pyproject.toml

[build-system]
requires = ['setuptools']
build-backend = 'setuptools.build_meta'

[project]
name = 'LoopStructural'
description = '3D geological modelling'
authors = [{ name = 'Lachlan Grose', email = 'lachlan.grose@monash.edu' }]
readme = 'README.md'
requires-python = '>=3.9'
keywords = [
    "earth sciences",
    "geology",
    "3-D modelling",
    "structural geology",
    "uncertainty",

]
license = { text = 'MIT' }
classifiers = [
    'Development Status :: 5 - Production/Stable',
    'Intended Audience :: Science/Research',
    'Topic :: Scientific/Engineering :: Information Analysis',
    'License :: OSI Approved :: MIT License',
    'Operating System :: Microsoft :: Windows',
    'Operating System :: POSIX',
    'Operating System :: MacOS',
    'Programming Language :: Python :: 3.8',
    'Programming Language :: Python :: 3.9',
    'Programming Language :: Python :: 3.10',
    'Programming Language :: Python :: 3.11',
    'Programming Language :: Python :: 3.12',
]
dependencies = [
    "loop-common>=0.1.0,<0.2.0",
    "loop-interpolation>=0.1.0,<0.2.0",
    "numpy>=1.18",
    "pandas",
    "scipy",
    "scikit-image",
    "scikit-learn",
]
dynamic = ['version']

[project.optional-dependencies]
all = ['loopstructural[inequalities]', 'tqdm']
visualisation = ["matplotlib", "pyvista", "loopstructuralvisualisation>=0.1.14"]
export = ["geoh5py", "pyevtk", "dill"]
jupyter = ["pyvista[all]"]
inequalities = ["loopsolver"]
tests = ['pytest']
dev = ['ruff']
docs = [
    "pyvista[all]",
    "pydata-sphinx-theme",
    "meshio",
    "loopstructuralvisualisation[all]",
    "networkx",
    "scikit-learn",
    "scikit-image",
    "sphinx",
    "sphinx-gallery",
    "geoh5py",
    "geopandas",
    "pillow>=10.4.0",
    "sphinxcontrib-bibtex",
    "myst-parser",
    "sphinx-design",
]
[project.urls]
Documentation = 'https://Loop3d.org/LoopStructural/'
"Bug Tracker" = 'https://github.com/loop3d/loopstructural/issues'
"Source Code" = 'https://github.com/loop3d/loopstructural'

[tool.setuptools.dynamic]
version = { attr = 'LoopStructural.version.__version__' }

[tool.setuptools.packages.find]
include = ['LoopStructural', 'LoopStructural.*']

[tool.setuptools.package-data]
LoopStructural = [
    "datasets/data/fault_trace/*",
    "datasets/data/*.csv",
    "datasets/data/*.txt",
    "datasets/data/geological_map_data/*.csv",
    "datasets/data/geological_map_data/*.txt",
]

[tool.uv.workspace]
members = ["packages/*"]

[tool.uv.sources]
loop-common = { workspace = true }
loop-interpolation = { workspace = true }

[tool.pytest.ini_options]
addopts = "--import-mode=importlib"
testpaths = ["tests"]

[tool.isort]
profile = 'black'
line_length = 100
# Sort by name, don't cluster "from" vs "import"
force_sort_within_sections = true
# Combines "as" imports on the same line
combine_as_imports = true

[tool.black]
line-length = 100
skip-string-normalization = true
target-version = ['py39']
exclude = '\.eggs|\.git|\.mypy_cache|\.tox|\.venv|_build|buck-out|build|dist|node_modules'

[tool.blackdoc]
# From https://numpydoc.readthedocs.io/en/latest/format.html
# Extended discussion: https://github.com/pyvista/pyvista/pull/4129
# The length of docstring lines should be kept to 75 characters to facilitate
# reading the docstrings in text terminals.
line-length = 75

[tool.build_sphinx]
source-dir = 'doc'
build-dir = './doc/build'
all_files = 1

[tool.upload_sphinx]
upload-dir = 'doc/build/html'

