pyproject.toml

[build-system]
requires = ["setuptools>=42", "wheel", "setuptools-git-versioning"]
build-backend = "setuptools.build_meta"

[project]
name = "reaction-network"
description = "Reaction-network is a Python package for synthesis planning and predicting chemical reaction pathways in inorganic materials synthesis."
readme = "README.md"
keywords = [
    "reaction",
    "network",
    "computational",
    "graph",
    "inorganic",
    "materials",
    "retrosynthesis",
    "synthesis",
    "planning",
]
license = { text = "modified BSD" }
authors = [{ name = "Matthew McDermott", email = "mcdermott@lbl.gov" }]
dynamic = ["version"]
classifiers = [
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: BSD License",
    "Operating System :: OS Independent",
    "Topic :: Scientific/Engineering :: Information Analysis",
    "Topic :: Scientific/Engineering :: Physics",
    "Topic :: Scientific/Engineering :: Chemistry",
    "Topic :: Software Development :: Libraries :: Python Modules",
]
requires-python = ">=3.9"
dependencies = [
    "pymatgen>=2023.11.12",
    "numba>=0.58.1",
    "jobflow>=0.1.15",
    "ray>=2.9.0",
    "rustworkx>=0.13.2",
]

[project.optional-dependencies]
docs = [
    "autodoc_pydantic==2.0.1",
    "furo==2023.9.10",
    "ipython==8.16.1",
    "myst_parser==2.0.0",
    "nbsphinx==0.9.3",
    "sphinx-copybutton==0.5.2",
    "sphinx==7.2.6",
]
tests = [
    "mp-api==0.39.4",  # required for testing get_entry_set job
    "pytest==7.4.3",
    "pytest-cov==4.1.0",
    "pytest-xdist==3.5.0",
]
strict = [
    "pymatgen==2023.12.18",
    "numba==0.58.1",
    "jobflow==0.1.15",
    "ray==2.9.0",
    "rustworkx==0.13.2",
]

[project.urls]
homepage = "https://materialsproject.github.io/reaction-network/"
documentation = "https://materialsproject.github.io/reaction-network/"
repository = "https://github.com/materialsproject/reaction-network"
changelog = "https://github.com/materialsproject/reaction-network/blob/main/docs/CHANGELOG.md"

[tool.coverage.run]
include = ["src/*"]
parallel = true
branch = false

[tool.coverage.paths]
source = ["src/"]

[tool.coverage.report]
show_missing = true
skip_covered = true
exclude_also = [
    '\#\s*pragma: no cover',
    '^\s*assert False(,|$)',
    'if typing.TYPE_CHECKING:',
    '^\s*@overload( |$)',
    'if TYPE_CHECKING:',
]
omit = [
    "src/rxn_network/data/nist/generate_janaf_data.py",
    "src/rxn_network/network/visualize.py",
    "src/rxn_network/pathways/plotting.py",
]

[tool.ruff]
target-version = "py39"
line-length = 120

[tool.ruff.lint]
select = [
    "B",      # flake8-bugbear
    "C4",     # flake8-comprehensions
    "D",      # pydocstyle
    "E",      # pycodestyle error
    "EXE",    # flake8-executable
    "F",      # pyflakes
    "FA",     # flake8-future-annotations
    "FBT003", # boolean-positional-value-in-call
    "FLY",    # flynt
    "I",      # isort
    "ICN",    # flake8-import-conventions
    "ISC",    # flake8-implicit-str-concat
    "PD",     # pandas-vet
    "PERF",   # perflint
    "PIE",    # flake8-pie
    "PL",     # pylint
    "PT",     # flake8-pytest-style
    "PYI",    # flakes8-pyi
    "Q",      # flake8-quotes
    "RET",    # flake8-return
    "RSE",    # flake8-raise
    "RUF",    # Ruff-specific rules
    "SIM",    # flake8-simplify
    "SLOT",   # flake8-slots
    "TCH",    # flake8-type-checking
    "TID",    # flake8-tidy-imports
    "UP",     # pyupgrade
    "W",      # pycodestyle warning
    "YTT",    # flake8-2020
]
ignore = [
    "B023",    # Function definition does not bind loop variable
    "B028",    # No explicit stacklevel keyword argument found
    "B904",    # Within an except clause, raise exceptions with ...
    "C408",    # unnecessary-collection-call
    "D105",    # Missing docstring in magic method
    "D205",    # 1 blank line required between summary line and description
    "D212",    # Multi-line docstring summary should start at the first line
    "PD011",   # pandas-use-of-dot-values
    "PD901",   # pandas-df-variable-name
    "PERF203", # try-except-in-loop
    "PERF401", # manual-list-comprehension (TODO fix these or wait for autofix)
    "PLR",     # pylint-refactor
    "PLW2901", # Outer for loop variable overwritten by inner assignment target
    "PT004",   # pytest-missing-fixture-name-underscore
    "PT006",   # pytest-parametrize-names-wrong-type
    "PT013",   # pytest-incorrect-pytest-import
    "PYI024",  # collections-named-tuple (TODO should maybe fix these)
    "RUF012",  # Disable checks for mutable class args. This is a non-problem.
    "RUF013",  # implicit-optional
    "SIM105",  # Use contextlib.suppress(OSError) instead of try-except-pass
]
pydocstyle.convention = "google"

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]
"**/tests/*" = ["D"]
"**/schemas/*" = ["FA", "TCH", "UP007"]
"**/schema.py" = ["FA", "TCH", "UP007"]

[tool.mypy]
ignore_missing_imports = true
namespace_packages = true
explicit_package_bases = true
no_implicit_optional = false
follow_imports = "skip"
disable_error_code = "annotation-unchecked"

[tool.pytest]
addopts = "--durations=10"

[tool.pytest.ini_options]
addopts = "-n auto"

[tool.setuptools.package-data]
rxn_network = ["py.typed"]

[tool.setuptools-git-versioning]
enabled = true