mirror of
https://github.com/NixOS/nixpkgs.git
synced 2026-10-10 22:30:59 +00:00
90 lines
1.7 KiB
Nix
90 lines
1.7 KiB
Nix
{
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lib,
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buildPythonPackage,
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fetchFromGitHub,
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python,
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# build-system
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cmake,
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cython,
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ninja,
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numpy,
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scikit-build-core,
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# nativeBuildInputs
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pkg-config,
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# buildInputs
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htslib,
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# dependencies
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click,
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coloredlogs,
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# tests
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pytestCheckHook,
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}:
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buildPythonPackage (finalAttrs: {
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pname = "cyvcf2";
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version = "0.34.0";
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pyproject = true;
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__structuredAttrs = true;
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src = fetchFromGitHub {
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owner = "brentp";
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repo = "cyvcf2";
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tag = "v${finalAttrs.version}";
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hash = "sha256-XDo2cEcZm5y6u9Gc2e7q2tg8pt3C/5cmnWRe6Dr5x7M=";
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};
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build-system = [
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cmake
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cython
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ninja
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numpy
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scikit-build-core
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];
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dontUseCmakeConfigure = true;
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nativeBuildInputs = [
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pkg-config
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];
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buildInputs = [
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htslib
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];
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env = {
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# Link against the system htslib instead of building the bundled submodule
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CYVCF2_HTSLIB_MODE = "EXTERNAL";
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};
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dependencies = [
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click
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coloredlogs
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numpy
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];
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pythonImportsCheck = [ "cyvcf2" ];
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nativeCheckInputs = [
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pytestCheckHook
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];
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# The test suite lives inside the package directory and relies on relative imports
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# (`from ..cyvcf2 import VCF`) as well as data files next to it, so it must run from the source
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# tree. Bring the compiled extension along.
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preCheck = ''
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cp $out/${python.sitePackages}/cyvcf2/cyvcf2*.so cyvcf2/
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'';
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meta = {
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description = "Cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files";
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homepage = "https://github.com/brentp/cyvcf2";
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changelog = "https://github.com/brentp/cyvcf2/blob/${finalAttrs.src.rev}/CHANGES.md";
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license = lib.licenses.mit;
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maintainers = with lib.maintainers; [ GaetanLepage ];
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};
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})
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