cbicall/pyproject.toml at main · CNAG-Biomedical-Informatics/cbicall · GitHub

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[build-system]
requires = ["hatchling>=1.27"]
build-backend = "hatchling.build"

[project]
name = "cbicall"
dynamic = ["version"]
description = "Configuration-driven framework for reproducible variant calling"
readme = "README.md"
requires-python = ">=3.8"
license = "GPL-3.0-only"
license-files = ["LICENSE"]
authors = [
  { name = "Manuel Rueda", email = "manuel.rueda@cnag.eu" },
]
keywords = [
  "bioinformatics",
  "genomics",
  "variant-calling",
  "workflow",
  "reproducibility",
]
classifiers = [
  "Development Status :: 5 - Production/Stable",
  "Environment :: Console",
  "Intended Audience :: Science/Research",
  "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
  "Operating System :: POSIX :: Linux",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.8",
  "Programming Language :: Python :: 3.9",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Programming Language :: Python :: 3.14",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
  "gdown>=5.0",
  "jsonschema>=4.18",
  "PyYAML>=6.0",
]

[project.optional-dependencies]
snakemake = [
  "pulp==2.6.0",
  "snakemake",
]
multiqc = ["multiqc"]
all = [
  "multiqc",
  "pulp==2.6.0",
  "snakemake",
]
test = [
  "pytest>=7",
  "pytest-cov>=4",
]
build = [
  "build>=1.2",
  "twine>=5",
]

[project.scripts]
cbicall = "cbicall.__main__:console_main"

[project.urls]
Homepage = "https://cnag-biomedical-informatics.github.io/cbicall/"
Documentation = "https://cnag-biomedical-informatics.github.io/cbicall/"
Repository = "https://github.com/CNAG-Biomedical-Informatics/cbicall"
Issues = "https://github.com/CNAG-Biomedical-Informatics/cbicall/issues"
Changelog = "https://github.com/CNAG-Biomedical-Informatics/cbicall/blob/main/CHANGELOG.md"

[tool.hatch.version]
path = "src/cbicall/__about__.py"

[tool.hatch.build.targets.wheel]
packages = ["src/cbicall"]

[tool.hatch.build.targets.wheel.force-include]
"browser/README" = "cbicall/_runtime/browser/README"
"browser/mtb2html.py" = "cbicall/_runtime/browser/mtb2html.py"
"browser/mtb2json.py" = "cbicall/_runtime/browser/mtb2json.py"
"mtdna/MToolBox_config.sh" = "cbicall/_runtime/mtdna/MToolBox_config.sh"
"workflows" = "cbicall/_runtime/workflows"
"resources" = "cbicall/_runtime/resources"
"tests/fixtures/integration" = "cbicall/_runtime/tests/fixtures/integration"
"examples/input/mit_cohort.yaml" = "cbicall/_runtime/examples/input/mit_cohort.yaml"
"examples/input/mit_single.yaml" = "cbicall/_runtime/examples/input/mit_single.yaml"
"examples/input/nf-core-demo.yaml" = "cbicall/_runtime/examples/input/nf-core-demo.yaml"
"examples/input/nf-core-sarek.yaml" = "cbicall/_runtime/examples/input/nf-core-sarek.yaml"
"examples/input/param.yaml" = "cbicall/_runtime/examples/input/param.yaml"
"examples/input/sample_map.tsv" = "cbicall/_runtime/examples/input/sample_map.tsv"
"examples/input/sarek_samplesheet.csv" = "cbicall/_runtime/examples/input/sarek_samplesheet.csv"
"examples/input/wes_cohort.yaml" = "cbicall/_runtime/examples/input/wes_cohort.yaml"
"examples/input/wes_cromwell.yaml" = "cbicall/_runtime/examples/input/wes_cromwell.yaml"
"examples/input/wes_single.yaml" = "cbicall/_runtime/examples/input/wes_single.yaml"
"examples/input/CNAG999_exome/CNAG99901P_ex/CNAG99901P_ex_S2_L001_R1_001.fastq.gz" = "cbicall/_runtime/examples/input/CNAG999_exome/CNAG99901P_ex/CNAG99901P_ex_S2_L001_R1_001.fastq.gz"
"examples/input/CNAG999_exome/CNAG99901P_ex/CNAG99901P_ex_S2_L001_R2_001.fastq.gz" = "cbicall/_runtime/examples/input/CNAG999_exome/CNAG99901P_ex/CNAG99901P_ex_S2_L001_R2_001.fastq.gz"
"scripts/download_cbicall_bundle.py" = "cbicall/_runtime/scripts/download_cbicall_bundle.py"

[tool.hatch.build.targets.sdist]
include = [
  "/bin/cbicall",
  "/browser/README",
  "/browser/mtb2html.py",
  "/browser/mtb2json.py",
  "/CHANGELOG.md",
  "/examples/input/*.csv",
  "/examples/input/*.tsv",
  "/examples/input/*.yaml",
  "/examples/input/CNAG999_exome/CNAG99901P_ex/*.fastq.gz",
  "/LICENSE",
  "/mtdna/MToolBox_config.sh",
  "/pyproject.toml",
  "/README.md",
  "/resources",
  "/scripts/download_cbicall_bundle.py",
  "/src/cbicall",
  "/tests/fixtures/integration",
  "/workflows",
]