Commit bf73b43d authored by Dmitry Kalinkin's avatar Dmitry Kalinkin
Browse files

snakemake: 8.29.2 -> 9.1.10

parent d4f2cc81

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

+28 −5
Original line number Diff line number Diff line
@@ -10,14 +10,14 @@ 


python3Packages.buildPythonApplication rec {

  pname = "snakemake";

  version = "8.29.2";

  version = "9.1.10";

  pyproject = true;



  src = fetchFromGitHub {

    owner = "snakemake";

    repo = "snakemake";

    tag = "v${version}";

    hash = "sha256-69NsbfHF29l92gwO8If9vp8Cdjac3BnO+hbY3b2bZ8E=";

    hash = "sha256-saEfclp6cRcBBUv/ssszr9Q8PGPapkSsjDwTUP9XOhg=";

  };



  postPatch = ''
@@ -25,13 +25,13 @@ python3Packages.buildPythonApplication rec { 
    substituteInPlace tests/common.py \

      --replace-fail 'os.environ["PYTHONPATH"] = os.getcwd()' "pass" \

      --replace-fail 'del os.environ["PYTHONPATH"]' "pass"

    substituteInPlace snakemake/unit_tests/__init__.py \

    substituteInPlace src/snakemake/unit_tests/__init__.py \

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

    substituteInPlace snakemake/assets/__init__.py \

    substituteInPlace src/snakemake/assets/__init__.py \

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

  '';



  build-system = with python3Packages; [ setuptools ];

  build-system = with python3Packages; [ setuptools-scm ];



  dependencies = with python3Packages; [

    appdirs
@@ -55,6 +55,7 @@ python3Packages.buildPythonApplication rec { 
    smart-open

    snakemake-interface-executor-plugins

    snakemake-interface-common

    snakemake-interface-logger-plugins

    snakemake-interface-storage-plugins

    snakemake-interface-report-plugins

    stopit
@@ -126,6 +127,20 @@ python3Packages.buildPythonApplication rec { 
      "test_deploy_sources"

      "test_output_file_cache_storage"

      "test_storage"



      # Tries to access internet

      "test_report_after_run"



      # Needs stress-ng

      "test_benchmark"

      "test_benchmark_jsonl"



      # Needs unshare

      "test_nodelocal"



      # Requires snakemake-storage-plugin-http

      "test_keep_local"

      "test_retrieve"

    ]

    ++ lib.optionals stdenv.hostPlatform.isDarwin [

      # Unclear failure:
@@ -144,6 +159,14 @@ python3Packages.buildPythonApplication rec { 
      "test_queue_input_forceall"

      "test_resources_submitted_to_cluster"

      "test_scopes_submitted_to_cluster"



      # Issue with /dev/stderr in sandbox

      "test_protected_symlink_output"



      # Unclear issue:

      #   pulp.apis.core.PulpSolverError: Pulp: cannot execute cbc cwd:

      # but pulp solver is not default

      "test_access_patterns"

    ];



  pythonImportsCheck = [ "snakemake" ];