Commit a019ba32 authored by Gaetan Lepage's avatar Gaetan Lepage
Browse files

snakemake: 8.20.1 -> 8.23.0 

Diff:
https://github.com/snakemake/snakemake/compare/refs/tags/v8.20.1...v8.23.0

Changelog:
https://github.com/snakemake/snakemake/blob/refs/tags/v8.23.0/CHANGELOG.md
parent 381bfca3

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

+70 −43
Original line number Diff line number Diff line 
{

  lib,

  stdenv,

  fetchPypi,

  python3,

  python3Packages,

  stress,

  versionCheckHook,

}:



python3.pkgs.buildPythonApplication rec {

python3Packages.buildPythonApplication rec {

  pname = "snakemake";

  version = "8.20.1";

  format = "setuptools";

  version = "8.23.0";



  pyproject = true;



  src = fetchPypi {

    inherit pname version;

    hash = "sha256-adNwIA1z/TwWsa0gQb4hAsUvHInjd30sm1dYKXvvXy8=";

    hash = "sha256-XENI9VJW62KyrxDGSwQiygggYZOu9yW2QSNyp4BO9Us=";

  };



  postPatch = ''
@@ -24,8 +27,13 @@ python3.pkgs.buildPythonApplication rec { 
      --replace-fail '"unit_tests/templates"' '"'"$PWD"'/snakemake/unit_tests/templates"'

  '';



  propagatedBuildInputs = with python3.pkgs; [

  build-system = with python3Packages; [

    setuptools

  ];



  dependencies = with python3Packages; [

    appdirs

    conda-inject

    configargparse

    connection-pool

    datrie
@@ -60,7 +68,7 @@ python3.pkgs.buildPythonApplication rec { 
  # for the current basic test suite. Slurm, Tibanna and Tes require extra

  # setup.



  nativeCheckInputs = with python3.pkgs; [

  nativeCheckInputs = with python3Packages; [

    numpy

    pandas

    pytestCheckHook
@@ -69,7 +77,9 @@ python3.pkgs.buildPythonApplication rec { 
    snakemake-executor-plugin-cluster-generic

    snakemake-storage-plugin-fs

    stress

    versionCheckHook

  ];

  versionCheckProgramArg = [ "--version" ];



  pytestFlagsArray = [

    "tests/tests.py"
@@ -80,38 +90,54 @@ python3.pkgs.buildPythonApplication rec { 
    "tests/test_api.py"

  ];



  # Some will be disabled via https://github.com/snakemake/snakemake/pull/3074

  disabledTests = [

    # requires graphviz

    "test_filegraph"

    # requires s3

    "test_storage"

    "test_default_storage"

    "test_output_file_cache_storage"

    # requires peppy and eido

    "test_pep"

    "test_modules_peppy"

    # requires perl

    "test_shadow"

    # requires snakemake-storage-plugin-http

  disabledTests =

    [

      # FAILED tests/tests.py::test_env_modules - AssertionError: expected successful execution

      "test_ancient"

    "test_modules_prefix"

    # requires snakemake-storage-plugin-s3

    "test_deploy_sources"

    # requires modules

      "test_conda_create_envs_only"

      "test_env_modules"

    # issue with locating template file

      "test_generate_unit_tests"

    # weird

      "test_modules_prefix"

      "test_strict_mode"

      # Requires perl

      "test_shadow"

      # Require peppy and eido

      "test_peppy"

      "test_modules_peppy"

      "test_pep_pathlib"



      # CalledProcessError

      "test_filegraph" # requires graphviz

      "test_github_issue1384"



      # AssertionError: assert 127 == 1

      "test_issue1256"

      "test_issue2574"

    "test_github_issue1384"

    # future-proofing

    "conda"

    "singularity"

    "apptainer"

    "container"



      # Require `snakemake-storage-plugin-fs` (circular dependency)

      "test_default_storage"

      "test_default_storage_local_job"

      "test_deploy_sources"

      "test_output_file_cache_storage"

      "test_storage"

    ]

    ++ lib.optionals stdenv.isDarwin [

      # Unclear failure:

      # AssertionError: expected successful execution

      # `__darwinAllowLocalNetworking` doesn't help

      "test_excluded_resources_not_submitted_to_cluster"

      "test_group_job_resources_with_pipe"

      "test_group_jobs_resources"

      "test_group_jobs_resources_with_limited_resources"

      "test_group_jobs_resources_with_max_threads"

      "test_issue850"

      "test_issue860"

      "test_multicomp_group_jobs"

      "test_queue_input"

      "test_queue_input_dryrun"

      "test_queue_input_forceall"

      "test_resources_submitted_to_cluster"

      "test_scopes_submitted_to_cluster"

    ];



  pythonImportsCheck = [
@@ -122,10 +148,11 @@ python3.pkgs.buildPythonApplication rec { 
    export HOME="$(mktemp -d)"

  '';



  meta = with lib; {

  meta = {

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

    license = licenses.mit;

    license = lib.licenses.mit;

    description = "Python-based execution environment for make-like workflows";

    changelog = "https://github.com/snakemake/snakemake/blob/v${version}/CHANGELOG.md";

    mainProgram = "snakemake";

    longDescription = ''

      Snakemake is a workflow management system that aims to reduce the complexity of
@@ -134,7 +161,7 @@ python3.pkgs.buildPythonApplication rec { 
      workflows are essentially Python scripts extended by declarative code to define

      rules. Rules describe how to create output files from input files.

    '';

    maintainers = with maintainers; [

    maintainers = with lib.maintainers; [

      helkafen

      renatoGarcia

      veprbl

pkgs/top-level/python-packages.nix

+1 −1
Original line number Diff line number Diff line
@@ -14536,7 +14536,7 @@ self: super: with self; { 
  });















  snakemake = toPythonModule (pkgs.snakemake.override {













    python3 = python;













    python3Packages = self;















  });





























  snakemake-executor-plugin-cluster-generic = callPackage ../development/python-modules/snakemake-executor-plugin-cluster-generic { };