truvari: 2.1.1 -> 4.0.0

{ lib

, fetchFromGitHub

, python3Packages

, runtimeShell

, bcftools

, htslib

}:

python3Packages.buildPythonApplication rec {

let

  ssshtest = fetchFromGitHub {

    owner = "ryanlayer";

    repo = "ssshtest";

    rev = "d21f7f928a167fca6e2eb31616673444d15e6fd0";

    hash = "sha256-zecZHEnfhDtT44VMbHLHOhRtNsIMWeaBASupVXtmrks=";

  };

in python3Packages.buildPythonApplication rec {

  pname = "truvari";

  version = "2.1.1";

  version = "4.0.0";

  src = fetchFromGitHub {

    owner = "spiralgenetics";

    owner = "ACEnglish";

    repo = "truvari";

    rev = "v${version}";

    sha256 = "14nsdbj063qm175xxixs34cihvsiskc9gym8pg7gbwsh13k5a00h";

    hash = "sha256-UJNMKEV5m2jFqnWvkVAtymkcE2TjPIXp7JqRZpMSqsE=";

  };

  postPatch = ''

    substituteInPlace setup.py \

      --replace 'python-Levenshtein==0.12.1' 'python-Levenshtein>=0.12.1'

      --replace "rich==" "rich>="

    substituteInPlace truvari/utils.py \

      --replace "/bin/bash" "${runtimeShell}"

    patchShebangs repo_utils/test_files

  '';

  propagatedBuildInputs = with python3Packages; [

    pyvcf

    levenshtein

    progressbar2

    rich

    edlib

    pysam

    pyfaidx

    intervaltree

    joblib

    numpy

    pytabix

    acebinf

    bwapy

    joblib

    pandas

  ];

  # no tests

  doCheck = false;

  makeWrapperArgs = [

    "--prefix" "PATH" ":" (lib.makeBinPath [ bcftools htslib ])

  ];

  pythonImportsCheck = [ "truvari" ];

  nativeCheckInputs = [

    bcftools

    htslib

  ] ++ (with python3Packages; [

    coverage

  ]);

  checkPhase = ''

    runHook preCheck

    ln -s ${ssshtest}/ssshtest .

    bash repo_utils/truvari_ssshtests.sh

    runHook postCheck

  '';

  meta = with lib; {

    description = "Structural variant comparison tool for VCFs";

    homepage = "https://github.com/spiralgenetics/truvari";

    homepage = "https://github.com/ACEnglish/truvari";

    license = licenses.mit;

    maintainers = with maintainers; [ scalavision ];

    longDescription = ''