gbanyan
150417ffcc
- Add matplotlib>=3.8.0 and seaborn>=0.13.0 to dependencies - Create visualizations.py with 3 plot functions and orchestrator - plot_score_distribution: histogram colored by confidence tier - plot_layer_contributions: bar chart of evidence layer coverage - plot_tier_breakdown: pie chart of tier distribution - Use Agg backend for headless/CLI safety - All plots saved at 300 DPI with proper figure cleanup - 6 tests covering file creation, edge cases, and return values
65 lines
1.4 KiB
TOML
65 lines
1.4 KiB
TOML
[build-system]
|
|
requires = ["setuptools>=61.0", "wheel"]
|
|
build-backend = "setuptools.build_meta"
|
|
|
|
[project]
|
|
name = "usher-pipeline"
|
|
version = "0.1.0"
|
|
description = "Reproducible pipeline for discovering under-studied cilia/Usher candidate genes"
|
|
requires-python = ">=3.11"
|
|
authors = [
|
|
{name = "Research Team"}
|
|
]
|
|
readme = "README.md"
|
|
license = {text = "MIT"}
|
|
classifiers = [
|
|
"Development Status :: 3 - Alpha",
|
|
"Intended Audience :: Science/Research",
|
|
"License :: OSI Approved :: MIT License",
|
|
"Programming Language :: Python :: 3.11",
|
|
"Programming Language :: Python :: 3.12",
|
|
"Topic :: Scientific/Engineering :: Bio-Informatics",
|
|
]
|
|
|
|
dependencies = [
|
|
"mygene>=3.2.0",
|
|
"requests>=2.31.0",
|
|
"requests-cache>=1.1.0",
|
|
"tenacity>=8.2.0",
|
|
"pydantic>=2.0",
|
|
"pydantic-yaml>=1.2.0",
|
|
"duckdb>=0.9.0",
|
|
"click>=8.1.0",
|
|
"polars>=0.19.0",
|
|
"pyarrow>=14.0.0",
|
|
"pyyaml>=6.0",
|
|
"httpx>=0.28",
|
|
"structlog>=25.0",
|
|
"biopython>=1.84",
|
|
"scipy>=1.14",
|
|
"matplotlib>=3.8.0",
|
|
"seaborn>=0.13.0",
|
|
]
|
|
|
|
[project.optional-dependencies]
|
|
dev = [
|
|
"pytest>=7.4.0",
|
|
"pytest-cov>=4.1.0",
|
|
]
|
|
expression = [
|
|
"cellxgene-census>=1.19",
|
|
]
|
|
|
|
[project.scripts]
|
|
usher-pipeline = "usher_pipeline.cli.main:cli"
|
|
|
|
[tool.setuptools]
|
|
packages = ["usher_pipeline"]
|
|
package-dir = {"" = "src"}
|
|
|
|
[tool.pytest.ini_options]
|
|
testpaths = ["tests"]
|
|
python_files = ["test_*.py"]
|
|
python_functions = ["test_*"]
|
|
addopts = "-v --strict-markers"
|