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# build-system cmake, cython, ninja, numpy, scikit-build-core,
# nativeBuildInputs pkg-config,
# buildInputs htslib,
# dependencies click, coloredlogs,
# tests pytestCheckHook,}:
buildPythonPackage (finalAttrs: { pname = "cyvcf2"; version = "0.34.0"; pyproject = true; __structuredAttrs = true;
src = fetchFromGitHub { owner = "brentp"; repo = "cyvcf2"; tag = "v${finalAttrs.version}"; hash = "sha256-XDo2cEcZm5y6u9Gc2e7q2tg8pt3C/5cmnWRe6Dr5x7M="; };
build-system = [ cmake cython ninja numpy scikit-build-core ]; dontUseCmakeConfigure = true;
nativeBuildInputs = [ pkg-config ];
buildInputs = [ htslib ];
env = { # Link against the system htslib instead of building the bundled submodule CYVCF2_HTSLIB_MODE = "EXTERNAL"; };
dependencies = [ click coloredlogs numpy ];
pythonImportsCheck = [ "cyvcf2" ];
nativeCheckInputs = [ pytestCheckHook ];
# The test suite lives inside the package directory and relies on relative imports # (`from ..cyvcf2 import VCF`) as well as data files next to it, so it must run from the source # tree. Bring the compiled extension along. preCheck = '' cp $out/${python.sitePackages}/cyvcf2/cyvcf2*.so cyvcf2/ '';
meta = { description = "Cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files"; homepage = "https://github.com/brentp/cyvcf2"; changelog = "https://github.com/brentp/cyvcf2/blob/${finalAttrs.src.rev}/CHANGES.md"; license = lib.licenses.mit; maintainers = with lib.maintainers; [ GaetanLepage ]; };})