a changelog entry.\n\nFor details, see: https://docs.plasmapy.org/en/latest/contributing/changelog_guide.html#adding-a-changelog-entry"
verify_pr_number = true
number_incorrect = "Changelog entry number ≠ PR number (see `changelog/README.rst`)"
number_incorrect_long = "The changelog entry number does not match this pull request's number.\n\nWhen purposefully editing the changelog entry for a different pull request, set the 'no changelog entry needed' label to ignore this check."
type_incorrect = "Incorrect changelog type (see `changelog/README.rst`)"
type_incorrect_long = "The filename of the changelog entry must be of the form `changelog/NUMBER.TYPE.rst` where `TYPE` is one of `feature`, `trivial`, `doc`, `internal`, `bugfix`, `breaking`, or `removal`.\n\nFor details, see: https://docs.plasmapy.org/en/latest/contributing/changelog_guide.html#adding-a-changelog-entry"

[tool.ruff]
target-version = "py310"
namespace-packages = [".github/workflows", "docs"]
output-format = "grouped"
show-fixes = true
extend-exclude = [
  "docs/plasmapy_sphinx",
  ".idea",
  ".hypothesis",
  ".jupyter",
  "__pycache__",
  "_dev",
]

[tool.ruff.format]
docstring-code-format = true
line-ending = "lf"

[tool.ruff.lint]
extend-select = [
  "A", # flake8-builtins
  "ANN204", # missing-return-type-special-method
  "ANN205", # missing-return-type-static-method
  "ANN206", # missing-return-type-class-method
  "ARG", # flake8-unused-arguments
  "ASYNC", # flake8-async
  "B", # flake8-bugbear
  "BLE", # flake8-blind-except
  "C4", # flake8-comprehensions
  "C90", # mccabe
  "COM818", # trailing-comma-on-bare-tuple
  "D", # pydocstyle
  "DTZ", # flake8-datetimez
  "EM", # flake8-errmsg
  "EXE", # flake8-executable
  "FA102", # flake8-required-type-annotation
  "FBT003", # flake8-boolean-trap
  "FIX", # flake8-fixme
  "FLY", # flynt
  "G", # flake8-logging-format
  "I", # isort
  "ICN", # flake8-import-conventions
  "INP", # flake8-no-pep420
  "INT", # flake8-gettext
  "ISC", # flake8-implicit-str-concat
  "N", # pep8-naming
  "NPY", # numpy-deprecated-type-alias
  "PD", # pandas-vet
  "PERF", # perflint
  "PGH", # pygrep-hooks
  "PIE", # flake8-pie
  "PLC", # pylint convention
  "PLE", # pylint errors
  "PLR", # pylint refactorings
  "PLW", # pylint warnings
  "PT", # flake8-pytest-style
  "PTH", # flake8-use-pathlib
  "PYI", # flake8-pyi
  "RET", # flake8-return
  "RSE", # flake8-raise
  "RUF005", # collection-literal-concatenation
  "RUF006", # asyncio-dangling-task
  "RUF007", # pairwise-over-zipped
  "RUF008", # mutable-dataclass-default
  "RUF009", # function-call-in-dataclass-default-argument
  "RUF010", # explicit-f-string-type-conversion
  "RUF012", # mutable-class-default
  "RUF013", # implicit-optional
  "RUF015", # unnecessary-iterable-allocation-for-first-element
  "RUF016", # invalid-index-type
  "RUF017", # quadratic-list-summation
  "RUF018", # assignment-in-assert
  "RUF019", # unnecessary-key-check
  "RUF020", # never-union
  "RUF100", # unused-noqa
  "RUF200", # invalid-pyproject-toml
  "S", # flake8-bandit
  "SIM", # flake8-simplify
  "SLF", # flake8-self
  "SLOT", # flake8-slots
  "T", # flake8-print
  "T100", # debugger
  "TCH", # flake8-type-checking
  "TD", # flake8-todos
  "TID", # flake8-tidy-imports
  "TRY", # tryceratops
  "UP", # pyupgrade
  "W", # pycodestyle warnings
  "YTT", # flake8-2020
]
ignore = [
  "B028", # no-explicit-stacklevel
  "D105", # undocumented-magic-method (enable later?)
  "D200", # fits-on-one-line (incompatible with multiline short summaries)
  "D202", # no-blank-line-after-function
  "D205", # blank-line-after-summary (incompatible with multiline short summaries)
  "D206", # indent-with-spaces (formatter conflict)
  "D401", # non-imperative-mood (enable later?)
  "E501", # line-too-long
  "EM101", # raw-string-in-exception (enable later in focused PR)
  "EM102", # f-string-in-exception (enable later in focused PR)
  "FIX002", # line-contains-todo
  "ISC001", # single-line-implicit-string-concatenation (formatter conflict)
  "N802", # invalid-function-name
  "N803", # invalid-argument-name
  "N806", # non-lowercase-variable-in-function
  "N816", # mixed-case-variable-in-global-scope
  "PERF203", # try-except-in-loop (remove when we require Python ≥ 3.11)
  "PLE0605", # invalid-all-format (flags `__all__ += __lite_funcs`, etc.)
  "PLR0913", # too-many-arguments
  "PLR2004", # magic-value-comparison
  "PT007", # pytest-parametrize-values-wrong-type
  "PT011", # pytest-raises-too-broad
  "PT012", # pytest-raises-multiple-statements (enable later?)
  "PT019", # pytest-fixture-param-without-value (enable later?)
  "PYI024", # collections-named-tuple (enable later)
  "RET501", # unnecessary-return-none
  "RET502", # implicit-return-value
  "RET505", # superfluous-else-return (enable later?)
  "RET506", # superfluous-else-raise (enable later?)
  "S101", # asserts
  "SIM117", # multiple-with-statements (remove for Python 3.10+)
  "SIM300", # yoda-conditions
  "TD002", # missing-todo-author
  "TD003", # missing-todo-link
  "TRY003", # raise-vanilla-args
  "TRY301", # raise-within-try
  "UP025", # unicode-kind-prefix
  "W191", # tab-indentation (formatter conflict)
  "W291", # trailing-whitespace (handled by formatter)
]
dummy-variable-rgx = "Z|mass_numb|request|event"
ignore-init-module-imports = true

