VCF-RDFizer/pyproject.toml at main · ecrum19/VCF-RDFizer · GitHub

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[build-system]
requires = ["setuptools>=77", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "vcf-rdfizer"
version = "3.3.0"
description = "Docker-first VCF to RDF conversion targeting the VCF Core vocabulary, with compressed queryable representations (HDT, COTTAS), semantic validation, and data linking"
readme = "README.md"
requires-python = ">=3.10"
license = "MIT"
license-files = ["LICENSE"]
authors = [
  { name = "VCF-RDFizer maintainers" }
]
keywords = ["bioinformatics", "vcf", "rdf", "rml", "docker", "hdt"]
classifiers = [
  "Development Status :: 4 - Beta",
  "Environment :: Console",
  "Intended Audience :: Science/Research",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
  "rich>=13.7.0",
  "rdflib>=7.0.0",
  "pyoxigraph>=0.3.18",
]

[project.urls]
Homepage = "https://github.com/ecrum19/VCF-RDFizer"
Issues = "https://github.com/ecrum19/VCF-RDFizer/issues"

[project.scripts]
vcf-rdfizer = "vcf_rdfizer:main"
vcf-rdfizer-rules = "vcf_rdfizer_rules:main"
vcf-rdfizer-link = "vcf_rdfizer_link:main"
vcf-rdfizer-policy = "vcf_rdfizer_policy:main"

[project.optional-dependencies]
dev = [
  "build>=1.2.2",
  "twine>=5.1.1",
]

[tool.setuptools]
py-modules = ["vcf_rdfizer", "vcf_rdfizer_gzip", "vcf_rdfizer_rules", "vcf_rdfizer_link", "vcf_rdfizer_policy", "vcf_rdfizer_vocab", "vcf_rdfizer_cottas"]
packages = ["vcf_rdfizer_data", "vcf_rdfizer_data.rules", "vcf_rdfizer_data.linkers", "vcf_rdfizer_data.policy", "vcf_rdfizer_linking", "vcf_rdfizer_policies"]
include-package-data = true

[tool.setuptools.package-data]
"vcf_rdfizer_data.rules" = ["default_rules.ttl"]
"vcf_rdfizer_data.linkers" = ["*/linker.ttl", "*/resolver.py", "*/genes.gff3", "*/*.tsv", "*/README.md"]
"vcf_rdfizer_data.policy" = ["*.ttl"]
# Vendored from the published vocabulary so SHACL validation works from an
# installed package with no separate checkout. Digests are pinned in
# vcf_rdfizer_data/VOCABULARY_PROVENANCE.json.
"vcf_rdfizer_data" = [
  "VOCABULARY_PROVENANCE.json",
  "shacl/*.shacl.ttl",
  "ontology/*.ttl",
]

[tool.coverage.run]
# Measure this project only.
#
# Without this, coverage measures whatever the interpreter executes, which
# includes scripts the tests themselves write into a temporary directory and
# import -- the linking tests write a resolver.py, run it, and let the
# TemporaryDirectory clean it up. By the time `coverage xml` runs, that file is
# gone, and coverage xml fails with "No source for code: .../resolver.py"
# and exit 1, on any platform.
#
# Scoping to the repository is the honest fix rather than ignoring the error:
# a throwaway script in a temp directory is not this project's code and was
# never meant to be in the coverage report.
source = ["."]
omit = [
  "*/.venv/*",
  "*/site-packages/*",
]