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{
lib,
fetchPypi,
buildPythonPackage,
stdenv,
pythonOlder,
overrideSDK,
rustPlatform,
bitstring,
cachetools,
cffi,
deprecation,
iconv,
matplotlib,
numpy,
scipy,
screed,
hypothesis,
pytest-xdist,
pyyaml,
pytestCheckHook,
}:
let
stdenv' =
if stdenv.hostPlatform.isDarwin then overrideSDK stdenv { darwinMinVersion = "10.14"; } else stdenv;
in
buildPythonPackage rec {
pname = "sourmash";
version = "4.8.11";
pyproject = true;
disabled = pythonOlder "3.9";
stdenv = stdenv';
src = fetchPypi {
inherit pname version;
hash = "sha256-GganbfRkuSaFd5qqpu0CpXe91zpKsyly6BNFgQNNNL8=";
};
cargoDeps = rustPlatform.fetchCargoTarball {
inherit src;
name = "${pname}-${version}";
hash = "sha256-im/TPxnT8c2QbWlzCY60wVwJFRIhSnVW7E4kv6bm0p4=";
};
nativeBuildInputs = with rustPlatform; [
cargoSetupHook
maturinBuildHook
bindgenHook
];
buildInputs = [ iconv ];
propagatedBuildInputs = [
bitstring
cachetools
cffi
deprecation
matplotlib
numpy
scipy
screed
];
pythonImportsCheck = [ "sourmash" ];
nativeCheckInputs = [
hypothesis
pytest-xdist
pytestCheckHook
pyyaml
];
# TODO(luizirber): Working on fixing these upstream
disabledTests = [
"test_compare_no_such_file"
"test_do_sourmash_index_multiscaled_rescale_fail"
"test_metagenome_kreport_out_fail"
];
meta = with lib; {
description = "Quickly search, compare, and analyze genomic and metagenomic data sets";
mainProgram = "sourmash";
homepage = "https://sourmash.bio";
changelog = "https://github.com/sourmash-bio/sourmash/releases/tag/v${version}";
maintainers = with maintainers; [ luizirber ];
license = licenses.bsd3;
};
}
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