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628 lines (614 loc) · 18.7 KB
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[build-system]
build-backend = "setuptools.build_meta"
requires = [
"setuptools>=77",
"setuptools-scm>=8.1",
"wheel>=0.43",
]
[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-files = [ "LICENSE.md" ]
# SPEC 0 recommends that projects drop support for Python versions 3
# years after their initial release. See:
# https://scientific-python.org/specs/spec-0000
requires-python = ">=3.12"
# Add classifiers from https://pypi.org/classifiers
classifiers = [
"Intended Audience :: Education",
"Intended Audience :: Science/Research",
"Natural Language :: English",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
"Programming Language :: Python :: 3.14",
"Topic :: Scientific/Engineering :: Astronomy",
"Topic :: Scientific/Engineering :: Physics",
]
dynamic = [ "version" ]
# SPEC 0 recommends that support for core packages should be dropped 2
# years after their initial release.
# 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 `nox -s lock` to upgrade the
# pinned environments in `uv.lock`.
dependencies = [
"astropy>=6.1.3,<8",
"h5py>=3.11",
"lmfit>=1.3",
"matplotlib>=3.8",
"mpmath>=1.3",
"numpy>=1.26",
"packaging>=24",
"pandas>=2.1.4",
"pytest==9.0.3",
"requests>=2.30",
"scipy>=1.11",
"tqdm>=4.65",
"wrapt>=1.15",
"xarray>=2024.5",
]
urls.Changelog = "https://docs.plasmapy.org/en/stable/whatsnew/index.html"
urls.Chat = "https://plasmapy.org/chat"
urls.Documentation = "https://docs.plasmapy.org/"
urls.Issues = "https://github.com/PlasmaPy/plasmapy/issues/"
urls.Source = "https://github.com/PlasmaPy/plasmapy"
urls.website = "https://www.plasmapy.org"
# Remove references to plasma calculator after mid-2026
scripts.plasma-calculator = "plasmapy.utils.calculator:main"
[dependency-groups]
# Define development dependencies using dependency groups (see PEP 735).
# Because dependency groups are excluded from built distributions of
# packages, SPEC 0 does not apply.
dev = [
{ include-group = "autotyping" },
{ include-group = "changelog" },
{ include-group = "docs" },
{ include-group = "lint" },
{ include-group = "manifest" },
{ include-group = "nox" },
{ include-group = "test" },
{ include-group = "type_check" },
{ include-group = "zizmor" },
]
test = [
"hypothesis>=6.150",
"pytest>=9.0.2",
"pytest-cov>=7",
"pytest-filter-subpackage>=0.2",
"pytest-regressions>=2.9.1",
"pytest-rerunfailures>=16.1",
"pytest-xdist>=3.8",
]
docs = [
"docutils>=0.22",
"ipykernel>=7.2",
"ipywidgets>=8.1.8",
"jinja2>=3.1.6",
"nbsphinx>=0.9.8",
"numpydoc>=1.10",
"pillow>=12.2",
"plasmapy-sphinx>=2026.1",
"pygments>=2.20",
"sphinx>=9.1",
"sphinx-changelog>=1.6",
"sphinx-codeautolink>=0.18.1",
"sphinx-copybutton>=0.5.2",
"sphinx-gallery>=0.21",
"sphinx-issues>=6",
"sphinx-notfound-page>=1.1",
"sphinx-reredirects>=1.1",
"sphinx-rtd-theme>=3.1",
"sphinx-tabs>=3.5",
"sphinx-toolbox>=4.2",
"sphinxcontrib-bibtex>=2.7",
"sphinxcontrib-globalsubs>=1.1",
"sphinxemoji>=0.3.2",
"unidecode>=1.4",
{ include-group = "changelog" },
]
autotyping = [
"autotyping>=24.9",
"typing-extensions>=4.15",
]
changelog = [
"towncrier>=24.8",
]
lint = [
"pre-commit>=4.5.1",
# Include ruff to make it available for IDEs in virtual environments
"ruff>=0.14.11",
]
manifest = [
"check-manifest>=0.51",
]
nox = [
"nox>=2026.4.10",
"nox-uv>=0.7",
]
type_check = [
"ty>=0.0.35",
{ include-group = "docs" },
{ include-group = "test" },
]
zizmor = [
"zizmor==1.22",
]
[tool.setuptools]
packages.find.where = [ "src" ]
packages.find.exclude = [ "docs/automodapi", "src/plasmapy/_dev" ]
packages.find.namespaces = false
include-package-data = true
package-data."plasmapy.particles.data" = [ "*" ]
package-data."plasmapy.tests" = [ "coveragerc" ]
[tool.setuptools_scm]
write_to = "src/plasmapy/_version.py"
[tool.uv]
# Prefer pre-built distributions when using lowest-direct resolution strategy or when using nightly wheels
no-build-package = [ "astropy", "h5py", "matplotlib", "numpy", "pandas", "scipy", "wrapt" ]
