python3Packages.snakemake: 9.16.3 -> 9.21.0 (#522808)

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

@@ -6,18 +6,20 @@
   stress,
   versionCheckHook,
   writableTmpDirAsHomeHook,
+  snakemake,
 }:
 
 python3Packages.buildPythonApplication (finalAttrs: {
   pname = "snakemake";
-  version = "9.16.3";
+  version = "9.21.0";
   pyproject = true;
+  __structuredAttrs = true;
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = "snakemake";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-+eEzpRY6ZEKB3v1/AkHDg4bOcM2Y6pt4UMrdKF6soac=";
+    hash = "sha256-+EO+BTMkui0mJvEf0TOaCRBH8MzLsit8xK+71gujHt0=";
   };
 
   postPatch = ''
@@ -33,6 +35,10 @@ python3Packages.buildPythonApplication (finalAttrs: {
 
   build-system = with python3Packages; [ setuptools-scm ];
 
+  pythonRelaxDeps = [
+    "packaging"
+    "sqlmodel"
+  ];
   dependencies = with python3Packages; [
     appdirs
     conda-inject
@@ -53,20 +59,24 @@ python3Packages.buildPythonApplication (finalAttrs: {
     requests
     reretry
     smart-open
-    snakemake-interface-executor-plugins
     snakemake-interface-common
+    snakemake-interface-executor-plugins
     snakemake-interface-logger-plugins
-    snakemake-interface-storage-plugins
     snakemake-interface-report-plugins
     snakemake-interface-scheduler-plugins
+    snakemake-interface-storage-plugins
+    sqlmodel
     stopit
     tabulate
+    tenacity
     throttler
     toposort
     wrapt
     yte
   ];
 
+  pythonImportsCheck = [ "snakemake" ];
+
   # See
   # https://github.com/snakemake/snakemake/blob/main/.github/workflows/main.yml#L99
   # for the current basic test suite. Slurm, Tibanna and Tes require extra
@@ -81,11 +91,15 @@ python3Packages.buildPythonApplication (finalAttrs: {
       requests-mock
       snakemake-executor-plugin-cluster-generic
       snakemake-storage-plugin-fs
+      snakemake-storage-plugin-http
+      snakemake-storage-plugin-s3
       stress
-      versionCheckHook
       polars
     ])
-    ++ [ writableTmpDirAsHomeHook ];
+    ++ [
+      versionCheckHook
+      writableTmpDirAsHomeHook
+    ];
 
   enabledTestPaths = [
     "tests/tests.py"
@@ -97,6 +111,9 @@ python3Packages.buildPythonApplication (finalAttrs: {
   ];
 
   disabledTests = [
+    # AssertionError: expected file "onerror_module2.log" not produced
+    "test_module_onerror"
+
     # FAILED tests/tests.py::test_env_modules - AssertionError: expected successful execution
     "test_ancient"
     "test_conda_create_envs_only"
@@ -119,13 +136,6 @@ python3Packages.buildPythonApplication (finalAttrs: {
     "test_issue1256"
     "test_issue2574"
 
-    # 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"
-
     # Tries to access internet
     "test_report_after_run"
 
@@ -136,10 +146,6 @@ python3Packages.buildPythonApplication (finalAttrs: {
     # Needs unshare
     "test_nodelocal"
 
-    # Requires snakemake-storage-plugin-http
-    "test_keep_local"
-    "test_retrieve"
-
     # Requires conda
     "test_jupyter_notebook"
     "test_jupyter_notebook_nbconvert"
@@ -179,7 +185,11 @@ python3Packages.buildPythonApplication (finalAttrs: {
     "test_issue1331"
   ];
 
-  pythonImportsCheck = [ "snakemake" ];
+  # Circular dependencies
+  doCheck = false;
+  passthru.tests.pytest = snakemake.overridePythonAttrs {
+    doCheck = true;
+  };
 
   meta = {
     homepage = "https://snakemake.github.io";

pkgs/by-name/xr/xrootd/package.nix

@@ -158,5 +158,6 @@ stdenv.mkDerivation (finalAttrs: {
     license = lib.licenses.lgpl3Plus;
     platforms = lib.platforms.all;
     maintainers = with lib.maintainers; [ ShamrockLee ];
+    mainProgram = "xrootd";
   };
 })

pkgs/development/python-modules/snakemake-executor-plugin-cluster-generic/default.nix

@@ -2,36 +2,69 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+
+  # build-system
   poetry-core,
-  snakemake-interface-executor-plugins,
+
+  # dependencies
   snakemake-interface-common,
+  snakemake-interface-executor-plugins,
+
+  # tests
+  pytestCheckHook,
+  snakemake,
+  writableTmpDirAsHomeHook,
 }:
 
-buildPythonPackage rec {
+buildPythonPackage (finalAttrs: {
   pname = "snakemake-executor-plugin-cluster-generic";
   version = "1.0.9";
   pyproject = true;
+  __structuredAttrs = true;
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = "snakemake-executor-plugin-cluster-generic";
-    tag = "v${version}";
+    tag = "v${finalAttrs.version}";
     hash = "sha256-RHMefoJOZb6TjRsFCORLFdHtI5ZpTsV6CHrjHKMat9o=";
   };
 
