pyproject.toml

[build-system]
requires = ["setuptools", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "TopoBenchmarkX"
dynamic = ["version"]
authors = [
    {name = "PyT-Team Authors", email = "tlscabinet@gmail.com"}
]
readme = "README.md"
description = "Topological Deep Learning"
license = {file = "LICENSE.txt"}
classifiers = [
    "License :: OSI Approved :: MIT License",
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Mathematics",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Natural Language :: English",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11"
]
requires-python = ">= 3.10"
dependencies=[
    "tqdm",
    "numpy",
    "scipy",
    "requests",
    "scikit-learn",
    "matplotlib",
    "networkx",
    "pandas",
    "decorator",
    "hypernetx < 2.0.0",
    "trimesh",
    "spharapy",
    "hydra-core==1.3.2",
    "hydra-colorlog==1.2.0",
    "hydra-optuna-sweeper==1.2.0",
    "wandb==0.16.4",
    "einops==0.7.0",
    "tabulate",
    "ipykernel",
    "notebook",
    "jupyterlab",
    "rich",
    "rootutils",
    "toponetx @ git+https://github.com/pyt-team/TopoNetX.git",
    "topomodelx @ git+https://github.com/pyt-team/TopoModelX.git",
    "topoembedx @ git+https://github.com/pyt-team/TopoEmbedX.git",
    "lightning",
]

[project.optional-dependencies]
doc = [
    "jupyter",
    "nbsphinx",
    "nbsphinx_link",
    "numpydoc",
    "sphinx",
    "sphinx_gallery",
    "pydata-sphinx-theme"
]
lint = [
    "pre-commit",
    "ruff"
]
test = [
    "pytest",
    "pytest-cov",
    "coverage",
    "jupyter",
    "mypy",
    "pytest-mock"
]

dev = ["TopoBenchmarkX[test, lint]"]
all = ["TopoBenchmarkX[dev, doc]"]

[project.urls]
homepage="https://github.com/pyt-team/TopoBenchmarkX"
repository="https://github.com/pyt-team/TopoBenchmarkX"

[tool.black]
line-length = 79  # PEP 8 standard for maximum line length
target-version = ['py310']

[tool.docformatter]
wrap-summaries = 79
wrap-descriptions = 79

[tool.ruff]
target-version = "py310"
#extend-include = ["*.ipynb"]
extend-exclude = ["test", "tutorials", "notebooks"]
line-length = 79  # PEP 8 standard for maximum line length

[tool.ruff.format]
docstring-code-format = false

[tool.ruff.lint]
select = [
    "F", # pyflakes errors
    "E", # code style
    "W", # warnings
    "I", # import order
    "UP", # pyupgrade rules
    "B", # bugbear rules
    "PIE", # pie rules
    "Q", # quote rules
    "RET", # return rules
    "SIM", # code simplifications
    "NPY", # numpy rules
    "PERF", # performance rules
    "RUF", # miscellaneous rules
]
fixable = ["ALL"]
ignore = [
    "E501",     # line too long
    "RET504",   # Unnecessary assignment before return
    "RET505",   # Unnecessary `elif` after `return` statement
    "NPY002",   # Replace legacy `np.random.seed` call with `np.random.Generator`
    "UP038",    # Use `X | Y` in `isinstance` call instead of `(X, Y)` -- not compatible with python 3.9 (even with __future__ import)
    "W293",     # Does not allow to have empty lines in multiline comments
    "PERF203",  # [TODO: fix all such issues] `try`-`except` within a loop incurs performance overhead
]

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

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F403"]

[tool.setuptools.dynamic]
version = {attr = "topobenchmarkx.__version__"}

[tool.setuptools.packages.find]
include = [
    "topobenchmarkx",
    "topobenchmarkx.*"
]

[tool.mypy]
warn_redundant_casts = true
warn_unused_ignores = true
show_error_codes = true
disable_error_code = ["import-untyped"]
plugins = "numpy.typing.mypy_plugin"

[[tool.mypy.overrides]]
module = [
    "torch_cluster.*","networkx.*","scipy.spatial","scipy.sparse","toponetx.classes.simplicial_complex"
]
ignore_missing_imports = true

[tool.pytest.ini_options]
addopts = "--capture=no"
pythonpath = [
  "."
]

[tool.numpydoc_validation]
checks = [
    "all",
    "GL01",
    "ES01",
    "EX01",
    "SA01"
]
exclude = [
    '\.undocumented_method$',
    '\.__init__$',
    '\.__repr__$',
]