# Use a dependency cooldown so that security vulnerabilities in upstream
# packages can be identified and yanked before we start using them.
exclude-newer = "3 days"
exclude-newer-package = { plasmapy-sphinx = false }
[tool.ruff]
target-version = "py312"
namespace-packages = [ ".github/workflows", "docs" ]
extend-exclude = [
".hypothesis",
".idea",
".jupyter",
"__pycache__",
"_dev",
]
show-fixes = true
output-format = "grouped"
format.line-ending = "lf"
format.docstring-code-format = true
# Using an IDE like PyCharm with a ruff plugin will make rule names appear as inlay hints
lint.extend-select = [
"A",
"ANN",
"ARG",
"ASYNC",
"B",
"BLE",
"C4",
"C90",
"COM",
"D",
# enable DOC rule set when it is no longer in preview
"DTZ",
"EM",
"EXE",
"FA102",
"FBT",
"FIX",
"FLY",
"FURB",
"G",
"I",
"ICN",
"INP",
"INT",
"ISC",
"N",
"NPY",
"PD",
"PERF",
"PGH",
"PIE",
"PLC",
"PLE",
"PLR",
"PLW",
"PT",
"PTH",
"PYI",
"Q",
"RET",
"RSE",
"RUF001",
"RUF002",
"RUF003",
"RUF005",
"RUF006",
"RUF007",
"RUF008",
"RUF009",
"RUF010",
"RUF012",
"RUF013",
"RUF015",
"RUF016",
"RUF017",
"RUF018",
"RUF019",
"RUF020",
"RUF021",
"RUF023",
"RUF024",
"RUF026",
"RUF028",
"RUF030",
"RUF032",
"RUF033",
"RUF034",
"RUF037",
"RUF040",
"RUF041",
"RUF043",
"RUF046",
"RUF048",
"RUF049",
"RUF051",
"RUF053",
"RUF057",
"RUF058",
"RUF059",
"RUF060",
"RUF061",
"RUF064",
"RUF100",
"RUF101",
"RUF102",
"RUF103",
"RUF104",
"RUF200",
"S",
"SIM",
"SLF",
"SLOT",
"T10",
"T20",
"TC",
"TD",
"TID",
"TRY",
"UP",
"W",
"YTT",
]
lint.ignore = [
"ANN001", # add file-wide ignore comments?
"COM812", # handled by ruff format
"COM819", # adding trailing commas leads to simpler diffs
"D200", # incompatible with multiline short summaries
"D203", # handled by ruff format
"D205", # incompatible with multiline short summaries
"D206", # handled by ruff format
"D300", # handled by ruff format
"D401", # enable later?
"E111", # handled by ruff format
"E114", # handled by ruff format
"E117", # handled by ruff format
"E501", # handled by ruff format
"EM101", # enable later in focused PR
"EM102", # enable later in focused PR
"N802", # inconsistent with capitalization from physics notation
"N803", # inconsistent with capitalization from physics notation
"N806", # inconsistent with capitalization from physics notation
"N816", # inconsistent with capitalization from physics notation
"PLC2401", # flags variables used as mathematical symbols
"PLC2403", # flags variables used as mathematical symbols
"PLE0605", # flags `__all__ += __lite_funcs`
"PLR0913", # too many situations where lots of arguments are justified
"PLR2004", # would need case-by-case evaluations
"PT011", # would require using match keyword argument
"PT012", # enable later?
"PT019", # enable later?
"PYI024", # enable later?
"Q001", # handled by ruff format
"Q002", # handled by ruff format
"Q003", # handled by ruff format
"Q004", # handled by ruff format
"RET505", # enable later?
"RET506", # enable later?
"TD002", # enable later?
"TD003", # enable later?
"TRY003", # enable later?
