Unverified Commit f885cdd5 authored by emaryn's avatar emaryn Committed by GitHub
Browse files

snakemake: 8.23.0 -> 8.29.0 (#385979) 



Co-authored-by: default avataremaryn <emaryn@users.noreply.github.com>
parent 05de42c3

pkgs/by-name/sn/snakemake/package.nix

+27 −27
Original line number Diff line number Diff line 
{

  lib,

  stdenv,

  fetchPypi,

  fetchFromGitHub,

  python3Packages,

  stress,

  versionCheckHook,

  writableTmpDirAsHomeHook,

}:



python3Packages.buildPythonApplication rec {

  pname = "snakemake";

  version = "8.23.0";



  version = "8.29.0";

  pyproject = true;



  src = fetchPypi {

    inherit pname version;

    hash = "sha256-XENI9VJW62KyrxDGSwQiygggYZOu9yW2QSNyp4BO9Us=";

  src = fetchFromGitHub {

    owner = "snakemake";

    repo = "snakemake";

    tag = "v${version}";

    hash = "sha256-vGa0N5jbm+b4FH1rkvZI5yI005K0D5AP29JGK2wscps=";

  };



  postPatch = ''
@@ -25,11 +27,11 @@ python3Packages.buildPythonApplication rec { 
      --replace-fail 'del os.environ["PYTHONPATH"]' "pass"

    substituteInPlace snakemake/unit_tests/__init__.py \

      --replace-fail '"unit_tests/templates"' '"'"$PWD"'/snakemake/unit_tests/templates"'

    substituteInPlace snakemake/assets/__init__.py \

      --replace-fail "raise err" "return bytes('err','ascii')"

  '';



  build-system = with python3Packages; [

    setuptools

  ];

  build-system = with python3Packages; [ setuptools ];



  dependencies = with python3Packages; [

    appdirs
@@ -68,7 +70,8 @@ python3Packages.buildPythonApplication rec { 
  # for the current basic test suite. Slurm, Tibanna and Tes require extra

  # setup.



  nativeCheckInputs = with python3Packages; [

  nativeCheckInputs =

    (with python3Packages; [

      numpy

      pandas

      pytestCheckHook
@@ -78,7 +81,10 @@ python3Packages.buildPythonApplication rec { 
      snakemake-storage-plugin-fs

      stress

      versionCheckHook

  ];

      polars

    ])

    ++ [ writableTmpDirAsHomeHook ];



  versionCheckProgramArg = [ "--version" ];



  pytestFlagsArray = [
@@ -140,13 +146,7 @@ python3Packages.buildPythonApplication rec { 
      "test_scopes_submitted_to_cluster"

    ];



  pythonImportsCheck = [

    "snakemake"

  ];



  preCheck = ''

    export HOME="$(mktemp -d)"

  '';

  pythonImportsCheck = [ "snakemake" ];



  meta = {

    homepage = "https://snakemake.github.io";