pkgs/development/python-modules/sourmash/default.nix

   1 {
   2   lib,
   3   fetchPypi,
   4   buildPythonPackage,
   5   stdenv,
   6   pythonOlder,
   7   overrideSDK,
   8   rustPlatform,
   9   bitstring,
  10   cachetools,
  11   cffi,
  12   deprecation,
  13   iconv,
  14   matplotlib,
  15   numpy,
  16   scipy,
  17   screed,
  18   hypothesis,
  19   pytest-xdist,
  20   pyyaml,
  21   pytestCheckHook,
  22 }:
  23 let
  24   stdenv' =
  25     if stdenv.hostPlatform.isDarwin then overrideSDK stdenv { darwinMinVersion = "10.14"; } else stdenv;
  26 in
  27 buildPythonPackage rec {
  28   pname = "sourmash";
  29   version = "4.8.11";
  30   pyproject = true;
  31   disabled = pythonOlder "3.9";
  32
  33   stdenv = stdenv';
  34
  35   src = fetchPypi {
  36     inherit pname version;
  37     hash = "sha256-GganbfRkuSaFd5qqpu0CpXe91zpKsyly6BNFgQNNNL8=";
  38   };
  39
  40   cargoDeps = rustPlatform.fetchCargoTarball {
  41     inherit src;
  42     name = "${pname}-${version}";
  43     hash = "sha256-im/TPxnT8c2QbWlzCY60wVwJFRIhSnVW7E4kv6bm0p4=";
  44   };
  45
  46   nativeBuildInputs = with rustPlatform; [
  47     cargoSetupHook
  48     maturinBuildHook
  49     bindgenHook
  50   ];
  51
  52   buildInputs = [ iconv ];
  53
  54   propagatedBuildInputs = [
  55     bitstring
  56     cachetools
  57     cffi
  58     deprecation
  59     matplotlib
  60     numpy
  61     scipy
  62     screed
  63   ];
  64
  65   pythonImportsCheck = [ "sourmash" ];
  66   nativeCheckInputs = [
  67     hypothesis
  68     pytest-xdist
  69     pytestCheckHook
  70     pyyaml
  71   ];
  72
  73   # TODO(luizirber): Working on fixing these upstream
  74   disabledTests = [
  75     "test_compare_no_such_file"
  76     "test_do_sourmash_index_multiscaled_rescale_fail"
  77     "test_metagenome_kreport_out_fail"
  78   ];
  79
  80   meta = with lib; {
  81     description = "Quickly search, compare, and analyze genomic and metagenomic data sets";
  82     mainProgram = "sourmash";
  83     homepage = "https://sourmash.bio";
  84     changelog = "https://github.com/sourmash-bio/sourmash/releases/tag/v${version}";
  85     maintainers = with maintainers; [ luizirber ];
  86     license = licenses.bsd3;
  87   };
  88 }