pyproject.toml

[build-system]
requires = ["setuptools>=64"]
build-backend = "setuptools.build_meta"

[project]
name = "invert4geom"
authors = [
  { name = "Matt Tankersley", email = "matt.d.tankersley@gmail.com" },
]
description = "Constrained gravity inversion to recover the geometry of a density contrast."
requires-python = ">=3.9"
classifiers = [
  "Development Status :: 1 - Planning",
  "Intended Audience :: Science/Research",
  "Intended Audience :: Developers",
  "License :: OSI Approved :: MIT License",
  "Operating System :: OS Independent",
  "Programming Language :: Python",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.9",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Topic :: Scientific/Engineering",
  "Typing :: Typed",
]
readme = "README.md"
version = "0.10.0"
license = {file = "LICENSE"}

keywords = ["inversion", "gravity", "geometry", "density", "Moho", "sediment", "geophysics", "geology", "geoscience"]

dependencies = [
###
# core
###
  "numpy",
  "pandas",
  "xarray",
  "verde>=1.8.0",
  "rioxarray",
  "pykdtree",
  "xrft>=1.0",
  "harmonica>=0.6.0",
  "polartoolkit",
  "numba",
  "scipy<1.14", # issue with UQpy import
  "numba_progress",
  "tqdm",
  "pygmt",
  "dask",
  "deprecation",
  "pooch",
  "scikit-learn",
###
# optimization
###
  "optuna>=3.1.0", # need JournalStorage
  "optuna-integration",
  "botorch>=0.8.1", # need logie_candidates_func
  "joblib",
  "psutil",
###
# visualization
###
  "pyvista",
  "trame",
  "ipywidgets",
  "matplotlib",
  "seaborn",
  "ipython",
  "plotly",
###
# uncertainty
###
  "UQpy",
]

[project.optional-dependencies]
synth = [
  "xesmf",
]
test = [
  "pytest >=6",
  "pytest-cov >=3",
  "invert4geom",
]
docs = [
  "sphinx>=4.0",
  "myst_parser",
  "sphinx_copybutton",
  "sphinx_autoapi",
  "sphinx_autodoc_typehints",
  "sphinx-book-theme>=0.3",
  "sphinx_design",
  "nbsphinx",
  "nbconvert",
  "sphinxcontrib-bibtex",
]
dev = [
  "invert4geom[test,docs, synth]",
  "ruff",
  "nox",
  "pre-commit",
  "pylint>=3.2",
  "python-semantic-release >=8",
  "ipykernel",
  "jupyterlab",
  "mypy",
]
all = [
  "invert4geom[test,dev,docs,synth]",
]

[project.urls]
Homepage = "https://github.com/mdtanker/invert4geom"
Documentation = "https://invert4geom.readthedocs.io/"
"Bug Tracker" = "https://github.com/mdtanker/invert4geom/issues"
Discussions = "https://github.com/mdtanker/invert4geom/discussions"
Changelog = "https://invert4geom.readthedocs.io/en/latest/changelog.html"

[tool.coverage]
run.source = ["invert4geom"]
port.exclude_lines = [
  'pragma: no cover',
  '\.\.\.',
  'if typing.TYPE_CHECKING:',
]

[tool.pytest.ini_options]
minversion = "6.0"
addopts = [
  "-rA",
  "--showlocals",
  "--strict-markers",
  "--strict-config",
  "--cov", "--cov-report", "term-missing",
  ]
xfail_strict = true
filterwarnings = [
  "error",
  "ignore::DeprecationWarning",
  "ignore::PendingDeprecationWarning",
  "ignore::FutureWarning",
]
log_cli_level = "INFO"
testpaths = [
  "tests",
]
markers = [
    "use_numba: mark test functions that call Numba jitted functions",
]

[tool.mypy]
files = ["src"]
python_version = "3.9"
warn_unused_configs = true
strict = true
enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
warn_unreachable = true
disallow_untyped_defs = false
disallow_incomplete_defs = false
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = "invert4geom.*"
disallow_untyped_defs = true
disallow_incomplete_defs = true