"W191", # handled by ruff format
]
lint.per-file-ignores."**/*.ipynb" = [ "T201", "T203" ]
lint.per-file-ignores.".github/scripts/*.py" = [ "D103", "INP001" ]
lint.per-file-ignores."__init__.py" = [ "D104", "E402", "F401", "F402", "F403" ] # ignore import errors
lint.per-file-ignores."docs/conf.py" = [ "D100", "D103", "E402", "EXE001", "EXE005", "F401" ]
# Most ruff rule violations in the following files should eventually be fixed
lint.per-file-ignores."docs/notebooks/analysis/fit_functions.ipynb" = [ "NPY002" ]
lint.per-file-ignores."docs/notebooks/analysis/nullpoint.ipynb" = [ "D103" ]
lint.per-file-ignores."docs/notebooks/analysis/swept_langmuir/find_floating_potential.ipynb" = [ "FBT003" ]
lint.per-file-ignores."docs/notebooks/diagnostics/charged_particle_radiography_film_stacks.ipynb" = [ "B007", "PTH123" ]
lint.per-file-ignores."docs/notebooks/diagnostics/charged_particle_radiography_particle_tracing.ipynb" = [
"D103",
"E741",
]
lint.per-file-ignores."docs/notebooks/diagnostics/charged_particle_radiography_particle_tracing_custom_source.ipynb" = [
"NPY002",
]
lint.per-file-ignores."docs/notebooks/diagnostics/charged_particle_radiography_particle_tracing_wire_mesh.ipynb" = [
"D103",
]
lint.per-file-ignores."docs/notebooks/diagnostics/thomson_fitting.ipynb" = [ "NPY002", "PD011" ]
lint.per-file-ignores."docs/notebooks/dispersion/dispersion_function.ipynb" = [ "D103" ]
lint.per-file-ignores."docs/notebooks/dispersion/stix_dispersion.ipynb" = [ "FBT003" ]
lint.per-file-ignores."docs/notebooks/formulary/cold_plasma_tensor_elements.ipynb" = [ "FBT003" ]
lint.per-file-ignores."docs/notebooks/formulary/ExB_drift.ipynb" = [ "B008", "D103" ]
lint.per-file-ignores."docs/notebooks/langmuir_samples/_generate_noisy.ipynb" = [ "ANN202", "NPY002", "PTH123" ]
lint.per-file-ignores."docs/notebooks/plasma/grids_cartesian.ipynb" = [ "NPY002", "PLW2901" ]
lint.per-file-ignores."docs/notebooks/plasma/grids_nonuniform.ipynb" = [ "NPY002" ]
lint.per-file-ignores."setup.py" = [ "D100" ]
lint.per-file-ignores."src/plasmapy/analysis/fit_functions.py" = [ "D301" ]
lint.per-file-ignores."src/plasmapy/analysis/swept_langmuir/__init__.py" = [ "E402" ]
lint.per-file-ignores."src/plasmapy/formulary/braginskii.py" = [ "C901", "RET503", "RET504" ]
lint.per-file-ignores."src/plasmapy/plasma/sources/*.py" = [ "D102" ]
lint.per-file-ignores."src/plasmapy/utils/_pytest_helpers/pytest_helpers.py" = [ "BLE001", "PLR", "SLF001" ]
lint.per-file-ignores."tests/**/__init__.py" = [ "D104" ]
lint.per-file-ignores."tests/**/test_*.py" = [
"D100",
"D101",
"D102",
"D103",
"D104",
"D209",
"D400",
"D401",
"DOC201",
"DOC501",
"INP001",
"N801",
"N802",
"PLC2701",
"PLR6301",
"RUF012",
"S101",
"SLF001",
]
lint.per-file-ignores."tests/formulary/collisions/test_coulomb.py" = [ "PT031" ]
lint.per-file-ignores."tests/formulary/test_distribution.py" = [ "ARG005" ]
lint.per-file-ignores."tests/formulary/test_transport.py" = [ "PT031" ]
lint.per-file-ignores."tests/particles/test_decorators.py" = [ "ARG001", "ARG002" ]
lint.per-file-ignores."tests/utils/_pytest_helpers/test_pytest_helpers.py" = [ "BLE001", "TRY002" ]
lint.per-file-ignores."tests/utils/decorators/test_converters.py" = [ "ARG001", "ARG005" ]
# Allow potentially ambiguous Unicode characters with valid uses in plasma science
lint.allowed-confusables = [
"×",
"–",
"′",
"∨",
"∪",
"∼",
"⊤",
"α",
"ℂ",
"ℰ",
"ℱ",
"γ",
"ℎ",
"ι",
"ℐ",
"ℑ",
"ℒ",
"ℓ",
"ℳ",
"ν",
"ℕ",
"ο",
"𝒪",
"ℚ",
"ρ",
"ℜ",
"ℝ",
"σ",
"τ",
"β",
"υ",
"ℤ",
]
lint.dummy-variable-rgx = "^(Z|mass_numb|request|event|_.*)$"
lint.flake8-annotations.allow-star-arg-any = true
lint.flake8-annotations.ignore-fully-untyped = true