[tool.ruff.lint.flake8-annotations]
allow-star-arg-any = true
ignore-fully-untyped = true
mypy-init-return = true
suppress-dummy-args = true
suppress-none-returning = true

[tool.ruff.lint.flake8-import-conventions]
banned-from = [
  "astropy.units",
  "matplotlib.pyplot",
  "numpy",
  "pytest",
  "warnings",
]

[tool.ruff.lint.flake8-import-conventions.aliases]
"astropy.constants" = "const"
"astropy.units" = "u"
"matplotlib" = "mpl"
"matplotlib.pyplot" = "plt"
numpy = "np"
pandas = "pd"

[tool.ruff.lint.flake8-unused-arguments]
ignore-variadic-names = true

[tool.ruff.lint.flake8-tidy-imports]
ban-relative-imports = "all"

[tool.ruff.lint.flake8-tidy-imports.banned-api]
"typing.Callable".msg = "Deprecated alias. Change to collections.abc.Callable"
"typing.Collection".msg = "Deprecated alias. Change to collections.abc.Collection"
"typing.DefaultDict".msg = "Deprecated alias. Change to collections.defaultdict"
"typing.Dict".msg = "Deprecated alias. Change to dict"
"typing.Generator".msg = "Deprecated alias. Change to collections.abc.Generator"
"typing.Iterable".msg = "Deprecated alias. Change to collections.abc.Iterable"
"typing.Iterator".msg = "Deprecated alias. Change to collections.abc.Iterator"
"typing.List".msg = "Deprecated alias. Change to list"
"typing.Mapping".msg = "Deprecated alias. Change to collections.abc.mapping"
"typing.MutableMapping".msg = "Deprecated alias. Change to collections.abc.MutableMapping"
"typing.Sequence".msg = "Deprecated alias. Change to collections.abc.Sequence"
"typing.Set".msg = "Deprecated alias. Change to set"
"typing.Tuple".msg = "Deprecated alias. Change to tuple"
"typing.Type".msg = "Deprecated alias. Change to type"

[tool.ruff.lint.isort]
known-first-party = ["plasmapy"]

[tool.ruff.lint.mccabe]
max-complexity = 10

[tool.ruff.lint.per-file-ignores]
".github/scripts/*.py" = ["D103", "INP001"]
"__init__.py" = ["D104", "E402", "F401", "F402", "F403"] # ignore import errors
"docs/conf.py" = ["D100", "D103", "E402", "EXE001", "EXE005", "F401"]
"setup.py" = ["D100"]
"src/plasmapy/analysis/fit_functions.py" = ["D301"]
"src/plasmapy/formulary/braginskii.py" = ["C901", "RET503", "RET504"]
"src/plasmapy/plasma/sources/*.py" = ["D102"]
"src/plasmapy/utils/_pytest_helpers/pytest_helpers.py" = ["BLE001", "PLR", "SLF001"]
"test_*" = ["D100", "D101", "D102", "D103", "D104", "D209", "D400", "D401", "N801", "RUF012", "SLF001"]
"tests/**/__init__.py" = ["D104"]
"tests/**/*.py" = ["INP001"]
"tests/formulary/test_distribution.py" = ["ARG005"]
"tests/particles/test_decorators.py" = ["ARG001", "ARG002"]
"tests/utils/_pytest_helpers/test_pytest_helpers.py" = ["BLE001", "TRY002"]
"tests/utils/decorators/test_converters.py" = ["ARG001", "ARG005"]

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

[tool.towncrier]
package = "plasmapy"
name = "PlasmaPy"
filename = "CHANGELOG.rst"
directory = "changelog/"
title_format = "{name} v{version} ({project_date})"
issue_format = ":pr:`{issue}`" # Despite the name mismatch, we use this for linking to PRs
wrap = true

[[tool.towncrier.type]]
directory = "feature"
name = "New Features"
showcontent = true

[[tool.towncrier.type]]
directory = "doc"
name = "Documentation Improvements"
showcontent = true

[[tool.towncrier.type]]
directory = "breaking"
name = "Backwards Incompatible Changes"
showcontent = true

[[tool.towncrier.type]]
directory = "removal"
name = "Deprecations and Planned Removals"
showcontent = true

[[tool.towncrier.type]]
directory = "bugfix"
name = "Bug Fixes"
showcontent = true

[[tool.towncrier.type]]
directory = "internal"
name = "Internal Changes and Refactorings"
showcontent = true

[[tool.towncrier.type]]
directory = "trivial"
name = "Additional Changes"
showcontent = true