[tool.ruff]
lint.select = [
  "E", "F", "W", # flake8
  "B",           # flake8-bugbear
  "I",           # isort
  "ARG",         # flake8-unused-arguments
  "C4",          # flake8-comprehensions
  "EM",          # flake8-errmsg
  "ICN",         # flake8-import-conventions
  "ISC",         # flake8-implicit-str-concat
  "G",           # flake8-logging-format
  "PGH",         # pygrep-hooks
  "PIE",         # flake8-pie
  "PL",          # pylint
  "PT",          # flake8-pytest-style
  "PTH",         # flake8-use-pathlib
  "RET",         # flake8-return
  "RUF",         # Ruff-specific
  "SIM",         # flake8-simplify
  "T20",         # flake8-print
  "UP",          # pyupgrade
  "YTT",         # flake8-2020
  "EXE",         # flake8-executable
  "NPY",         # NumPy specific rules
  "PD",          # pandas-vet
]
lint.ignore = [
  "PLR",    # Design related pylint codes
  "G004",   # Logging with f-strings
  "PD901",  # Bad variable name warning
  "PD003", # Changes .isna to .isnull
  "PD004", # Changes .notna to .notnull
  "PD011", # Changes .values() to .to_numpy()
  "ISC001", # Implicit string concatenation
]
src = ["src"]
lint.unfixable = [
  "T20",  # Removes print statements
  "F841", # Removes unused variables
  "PD003", # Changes .isna to .isnull
  "PD004", # Changes .notna to .notnull
  "PD011", # Changes .values() to .to_numpy()
]
exclude = ["docs/index.md", "CHANGELOG.md"]
line-length = 88 # Set the maximum line length to 88.
lint.flake8-unused-arguments.ignore-variadic-names = true
lint.isort.required-imports = ["from __future__ import annotations"]
# Uncomment if using a _compat.typing backport
# typing-modules = ["invert4geom._compat.typing"]
extend-include = ["*.ipynb"]
[tool.ruff.lint.per-file-ignores]
"tests/**" = ["T20"]
"noxfile.py" = ["T20"]
"*.ipynb" = ["E402", "B018", "T201", "C408", "E712",]

[tool.ruff.lint.flake8-pytest-style]
mark-parentheses = true

[tool.pylint]
py-version = "3.9"
# ignore-patterns = [".*.md",]
reports.output-format = "colorized"
similarities.ignore-imports = "yes"
similarities.min-similarity-lines = 5
messages_control.disable = [
  "design",
  "fixme",
  "line-too-long",
  "missing-module-docstring",
  "wrong-import-position",
  "cyclic-import",
]

[tool.semantic_release]
version_variables = ["src/invert4geom/__init__.py:__version__"]
version_toml = ["pyproject.toml:project.version"]
major_on_zero = false
build_command = """
    python -m pip install build
    python -m build .
"""
commit_parser = "angular"

[tool.semantic_release.branches.main]
match = "main"
prerelease = false

[tool.semantic_release.branches.notmain]
match = "(?!main)"
prerelease = true

[tool.semantic_release.changelog]
template_dir = "templates"

[tool.semantic_release.changelog.environment]
trim_blocks = true

[tool.semantic_release.commit_parser_options]
allowed_tags = [
    "build",    # Changes that affect the build system or external dependencies
    "chore",    # Changes to the build process or auxiliary tools and libraries such as documentation generation
    "ci",       # CI related changes
    "docs",     # Documentation only changes
    "feat",     # A new feature
    "fix",      # A bug fix
    "perf",     # A code change that improves performance
    "style",    # Changes that do not affect the meaning of the code (white-space, formatting, missing semi-colons, etc)
    "refactor", # A code change that neither fixes a bug nor adds a feature
    "test",     # Adding missing or correcting existing tests
]
# including BREAKING CHANGE: in the commit message will trigger a major release
minor_tags = ["feat"] # tags which result in minor releases
patch_tags = ["fix", "perf"] # tags which result in patch releases