snakemake: 8.14.0 -> 8.20.1 (#339931)

pkgs/applications/science/misc/snakemake/default.nix

@@ -1,30 +1,28 @@
 { lib
-, fetchFromGitHub
+, fetchPypi
+, fetchpatch
 , python3
 , runtimeShell
+, stress
 }:
 
 python3.pkgs.buildPythonApplication rec {
   pname = "snakemake";
-  version = "8.14.0";
+  version = "8.20.1";
   format = "setuptools";
 
-  src = fetchFromGitHub {
-    owner = "snakemake";
-    repo = pname;
-    rev = "refs/tags/v${version}";
-    hash = "sha256-6oguN4u4OUDXpDsbueSBNwtWgLCaKmgq3w/d/MsMh7Y=";
-    # https://github.com/python-versioneer/python-versioneer/issues/217
-    postFetch = ''
-      sed -i "$out"/snakemake/_version.py -e 's#git_refnames = ".*"#git_refnames = " (tag: v${version})"#'
-    '';
+  src = fetchPypi {
+    inherit pname version;
+    hash = "sha256-adNwIA1z/TwWsa0gQb4hAsUvHInjd30sm1dYKXvvXy8=";
   };
 
   postPatch = ''
     patchShebangs --build tests/
-    patchShebangs --host snakemake/executors/jobscript.sh
-    substituteInPlace snakemake/shell.py \
-      --replace "/bin/sh" "${runtimeShell}"
+    substituteInPlace tests/common.py \
+      --replace-fail 'os.environ["PYTHONPATH"] = os.getcwd()' "pass" \
+      --replace-fail 'del os.environ["PYTHONPATH"]' "pass"
+    substituteInPlace snakemake/unit_tests/__init__.py \
+      --replace-fail '"unit_tests/templates"' '"'"$PWD"'/snakemake/unit_tests/templates"'
   '';
 
   propagatedBuildInputs = with python3.pkgs; [
@@ -41,6 +39,7 @@ python3.pkgs.buildPythonApplication rec {
     nbformat
     psutil
     pulp
+    pygments
     pyyaml
     requests
     reretry
@@ -66,16 +65,54 @@ python3.pkgs.buildPythonApplication rec {
     numpy
     pandas
     pytestCheckHook
+    pytest-mock
     requests-mock
     snakemake-executor-plugin-cluster-generic
+    snakemake-storage-plugin-fs
+    stress
   ];
 
-  disabledTestPaths = [
-    "tests/test_conda_python_3_7_script/test_script.py"
+  pytestFlagsArray = [
+    "tests/tests.py"
+    "tests/test_expand.py"
+    "tests/test_io.py"
+    "tests/test_schema.py"
+    "tests/test_executor_test_suite.py"
+    "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
+    "test_ancient"
+    "test_modules_prefix"
+    # requires snakemake-storage-plugin-s3
     "test_deploy_sources"
+    # requires modules
+    "test_env_modules"
+    # issue with locating template file
+    "test_generate_unit_tests"
+    # weird
+    "test_strict_mode"
+    "test_issue1256"
+    "test_issue2574"
+    "test_github_issue1384"
+    # future-proofing
+    "conda"
+    "singularity"
+    "apptainer"
+    "container"
   ];
 
   pythonImportsCheck = [

pkgs/development/python-modules/snakemake-storage-plugin-fs/default.nix

@@ -0,0 +1,44 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  poetry-core,
+  snakemake,
+  snakemake-interface-storage-plugins,
+  snakemake-interface-common,
+  sysrsync,
+}:
+
+buildPythonPackage rec {
+  pname = "snakemake-storage-plugin-fs";
+  version = "1.0.6";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "snakemake";
+    repo = pname;
+    rev = "refs/tags/v${version}";
+    hash = "sha256-9A2W+V0d9K1Ei4WXqIZfIcOYsWgpGVP7P/ANy8jOGu0=";
+  };
+
+  build-system = [ poetry-core ];
+
+  dependencies = [
+    snakemake-interface-storage-plugins
+    snakemake-interface-common
+    sysrsync
+  ];
+
+  # The current tests are not worth dealing with cyclic dependency on snakemake
+  doCheck = false;
+
+  # Use nothing due to a cyclic dependency on snakemake
+  pythonImportsCheck = [ ];
+
+  meta = with lib; {
+    description = "A Snakemake storage plugin that reads and writes from a locally mounted filesystem using rsync";
+    homepage = "https://github.com/snakemake/snakemake-storage-plugin-fs";
+    license = licenses.mit;
+    maintainers = with maintainers; [ veprbl ];
+  };
+}

pkgs/development/python-modules/sysrsync/default.nix

@@ -0,0 +1,45 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  poetry-core,
+  setuptools,
+  rsync,
+  toml,
+}:
+
+buildPythonPackage rec {
+  pname = "sysrsync";
+  version = "1.1.1";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "gchamon";
+    repo = pname;
+    rev = "refs/tags/${version}";
+    hash = "sha256-2Sz3JrNmIGOnad+qjRzbAgsFEzDtwBT0KLEFyQKZra4=";
+  };
+
+  postPatch = ''
+    substituteInPlace sysrsync/command_maker.py \
+      --replace-fail "'rsync'" "'${rsync}/bin/rsync'"
+  '';
+
+  build-system = [
+    poetry-core
+    setuptools
+  ];
+
+  dependencies = [
+    toml
+  ];
+
+  pythonImportsCheck = [ "sysrsync" ];
+
+  meta = with lib; {
+    description = "Simple and safe system's rsync wrapper for Python";
+    homepage = "https://github.com/gchamon/sysrsync";
+    license = licenses.mit;
+    maintainers = with maintainers; [ veprbl ];
+  };
+}

pkgs/top-level/python-packages.nix

@@ -14384,6 +14384,8 @@ self: super: with self; {
 
   snakemake-interface-storage-plugins = callPackage ../development/python-modules/snakemake-interface-storage-plugins { };
 
+  snakemake-storage-plugin-fs = callPackage ../development/python-modules/snakemake-storage-plugin-fs { };
+
   snakemake-storage-plugin-s3 = callPackage ../development/python-modules/snakemake-storage-plugin-s3 { };
 
   snakemake-storage-plugin-xrootd = callPackage ../development/python-modules/snakemake-storage-plugin-xrootd { };
@@ -15065,6 +15067,8 @@ self: super: with self; {
 
   syslog-rfc5424-formatter = callPackage ../development/python-modules/syslog-rfc5424-formatter { };
 
+  sysrsync = callPackage ../development/python-modules/sysrsync { };
+
   systembridge = callPackage ../development/python-modules/systembridge { };
 
   systembridgeconnector = callPackage ../development/python-modules/systembridgeconnector { };