[tool.pydocstyle]
match = '(?!coverage).*.py'
convention = "numpy"
add-ignore = ["D404"]

[tool.codespell]
skip = '*.pyc,*.txt,*.gif,*.png,*.jpg,*.ply,*.vtk,*.vti,*.vtu,*.js,*.html,*.doctree,*.ttf,*.woff,*.woff2,*.eot,*.mp4,*.inv,*.pickle,*.ipynb,flycheck*,./.git/*,./.hypothesis/*,*.yml,doc/_build/*,./doc/images/*,./dist/*,*~,.hypothesis*,./doc/examples/*,*.mypy_cache/*,*cover,./tests/tinypages/_build/*,*/_autosummary/*'
quiet-level = 3


[tool.ruff]
exclude = ['.git', 'pycache__', 'build', 'dist', 'doc/examples', 'doc/_build']
line-length = 100
indent-width = 4
target-version = 'py39'

[tool.ruff.lint]
external = ["E131", "D102", "D105"]

ignore = [
    # whitespace before ':'
    "E203",
    # line break before binary operator
    # "W503",
    # line length too long
    "E501",
    # do not assign a lambda expression, use a def
    "E731",
    # too many leading '#' for block comment
    "E266",
    # ambiguous variable name
    "E741",
    # module level import not at top of file
    "E402",
    # Quotes (temporary)
    "Q0",
    # we already check black
    # "BLK100",
    # 'from module import *' used; unable to detect undefined names
    "F403",
    # invalid module name: the PyPI project name (LoopStructural) is
    # intentionally CamelCase and shared by the top-level package/modules
    "N999",
]
fixable = ["ALL"]
unfixable = []
extend-select = [
    "B006",
    "B007",
    "B008",
    "B010",
    "C4",
    "D",
    "ANN",
    "F",
    "NPY",
    "PGH004",
    "RSE",
    "RUF100",
    "FA",
]