lint.flake8-annotations.suppress-dummy-args = true
lint.flake8-annotations.suppress-none-returning = true
lint.flake8-import-conventions.aliases."astropy.constants" = "const"
lint.flake8-import-conventions.aliases."astropy.units" = "u"
lint.flake8-import-conventions.aliases."matplotlib.pyplot" = "plt"
lint.flake8-import-conventions.aliases.matplotlib = "mpl"
lint.flake8-import-conventions.aliases.numpy = "np"
lint.flake8-import-conventions.aliases.pandas = "pd"
lint.flake8-import-conventions.banned-from = [
"astropy.units",
"matplotlib.pyplot",
"numpy",
"pytest",
"warnings",
]
lint.flake8-tidy-imports.ban-relative-imports = "all"
lint.flake8-tidy-imports.banned-api."typing.Callable".msg = "Deprecated alias. Change to collections.abc.Callable"
lint.flake8-tidy-imports.banned-api."typing.Collection".msg = "Deprecated alias. Change to collections.abc.Collection"
lint.flake8-tidy-imports.banned-api."typing.DefaultDict".msg = "Deprecated alias. Change to collections.defaultdict"
lint.flake8-tidy-imports.banned-api."typing.Dict".msg = "Deprecated alias. Change to dict"
lint.flake8-tidy-imports.banned-api."typing.Generator".msg = "Deprecated alias. Change to collections.abc.Generator"
lint.flake8-tidy-imports.banned-api."typing.Iterable".msg = "Deprecated alias. Change to collections.abc.Iterable"
lint.flake8-tidy-imports.banned-api."typing.Iterator".msg = "Deprecated alias. Change to collections.abc.Iterator"
lint.flake8-tidy-imports.banned-api."typing.List".msg = "Deprecated alias. Change to list"
lint.flake8-tidy-imports.banned-api."typing.Mapping".msg = "Deprecated alias. Change to collections.abc.mapping"
lint.flake8-tidy-imports.banned-api."typing.MutableMapping".msg = "Deprecated alias. Change to collections.abc.MutableMapping"
lint.flake8-tidy-imports.banned-api."typing.Sequence".msg = "Deprecated alias. Change to collections.abc.Sequence"
lint.flake8-tidy-imports.banned-api."typing.Set".msg = "Deprecated alias. Change to set"
lint.flake8-tidy-imports.banned-api."typing.Tuple".msg = "Deprecated alias. Change to tuple"
lint.flake8-tidy-imports.banned-api."typing.Type".msg = "Deprecated alias. Change to type"
lint.flake8-unused-arguments.ignore-variadic-names = true
lint.isort.known-first-party = [ "plasmapy" ]
lint.mccabe.max-complexity = 10
lint.pydocstyle.convention = "numpy"
[tool.codespell]
# Add false positives found by codespell to ignore-words-list
ignore-words-list = """
aas,
aci,
afe,
anc,
ans,
ba,
bale,
bu,
circularly,
ded,
dne,
ect,
explin,
fo,
fof,
gud,
hax,
hist,
hve,
ine,
inpt,
nd,
noo,
nwo,
ot,
recuse,
ro,
te,
tru,
ue,
ue,
windo"""
skip = "*.png,*cache*,*egg*,.git,.hypothesis,.idea,.nox,.tox,_build,*charged_particle*.ipynb,venv"
[tool.check-manifest]
ignore = [
"#*",
"*#",
"*~",
"*checkpoint*",
"*TEMP*",
".mailmap",
"docs/*build/**",
"src/plasmapy/_version.py",
"Untitled*",
]
[tool.ty]
# Ignore ty errors in certain notebooks until these can be fixed later
src.exclude = [
"docs/notebooks/analysis/fit_functions.ipynb",
"docs/notebooks/analysis/nullpoint.ipynb",
"docs/notebooks/analysis/swept_langmuir/find_floating_potential.ipynb",
"docs/notebooks/diagnostics/charged_particle_radiography_film_stacks.ipynb",
"docs/notebooks/diagnostics/charged_particle_radiography_particle_tracing.ipynb",
"docs/notebooks/diagnostics/charged_particle_radiography_particle_tracing_custom_source.ipynb",
"docs/notebooks/diagnostics/charged_particle_radiography_particle_tracing_wire_mesh.ipynb",
"docs/notebooks/diagnostics/thomson.ipynb",
"docs/notebooks/dispersion/dispersion_function.ipynb",
"docs/notebooks/dispersion/two_fluid_dispersion.ipynb",
