kompot/pyproject.toml at main · settylab/kompot · GitHub

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[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[tool.setuptools]
packages = {find = {exclude = ["tests*", "docs*", "examples*", "wheel_contents*"]}}
package-dir = {"" = "."}
package-data = {"kompot" = ["py.typed", "reporter/templates/*.html", "reporter/templates/css/*.css", "reporter/templates/js/*.js", "cli/templates/*.yaml"]}
include-package-data = false

[tool.pytest.ini_options]
testpaths = ["tests"]
# Coverage disabled by default for speed - enable with: pytest --cov=kompot
addopts = "-v --tb=short"
python_files = "test_*.py"
markers = [
    "slow: marks tests as slow (deselect with '-m not slow')",
    "integration: marks tests as integration tests (deselect with '-m not integration')",
    "memory: marks tests that measure memory usage",
]
# Filter warnings to keep output clean
filterwarnings = [
    "ignore::DeprecationWarning",
    "ignore::PendingDeprecationWarning",
    "ignore::FutureWarning",
    "ignore:Transforming to str index:anndata._core.aligned_df.ImplicitModificationWarning",
    "ignore:Series.__getitem__ treating keys as positions is deprecated:FutureWarning",
]

[tool.coverage.run]
omit = [
    "kompot/anndata/_legacy_*.py",
    "kompot/cli/__main__.py",
    "kompot/cli/main.py",
    "kompot/plot/stringdb.py",
    "kompot/plot/volcano.py",
    "kompot/plot/heatmap.py",
    "kompot/plot/__init__.py",
    "kompot/anndata/utils.py",
]

[tool.flake8]
max-line-length = 100
exclude = [".tox", "*.egg", "build", "temp"]
select = ["E", "W", "F"]
doctests = true
verbose = 2
ignore = ["E203", "W503"]

[project]
name = "kompot"
version = "0.7.0"
description = "Differential abundance and gene expression analysis using Mahalanobis distance with JAX backend"
readme = "README.md"
authors = [
    {name = "Dominik Otto", email = "dotto@fredhutch.org"},
]
requires-python = ">=3.10"
license = "GPL-3.0-or-later"
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
    "numpy>=1.20.0",
    "scipy>=1.7.0",
    "pandas>=1.3.0",
    "scikit-learn>=1.0.0",
    "jax>=0.3.0",
    "jaxlib>=0.3.0",
    "mellon>=1.7.1",
    "matplotlib>=3.5.0",
    "tqdm>=4.60.0",
    "anndata>=0.8.0",
    "pynndescent>=0.5.0",
    "python-igraph>=0.10.0",
    "psutil>=5.9.0",
    "filelock>=3.12.0",
    "pyyaml>=5.0.0",
]

[project.urls]
"Homepage" = "https://github.com/settylab/kompot"
"Documentation" = "https://kompot.readthedocs.io/"
"Bug Tracker" = "https://github.com/settylab/kompot/issues"

[project.scripts]
kompot = "kompot.cli:main"

[project.optional-dependencies]
docs = [
    "sphinx>=7.0.0,<8.3.0",
    "nbsphinx>=0.9.0",
    "furo>=2024.0.0",
    "sphinx-github-style>=1.2.0",
    "lxml[html_clean]",
    "IPython",
]
plot = [
    "scanpy>=1.9.0",
    "matplotlib>=3.5.0",
    "requests>=2.28.0",
    "IPython>=7.0.0",
    "json5~=0.9.14",
]
recommended = [
    "palantir>=1.0.0",
    "dask>=2024.4.0",
]
dask = [
    "dask>=2024.4.0",
]
dev = [
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0",
]
all = [
    "scanpy>=1.9.0",
    "matplotlib>=3.5.0",
    "requests>=2.28.0",
    "IPython>=7.0.0",
    "json5~=0.9.14",
    "palantir>=1.0.0",
    "dask>=2024.4.0",
]