snakemake: 8.29.2 -> 9.1.10 (#398494)

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

@@ -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" ];

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

@@ -0,0 +1,35 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  hatchling,
+  snakemake-interface-common,
+}:
+
+buildPythonPackage rec {
+  pname = "snakemake-interface-logger-plugins";
+  version = "1.2.3";
+  format = "pyproject";
+
+  src = fetchFromGitHub {
+    owner = "snakemake";
+    repo = pname;
+    tag = "v${version}";
+    hash = "sha256-VHbta+R2a/K2L03IRu/Ya7dJzshIAvyK9cNIRbx8QqM=";
+  };
+
+  nativeBuildInputs = [ hatchling ];
+
+  propagatedBuildInputs = [
+    snakemake-interface-common
+  ];
+
+  pythonImportsCheck = [ "snakemake_interface_logger_plugins" ];
+
+  meta = with lib; {
+    description = "A stable interface for interactions between Snakemake and its logger plugins";
+    homepage = "https://github.com/snakemake/snakemake-interface-logger-plugins";
+    license = licenses.mit;
+    maintainers = with maintainers; [ veprbl ];
+  };
+}

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

@@ -3,6 +3,7 @@
   buildPythonPackage,
   fetchFromGitHub,
   poetry-core,
+  humanfriendly,
   reretry,
   snakemake-interface-common,
   throttler,
@@ -11,19 +12,20 @@
 
 buildPythonPackage rec {
   pname = "snakemake-interface-storage-plugins";
-  version = "3.3.0";
+  version = "4.2.1";
   format = "pyproject";
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = pname;
     tag = "v${version}";
-    hash = "sha256-qjQZc7DIXIPmqXq+Fjslgrq2LbjbdRS/twGsp/jrxRY=";
+    hash = "sha256-mGpKmKWWL4ue9Dddjs4fXCaITrC97yHC58Jh2vclXAY=";
   };
 
   nativeBuildInputs = [ poetry-core ];
 
   propagatedBuildInputs = [
+    humanfriendly
     reretry
     snakemake-interface-common
     throttler

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

@@ -10,14 +10,14 @@
 
 buildPythonPackage rec {
   pname = "snakemake-storage-plugin-fs";
-  version = "1.0.6";
+  version = "1.1.1";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = pname;
     tag = "v${version}";
-    hash = "sha256-9A2W+V0d9K1Ei4WXqIZfIcOYsWgpGVP7P/ANy8jOGu0=";
+    hash = "sha256-Y+Fofz4D/CWgdG3lOneadRu/VfJ23D4Dz751j9rUKNo=";
   };
 
   build-system = [ poetry-core ];

pkgs/development/python-modules/snakemake-storage-plugin-s3/default.nix

@@ -13,14 +13,14 @@
 
 buildPythonPackage rec {
   pname = "snakemake-storage-plugin-s3";
-  version = "0.3.1";
+  version = "0.3.3";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = "snakemake-storage-plugin-s3";
     tag = "v${version}";
-    hash = "sha256-WbGlXu6/7e9U2GfVd4IF86bRfulNxjP1Tw5pVHpEj/g=";
+    hash = "sha256-jIz8Stx2Abd+xGx6kEwlgq3KGsFO13Lk2N8eLB8marA=";
   };
 
   build-system = [ poetry-core ];

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

@@ -2,7 +2,8 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
-  poetry-core,
+  hatch-vcs,
+  hatchling,
   snakemake,
   snakemake-interface-storage-plugins,
   snakemake-interface-common,
@@ -11,20 +12,23 @@
 
 buildPythonPackage rec {
   pname = "snakemake-storage-plugin-xrootd";
-  version = "0.1.4";
+  version = "0.4.1";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = pname;
     tag = "v${version}";
-    hash = "sha256-1plBss9jRzIIGQE7rXDEnAomFxNzSUKsw0VyhYA2mIc=";
+    hash = "sha256-vfMAgOTmT3uzUZHXeKsd8Ze3+b3nFsVHDhkPG+xvz+k=";
   };
 
   # xrootd<6.0.0,>=5.6.4 not satisfied by version 5.7rc20240303
   pythonRelaxDeps = [ "xrootd" ];
 
-  build-system = [ poetry-core ];
+  build-system = [
+    hatch-vcs
+    hatchling
+  ];
 
   dependencies = [
     snakemake-interface-storage-plugins

pkgs/top-level/python-packages.nix

@@ -15968,6 +15968,10 @@ self: super: with self; {
     callPackage ../development/python-modules/snakemake-interface-executor-plugins
       { };
 
+  snakemake-interface-logger-plugins =
+    callPackage ../development/python-modules/snakemake-interface-logger-plugins
+      { };
+
   snakemake-interface-report-plugins =
     callPackage ../development/python-modules/snakemake-interface-report-plugins
       { };