kinematic-morphospace/pyproject.toml at main · LydiaFrance/kinematic-morphospace · GitHub

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[build-system]
requires = ["setuptools>=61"]
build-backend = "setuptools.build_meta"
[project]
name = "kinematic-morphospace"
version = "0.1.0"
authors = [
  { name = "Lydia France", email = "lydia.france@biology.ox.ac.uk" },
]
description = "PCA-based decomposition of morphing shape changes in animal locomotion from motion capture data."
readme = "README.md"
requires-python = ">=3.10"
classifiers = [
  "Development Status :: 3 - Alpha",
  "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 :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Topic :: Scientific/Engineering",
]
keywords = [
  "PCA",
  "principal-component-analysis",
  "bird-flight",
  "morphing-wings",
  "biomechanics",
  "motion-capture",
  "kinematics",
]
dependencies = [
  "numpy>=1.24,<3",
  "pandas>=1.5,<3",
  "pyarrow>=15",
  "scikit-learn>=1.2,<2",
  "pyyaml>=6.0",
  "morphing_birds @ git+https://github.com/LydiaFrance/morphing_birds.git",
  "ipykernel>=7.2.0",
  "tqdm>=4.67.3",
  "coloredlogs>=15.0.1",
  "seaborn>=0.13.2",
  "ipympl>=0.10.0",
  "requests>=2.32.5",
  "kaleido>=1.0",
]

[project.optional-dependencies]
plot = [
  "matplotlib>=3.6",
  "seaborn>=0.12",
  "plotly>=5.0",
  "kaleido>=1.0",
  "ipympl>=0.9",
  "Pillow>=9.0",
]
notebook = [
  "kinematic-morphospace[plot]",
  "ipykernel",
  "jupyter",
  "notebook",
]
test = [
  "pytest>=6",
  "pytest-cov>=3",
  "coloredlogs",
]
preprocessing = [
  "scipy>=1.10",
  "mat73>=0.60",
  "h5py>=3.8",
  "ezc3d>=1.5",
]
docs = [
  "mkdocs>=1.6",
  "mkdocs-material>=9.5",
  "mkdocstrings[python]>=0.27",
  "mkdocs-section-index>=0.3",
]
dev = [
  "pytest>=6",
  "pytest-cov>=3",
  "pre-commit",
]

[project.urls]
Homepage = "https://github.com/LydiaFrance/kinematic-morphospace"
"Bug Tracker" = "https://github.com/LydiaFrance/kinematic-morphospace/issues"
Discussions = "https://github.com/LydiaFrance/kinematic-morphospace/discussions"
Changelog = "https://github.com/LydiaFrance/kinematic-morphospace/releases"

[tool.pytest.ini_options]
minversion = "6.0"
addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
xfail_strict = true
filterwarnings = [
  "error",
]
log_cli_level = "INFO"
testpaths = [
  "tests",
]

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

[tool.setuptools]
package-dir = {"" = "src"}
packages = ["kinematic_morphospace", "kinematic_morphospace.plotting", "kinematic_morphospace.preprocessing"]

[tool.ruff]
src = ["src"]
exclude = []
line-length = 88  # how long you want lines to be

[tool.ruff.format]
docstring-code-format = true  # code snippets in docstrings will be formatted

[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
  "RET",         # flake8-return
  "RUF",         # Ruff-specific
  "SIM",         # flake8-simplify
  "UP",          # pyupgrade
  "YTT",         # flake8-2020
  "EXE",         # flake8-executable
  "D",           # pydocstyle (Google convention — see below)
]
ignore = [
  "PLR",    # Design related pylint codes
  "ISC001", # Conflicts with formatter
]
unfixable = [
  "F401",   # Would remove unused imports
  "F841",   # Would remove unused variables
]
flake8-unused-arguments.ignore-variadic-names = true  # allow unused *args/**kwargs

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

[dependency-groups]
dev = [
    "coloredlogs>=15.0.1",
    "ruff>=0.15.8",
    "ty>=0.0.26",
]