"docs/notebooks/plasma/grids_cartesian.ipynb",
"docs/notebooks/plasma/grids_nonuniform.ipynb",
]
environment.python-platform = "all"
# Because astropy.units.Quantity[u.kg] is not recognized
rules.invalid-type-form = "ignore"
# Because astropy.constants.m_p, etc. are not recognized
rules.unresolved-attribute = "ignore"
analysis.allowed-unresolved-imports = [ "astropy.constants.**" ]
[tool.pytest] # https://docs.pytest.org/en/stable/reference/customize.html#pyproject-toml
addopts = [
"--pyargs",
"--durations=5",
"--durations-min=0.4",
"--tb=short",
"--numprocesses=auto",
"--dist=loadfile",
"--keep-duplicates",
"--ignore=src/plasmapy/_dev",
"--ignore=src/plasmapy/version.py",
]
doctest_optionflags = [
"NORMALIZE_WHITESPACE",
"ELLIPSIS",
"NUMBER",
"IGNORE_EXCEPTION_DETAIL",
]
empty_parameter_set_mark = "fail_at_collect"
filterwarnings = [
# To prevent the number of warnings issue during tests from ballooning,
# treat warnings as errors unless otherwise specified. Please raise a
# GitHub issue when ignoring a FutureWarning or DeprecationWarning,
# and label it with "needed for release".
"error",
# ubiquitous warning in particle tracker (see issue #2514)
"ignore:.*Quantities should go to zero at edges of grid.*:RuntimeWarning",
# occasional warning from downloader tests
"once:.*API rate limit exceeded.*:UserWarning",
# for numpy.reshape calls, newshape kwarg is deprecated; use shape instead or pass positionally
"once:.*MultiIndex.*:FutureWarning",
# warnings that have occurred sporadically but probably aren't important
"once:unclosed:ResourceWarning",
"once::pytest.PytestUnraisableExceptionWarning",
"once:XDG_CONFIG_HOME:astropy.utils.exceptions.AstropyUserWarning",
]
markers = [
"slow: marks tests as slow (deselect with '-m \"not slow\"')",
]
strict = true
testpaths = [ "tests", "src/plasmapy" ]
[tool.coverage]
run.branch = true
run.omit = [
"*/plasmapy/*version.py",
"*/plasmapy/_dev/*",
"*/plasmapy/tests/*",
]
run.source = [ "src" ]
report.exclude_lines = [
"@abstractmethod",
"coverage: ignore",
"if TYPE_CHECKING",
"if typing.TYPE_CHECKING",
"ImportError",
"ModuleNotFoundError",
"raise NotImplementedError",
]
[tool.towncrier]
name = "PlasmaPy"
package = "plasmapy"
directory = "changelog"
filename = "CHANGELOG.rst"
title_format = "{name} v{version} ({project_date})"
# Despite the name mismatch, we use `issue_format` for linking to PRs
issue_format = ":pr:`{issue}`"
wrap = true
# Changes to changelog tags need to be propagated into .github/workflows/changelog.yml
type = [
{ directory = "feature", name = "New Features", showcontent = true },
{ directory = "doc", name = "Documentation Improvements", showcontent = true },
{ directory = "breaking", name = "Backwards Incompatible Changes", showcontent = true },
{ directory = "removal", name = "Deprecations and Planned Removals", showcontent = true },
{ directory = "bugfix", name = "Bug Fixes", showcontent = true },
{ directory = "internal", name = "Internal Changes and Refactorings", showcontent = true },
{ directory = "test", name = "Updates to Software Testing", showcontent = true },
{ directory = "misc", name = "Miscellaneous Changes", showcontent = true },
]
[tool.build_docs]
source-dir = "docs"
build-dir = "docs/_build"
all_files = "1"
[tool.changelog-bot]
towncrier_changelog.enabled = true
towncrier_changelog.verify_pr_number = true
towncrier_changelog.changelog_skip_label = "no changelog entry needed"
towncrier_changelog.changelog_noop_label = "skip changelog checks"
towncrier_changelog.whatsnew_label = "needs changelog entry"
towncrier_changelog.whatsnew_pattern = "changelog\\/\\d+\\.[a-zA-Z]+(\\.\\d+)?\\.rst"