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

[tool.ruff.lint.flake8-comprehensions]
allow-dict-calls-with-keyword-arguments = true
[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]
# D (docstrings) / ANN (type hints) are enforced going forward per Stage 1c
# of ROADMAP.md; existing files are grandfathered here rather than
# retroactively fixed in bulk. Any *new* file under LoopStructural/ is not
# in this list and is enforced immediately. Remove an entry once that
# file's public surface has been brought up to standard.
# Stage 2 keeps lint hardening scoped to LoopStructural/; extracted workspace
# packages are currently grandfathered for D/ANN and will get dedicated lint
# policy in a later stage.
"packages/loop_common/src/**/*.py" = ["D", "ANN"]
"packages/loop_interpolation/src/**/*.py" = ["D", "ANN"]
"LoopStructural/__init__.py" = ["D", "ANN"]
"LoopStructural/datasets/__init__.py" = ["D", "ANN"]
"LoopStructural/datasets/_base.py" = ["D", "ANN"]
"LoopStructural/datasets/_example_models.py" = ["D", "ANN"]
"LoopStructural/datatypes/__init__.py" = ["D", "ANN"]
"LoopStructural/export/exporters.py" = ["D", "ANN"]
"LoopStructural/export/file_formats.py" = ["D", "ANN"]
"LoopStructural/export/geoh5.py" = ["D", "ANN"]
"LoopStructural/export/gocad.py" = ["D", "ANN"]
"LoopStructural/export/omf_wrapper.py" = ["D", "ANN"]
"LoopStructural/geometry/__init__.py" = ["D", "ANN"]
"LoopStructural/geometry/_bounding_box.py" = ["D", "ANN"]
"LoopStructural/geometry/_structured_grid.py" = ["D", "ANN"]
"LoopStructural/interpolators/__init__.py" = ["D", "ANN"]
"LoopStructural/interpolators/_api.py" = ["D", "ANN"]
"LoopStructural/interpolators/_builders.py" = ["D", "ANN"]
"LoopStructural/interpolators/_constant_norm.py" = ["D", "ANN"]
"LoopStructural/interpolators/_cython/__init__.py" = ["D", "ANN"]
"LoopStructural/interpolators/_discrete_fold_interpolator.py" = ["D", "ANN"]
"LoopStructural/interpolators/_discrete_interpolator.py" = ["D", "ANN"]
"LoopStructural/interpolators/_finite_difference_interpolator.py" = ["D", "ANN"]
"LoopStructural/interpolators/_geological_interpolator.py" = ["D", "ANN"]
"LoopStructural/interpolators/_interpolator_builder.py" = ["D", "ANN"]
"LoopStructural/interpolators/_interpolator_factory.py" = ["D", "ANN"]
"LoopStructural/interpolators/_interpolatortype.py" = ["D", "ANN"]
"LoopStructural/interpolators/_operator.py" = ["D", "ANN"]
"LoopStructural/interpolators/_p1interpolator.py" = ["D", "ANN"]
"LoopStructural/interpolators/_p2interpolator.py" = ["D", "ANN"]
"LoopStructural/interpolators/_surfe_wrapper.py" = ["D", "ANN"]
"LoopStructural/modelling/__init__.py" = ["D", "ANN"]
"LoopStructural/modelling/core/__init__.py" = ["D", "ANN"]
"LoopStructural/modelling/core/_feature_registry.py" = ["D", "ANN"]
"LoopStructural/modelling/core/fault_topology.py" = ["D", "ANN"]
"LoopStructural/modelling/core/geological_model.py" = ["D", "ANN"]
"LoopStructural/modelling/core/stratigraphic_column.py" = ["D", "ANN"]
"LoopStructural/modelling/features/__init__.py" = ["D", "ANN"]
"LoopStructural/modelling/features/_analytical_feature.py" = ["D", "ANN"]
"LoopStructural/modelling/features/_base_geological_feature.py" = ["D", "ANN"]
"LoopStructural/modelling/features/_cross_product_geological_feature.py" = ["D", "ANN"]
"LoopStructural/modelling/features/_feature_converters.py" = ["D", "ANN"]
"LoopStructural/modelling/features/_geological_feature.py" = ["D", "ANN"]
"LoopStructural/modelling/features/_lambda_geological_feature.py" = ["D", "ANN"]
"LoopStructural/modelling/features/_projected_vector_feature.py" = ["D", "ANN"]
"LoopStructural/modelling/features/_region.py" = ["D", "ANN"]
"LoopStructural/modelling/features/_structural_frame.py" = ["D", "ANN"]
"LoopStructural/modelling/features/_unconformity_feature.py" = ["D", "ANN"]
"LoopStructural/modelling/features/builders/__init__.py" = ["D", "ANN"]
"LoopStructural/modelling/features/builders/_analytical_fold_builder.py" = ["D", "ANN"]
