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pyproject.toml
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pyproject.toml
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[build-system]
build-backend = "setuptools.build_meta"
requires = [ "setuptools>=64", "setuptools-scm>=8" ]
[project]
name = "hetnet-analysis"
description = "Demonstrating Pythonic uv usage with dynamic versioning."
readme = "README.md"
requires-python = ">=3.11"
classifiers = [
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
]
dynamic = [ "version" ]
dependencies = [
"black>=24.10",
"duckdb>=1.1.3",
"hetmatpy>=0.1",
"ipywidgets>=8.1.5",
"isort>=5.13.2",
"joblib>=1.4.2",
"jupyterlab>=4.3",
"jupyterlab-code-formatter>=3.0.2",
"jupytext>=1.16.4",
"lancedb>=0.15",
"neo4j>=5.26",
"requests>=2.32.3",
]
[tool.setuptools_scm]
root = "."
[tool.ruff]
target-version = "py38"
line-length = 88
fix = true
lint.select = [
# flake8-builtins
"A",
# flake8-annotations
"ANN",
# flake8-comprehensions
"C4",
# mccabe
"C90",
# pycodestyle
"E",
# pyflakes
"F",
# isort
"I",
# pylint
"PL",
# ruff
"RUF",
# flake8-simplify
"SIM",
"W",
]
# Ignore `E402` and `F401` (unused imports) in all `__init__.py` files
lint.per-file-ignores."__init__.py" = [ "F401" ]
# ignore typing rules for tests
lint.per-file-ignores."tests/*" = [ "ANN201", "PLR0913", "PLR2004" ]
[tool.jupytext]
formats = "ipynb,py:light"
[tool.uv]
dev-dependencies = [
"setuptools-scm>=8.1.0",
"poethepoet>=0.29",
"pre-commit>=4.0.1",
"pytest>=8.3.3",
]
[tool.poe.tasks]
# install the project for development purposes
setup.shell = """
uv pip install '.[dev]'
"""
# run testing on development source
test.shell = """
uv run pre-commit run -a
uv run pytest
"""
# run the gene metapath extraction
run_bioproc_gene_metapath_test.shell = """
uv run python src/bioprocess_metapath_to_gene_pval_and_dwpc/gather_subset_data_metapath_BPpGdAdG.py
"""
# run path count table extraction
run_pathcount_extract.shell = """
cd src/connectivity_search_PathCount_table
uv run python get_table.py
"""