-  nativeBuildInputs = [ poetry-core ];
+  build-system = [
+    poetry-core
+  ];
 
-  propagatedBuildInputs = [
-    snakemake-interface-executor-plugins
+  dependencies = [
     snakemake-interface-common
+    snakemake-interface-executor-plugins
   ];
 
   pythonImportsCheck = [ "snakemake_executor_plugin_cluster_generic" ];
 
+  nativeCheckInputs = [
+    pytestCheckHook
+    snakemake
+    writableTmpDirAsHomeHook
+  ];
+
+  enabledTestPaths = [ "tests/tests.py" ];
+
+  disabledTestPaths = [
+    # Failed to setup log file: [Errno 13] Permission denied: '/build/pytest-of-nixbld/pytest-0/test_group_workflow5/groups/.snakemake'
+    "tests/tests.py::TestWorkflowsCancelCmd::test_group_workflow"
+    "tests/tests.py::TestWorkflowsCancelCmd::test_simple_workflow"
+    "tests/tests.py::TestWorkflowsSidecar::test_group_workflow"
+    "tests/tests.py::TestWorkflowsSidecar::test_simple_workflow"
+    "tests/tests.py::TestWorkflowsStatusCmd::test_group_workflow"
+    "tests/tests.py::TestWorkflowsStatusCmd::test_simple_workflow"
+    "tests/tests.py::TestWorkflowsSubmitCmdOnly::test_group_workflow"
+    "tests/tests.py::TestWorkflowsSubmitCmdOnly::test_simple_workflow"
+  ];
+
   meta = {
     description = "Generic cluster executor for Snakemake";
     homepage = "https://github.com/snakemake/snakemake-executor-plugin-cluster-generic";
+    changelog = "https://github.com/snakemake/snakemake-executor-plugin-cluster-generic/releases/tag/${finalAttrs.src.tag}";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ veprbl ];
   };
-}
+})

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

@@ -1,22 +1,34 @@
 {
   lib,
-  argparse-dataclass,
   buildPythonPackage,
-  configargparse,
   fetchFromGitHub,
   fetchpatch,
+
+  # build-system
   setuptools,
+
+  # dependencies
+  argparse-dataclass,
+  configargparse,
+
+  # tests
+  pytestCheckHook,
+  snakemake,
+
+  # passthru
+  snakemake-interface-common,
 }:
 
-buildPythonPackage rec {
+buildPythonPackage (finalAttrs: {
   pname = "snakemake-interface-common";
   version = "1.23.0";
   pyproject = true;
+  __structuredAttrs = true;
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = "snakemake-interface-common";
-    tag = "v${version}";
+    tag = "v${finalAttrs.version}";
     hash = "sha256-D3vktJmn1CifdiEg5UPGpBuuigEIb+ja4yklHZA6ytQ=";
   };
 
@@ -29,7 +41,9 @@ buildPythonPackage rec {
     })
   ];
 
-  build-system = [ setuptools ];
+  build-system = [
+    setuptools
+  ];
 
   dependencies = [
     argparse-dataclass
@@ -38,16 +52,24 @@ buildPythonPackage rec {
 
   pythonImportsCheck = [ "snakemake_interface_common" ];
 
-  # test_snakemake_version: No module named 'snakemake'
-  # nativeCheckInputs = [ pytestCheckHook ];
+  nativeCheckInputs = [
+    pytestCheckHook
+    snakemake
+  ];
 
-  # enabledTestPaths = [ "tests/tests.py" ];
+  enabledTestPaths = [ "tests/tests.py" ];
+
+  # Circular dependency with snakemake
+  doCheck = false;
+  passthru.tests.pytest = snakemake-interface-common.overridePythonAttrs {
+    doCheck = true;
+  };
 
   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${version}";
+    changelog = "https://github.com/snakemake/snakemake-interface-common/releases/tag/${finalAttrs.src.tag}";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ veprbl ];
   };
-}
+})

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

@@ -2,39 +2,66 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+
+  # build-system
   poetry-core,
+
+  # dependencies
   argparse-dataclass,
-  throttler,
   snakemake-interface-common,
+  throttler,
+
+  # tests
+  pytestCheckHook,
+  snakemake-executor-plugin-cluster-generic,
+
+  # passthru
+  snakemake-interface-executor-plugins,
 }:
 
-buildPythonPackage rec {
+buildPythonPackage (finalAttrs: {
   pname = "snakemake-interface-executor-plugins";
   version = "9.4.0";
   pyproject = true;
+  __structuredAttrs = true;
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = "snakemake-interface-executor-plugins";
-    tag = "v${version}";
+    tag = "v${finalAttrs.version}";
     hash = "sha256-ePbdHMYB2LfCOglz87ZnsUkJH7B97hhSmNBGzwtl5OM=";
   };
 
-  build-system = [ poetry-core ];
+  build-system = [
+    poetry-core
+  ];
 
   dependencies = [
     argparse-dataclass
-    throttler
     snakemake-interface-common
+    throttler
   ];
 
   pythonImportsCheck = [ "snakemake_interface_executor_plugins" ];
 