"LoopStructural/modelling/features/builders/_base_builder.py" = ["D", "ANN"]
"LoopStructural/modelling/features/builders/_fault_builder.py" = ["D", "ANN"]
"LoopStructural/modelling/features/builders/_folded_feature_builder.py" = ["D", "ANN"]
"LoopStructural/modelling/features/builders/_geological_feature_builder.py" = ["D", "ANN"]
"LoopStructural/modelling/features/builders/_structural_frame_builder.py" = ["D", "ANN"]
"LoopStructural/modelling/features/fault/__init__.py" = ["D", "ANN"]
"LoopStructural/modelling/features/fault/_fault_function.py" = ["D", "ANN"]
"LoopStructural/modelling/features/fault/_fault_function_feature.py" = ["D", "ANN"]
"LoopStructural/modelling/features/fault/_fault_segment.py" = ["D", "ANN"]
"LoopStructural/modelling/features/fold/__init__.py" = ["D", "ANN"]
"LoopStructural/modelling/features/fold/_fold.py" = ["D", "ANN"]
"LoopStructural/modelling/features/fold/_fold_rotation_angle_feature.py" = ["D", "ANN"]
"LoopStructural/modelling/features/fold/_foldframe.py" = ["D", "ANN"]
"LoopStructural/modelling/features/fold/_svariogram.py" = ["D", "ANN"]
"LoopStructural/modelling/features/fold/fold_function/__init__.py" = ["D", "ANN"]
"LoopStructural/modelling/features/fold/fold_function/_base_fold_rotation_angle.py" = ["D", "ANN"]
"LoopStructural/modelling/features/fold/fold_function/_fourier_series_fold_rotation_angle.py" = ["D", "ANN"]
"LoopStructural/modelling/features/fold/fold_function/_lambda_fold_rotation_angle.py" = ["D", "ANN"]
"LoopStructural/modelling/features/fold/fold_function/_trigo_fold_rotation_angle.py" = ["D", "ANN"]
"LoopStructural/modelling/input/__init__.py" = ["D", "ANN"]
"LoopStructural/modelling/input/fault_network.py" = ["D", "ANN"]
"LoopStructural/modelling/input/map2loop_processor.py" = ["D", "ANN"]
"LoopStructural/modelling/input/process_data.py" = ["D", "ANN"]
"LoopStructural/modelling/input/project_file.py" = ["D", "ANN"]
"LoopStructural/modelling/intrusions/__init__.py" = ["D", "ANN"]
"LoopStructural/modelling/intrusions/geom_conceptual_models.py" = ["D", "ANN"]
"LoopStructural/modelling/intrusions/geometric_scaling_functions.py" = ["D", "ANN"]
"LoopStructural/modelling/intrusions/intrusion_builder.py" = ["D", "ANN"]
"LoopStructural/modelling/intrusions/intrusion_feature.py" = ["D", "ANN"]
"LoopStructural/modelling/intrusions/intrusion_frame.py" = ["D", "ANN"]
"LoopStructural/modelling/intrusions/intrusion_frame_builder.py" = ["D", "ANN"]
"LoopStructural/modelling/intrusions/intrusion_support_functions.py" = ["D", "ANN"]
"LoopStructural/utils/__init__.py" = ["D", "ANN"]
"LoopStructural/utils/_api_registry.py" = ["D", "ANN"]
"LoopStructural/utils/_log_sinks.py" = ["D", "ANN"]
"LoopStructural/utils/_log_timing.py" = ["D", "ANN"]
"LoopStructural/utils/_surface.py" = ["D", "ANN"]
"LoopStructural/utils/_transformation.py" = ["D", "ANN"]
"LoopStructural/utils/colours.py" = ["D", "ANN"]
"LoopStructural/utils/config.py" = ["D", "ANN"]
"LoopStructural/utils/dtm_creator.py" = ["D", "ANN"]
"LoopStructural/utils/exceptions.py" = ["D", "ANN"]
"LoopStructural/utils/features.py" = ["D", "ANN"]
"LoopStructural/utils/helper.py" = ["D", "ANN"]
"LoopStructural/utils/json_encoder.py" = ["D", "ANN"]
"LoopStructural/utils/linalg.py" = ["D", "ANN"]
"LoopStructural/utils/logging.py" = ["D", "ANN"]
"LoopStructural/utils/maths.py" = ["D", "ANN"]
"LoopStructural/utils/observer.py" = ["D", "ANN"]
"LoopStructural/utils/regions.py" = ["D", "ANN"]
"LoopStructural/utils/typing.py" = ["D", "ANN"]
"LoopStructural/utils/utils.py" = ["D", "ANN"]
"LoopStructural/version.py" = ["D", "ANN"]
"LoopStructural/visualisation/__init__.py" = ["D", "ANN"]
# D/ANN are not enforced outside the library package.
"tests/*" = ["D", "ANN"]
"examples/*" = ["D", "ANN"]
"docs/*" = ["D", "ANN"]
"setup.py" = ["D", "ANN"]
"packages/loop_common/tests/*" = ["D", "ANN"]
"packages/loop_interpolation/tests/*" = ["D", "ANN"]