Unverified Commit 0ae547b1 authored by Dmitry Kalinkin's avatar Dmitry Kalinkin Committed by GitHub
Browse files

snakemake: 9.5.1 -> 9.11.8 (#446245)

parents 96a6230e 0c1fde6f

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

+8 −2
Original line number Diff line number Diff line
@@ -10,14 +10,14 @@ 


python3Packages.buildPythonApplication rec {

  pname = "snakemake";

  version = "9.5.1";

  version = "9.11.8";

  pyproject = true;



  src = fetchFromGitHub {

    owner = "snakemake";

    repo = "snakemake";

    tag = "v${version}";

    hash = "sha256-cSFqPSLeM7hw1bxQZ2FhlHUP+O3iyrwBz4+Jz90Zck8=";

    hash = "sha256-fQCpQ3LB0Q1USZ9YTEniR5iKq68Zri9+14zqa/jzO2o=";

  };



  postPatch = ''
@@ -58,6 +58,7 @@ python3Packages.buildPythonApplication rec { 
    snakemake-interface-logger-plugins

    snakemake-interface-storage-plugins

    snakemake-interface-report-plugins

    snakemake-interface-scheduler-plugins

    stopit

    tabulate

    throttler
@@ -140,6 +141,11 @@ python3Packages.buildPythonApplication rec { 
    # Requires snakemake-storage-plugin-http

    "test_keep_local"

    "test_retrieve"



    # Requires conda

    "test_jupyter_notebook"

    "test_jupyter_notebook_nbconvert"

    "test_jupyter_notebook_draft"

  ]

  ++ lib.optionals stdenv.hostPlatform.isDarwin [

    # Unclear failure:

pkgs/development/python-modules/snakemake-interface-common/default.nix

+11 −14
Original line number Diff line number Diff line
@@ -4,43 +4,40 @@ 
  buildPythonPackage,

  configargparse,

  fetchFromGitHub,

  poetry-core,

  pythonOlder,

  pytestCheckHook,

  setuptools,

}:



buildPythonPackage rec {

  pname = "snakemake-interface-common";

  version = "1.17.4";

  version = "1.22.0";

  pyproject = true;



  disabled = pythonOlder "3.8";



  src = fetchFromGitHub {

    owner = "snakemake";

    repo = "snakemake-interface-common";

    tag = "v${version}";

    hash = "sha256-PMEs7yeVfSnZKbabLrbXfIKCIPteNV1wzbt9RIDG3qU=";

    hash = "sha256-DxbB/UaBkLbG18CGHyDMo7dmRlVY2tD3BhO0MShbnq4=";

  };



  build-system = [ poetry-core ];

  build-system = [ setuptools ];



  dependencies = [

    argparse-dataclass

    configargparse

  ];



  nativeCheckInputs = [ pytestCheckHook ];



  pythonImportsCheck = [ "snakemake_interface_common" ];



  enabledTestPaths = [ "tests/tests.py" ];

  # test_snakemake_version: No module named 'snakemake'

  # nativeCheckInputs = [ pytestCheckHook ];



  # enabledTestPaths = [ "tests/tests.py" ];



  meta = with lib; {

  meta = {

    description = "Common functions and classes for Snakemake and its plugins";

    homepage = "https://github.com/snakemake/snakemake-interface-common";

    changelog = "https://github.com/snakemake/snakemake-interface-common/releases/tag/v${version}";

    license = licenses.mit;

    maintainers = with maintainers; [ veprbl ];

    license = lib.licenses.mit;

    maintainers = with lib.maintainers; [ veprbl ];

  };

}

pkgs/development/python-modules/snakemake-interface-scheduler-plugins/default.nix

0 → 100644
+42 −0
Original line number Diff line number Diff line 
{

  lib,

  buildPythonPackage,

  fetchFromGitHub,

  hatchling,

  snakemake-interface-common,

}:



let

  version = "2.0.1";



  src = fetchFromGitHub {

    owner = "snakemake";

    repo = "snakemake-interface-scheduler-plugins";

    tag = "v${version}";

    hash = "sha256-Z/rJGkby9AcYB+Gil00xhbrySChqEIEOtzLyzQPhObk=";

  };

in

buildPythonPackage {

  pname = "snakemake-interface-scheduler-plugins";

  inherit version src;

  pyproject = true;



  build-system = [ hatchling ];



  dependencies = [ snakemake-interface-common ];



  pythonImportsCheck = [ "snakemake_interface_scheduler_plugins" ];



  # test_scheduler: No module named 'snakemake'

  # nativeCheckInputs = [ pytestCheckHook ];



  # enabledTestPaths = [ "tests/tests.py" ];



  meta = {

    description = "Provides a stable interface for interactions between Snakemake and its scheduler plugins";

    homepage = "https://github.com/snakemake/snakemake-interface-scheduler-plugins";

    changelog = "https://github.com/snakemake/snakemake-interface-scheduler-plugins/blob/${src.rev}/CHANGELOG.md";

    license = lib.licenses.mit;

    maintainers = with lib.maintainers; [ kyehn ];

  };

}

pkgs/top-level/python-packages.nix

+4 −0
Original line number Diff line number Diff line
@@ -17032,6 +17032,10 @@ self: super: with self; { 
    callPackage ../development/python-modules/snakemake-interface-report-plugins

      { };













  snakemake-interface-scheduler-plugins =













    callPackage ../development/python-modules/snakemake-interface-scheduler-plugins













      { };



























  snakemake-interface-storage-plugins =















    callPackage ../development/python-modules/snakemake-interface-storage-plugins















      { };