+  nativeCheckInputs = [
+    pytestCheckHook
+    snakemake-executor-plugin-cluster-generic
+  ];
+
+  enabledTestPaths = [ "tests/tests.py" ];
+
+  # Circular dependency with snakemake
+  doCheck = false;
+  passthru.tests.pytest = snakemake-interface-executor-plugins.overridePythonAttrs {
+    doCheck = true;
+  };
+
   meta = {
-    description = "This package provides a stable interface for interactions between Snakemake and its executor plugins";
+    description = "Stable interface for interactions between Snakemake and its executor plugins";
     homepage = "https://github.com/snakemake/snakemake-interface-executor-plugins";
-    changelog = "https://github.com/snakemake/snakemake-interface-executor-plugins/blob/${src.tag}/CHANGELOG.md";
+    changelog = "https://github.com/snakemake/snakemake-interface-executor-plugins/blob/${finalAttrs.src.tag}/CHANGELOG.md";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ veprbl ];
   };
-}
+})

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

@@ -2,34 +2,62 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+
+  # build-system
   hatchling,
+
+  # dependencies
   snakemake-interface-common,
+
+  # tests
+  pytestCheckHook,
+  snakemake-logger-plugin-rich,
+
+  # passthru
+  snakemake-interface-logger-plugins,
 }:
 
-buildPythonPackage rec {
+buildPythonPackage (finalAttrs: {
   pname = "snakemake-interface-logger-plugins";
-  version = "2.0.1";
+  version = "2.1.0";
   pyproject = true;
+  __structuredAttrs = true;
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = "snakemake-interface-logger-plugins";
-    tag = "v${version}";
-    hash = "sha256-yvEjd4xBjjCocGK/HD1j5jcuy+syyXcEJGdsEFA0H40=";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-UBdzJtKukR4Y9KPpu8qJv4HmN9ghncvEqGsTQnHk36k=";
   };
 
-  nativeBuildInputs = [ hatchling ];
+  build-system = [
+    hatchling
+  ];
 
-  propagatedBuildInputs = [
+  dependencies = [
     snakemake-interface-common
   ];
 
   pythonImportsCheck = [ "snakemake_interface_logger_plugins" ];
 
+  nativeCheckInputs = [
+    pytestCheckHook
+    snakemake-logger-plugin-rich
+  ];
+
+  enabledTestPaths = [ "tests/tests.py" ];
+
+  # Circular dependency with snakemake
+  doCheck = false;
+  passthru.tests.pytest = snakemake-interface-logger-plugins.overridePythonAttrs {
+    doCheck = true;
+  };
+
   meta = {
     description = "Stable interface for interactions between Snakemake and its logger plugins";
     homepage = "https://github.com/snakemake/snakemake-interface-logger-plugins";
+    changelog = "https://github.com/snakemake/snakemake-interface-logger-plugins/blob/${finalAttrs.src.tag}/CHANGELOG.md";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ veprbl ];
   };
-}
+})

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

@@ -2,32 +2,62 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+
+  # build-system
   poetry-core,
+
+  # dependencies
   snakemake-interface-common,
+
+  # tests
+  pytestCheckHook,
+  snakemake,
+
+  # passthru
+  snakemake-interface-report-plugins,
 }:
 
-buildPythonPackage rec {
+buildPythonPackage (finalAttrs: {
   pname = "snakemake-interface-report-plugins";
   version = "1.3.0";
   pyproject = true;
+  __structuredAttrs = true;
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = "snakemake-interface-report-plugins";
-    tag = "v${version}";
+    tag = "v${finalAttrs.version}";
     hash = "sha256-3ugEmdO1dcusKXXBZBRszlZXX5fhJyYSSF5Uj5CKJkQ=";
   };
 
-  nativeBuildInputs = [ poetry-core ];
+  build-system = [
+    poetry-core
+  ];
 
-  propagatedBuildInputs = [ snakemake-interface-common ];
+  dependencies = [
+    snakemake-interface-common
+  ];
 
   pythonImportsCheck = [ "snakemake_interface_report_plugins" ];
 
+  nativeCheckInputs = [
+    pytestCheckHook
+    snakemake
+  ];
+
+  enabledTestPaths = [ "tests/tests.py" ];
+
+  # Circular dependency with snakemake
+  doCheck = false;
+  passthru.tests.pytest = snakemake-interface-report-plugins.overridePythonAttrs {
+    doCheck = true;
+  };
+
   meta = {
     description = "Interface for Snakemake report plugins";
     homepage = "https://github.com/snakemake/snakemake-interface-report-plugins";
+    changelog = "https://github.com/snakemake/snakemake-interface-report-plugins/blob/${finalAttrs.src.tag}/CHANGELOG.md";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ veprbl ];
   };
-}
+})

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

@@ -2,41 +2,62 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+
+  # build-system
   hatchling,
+
+  # dependencies
   snakemake-interface-common,
+
+  # tests
+  pytestCheckHook,
+  snakemake,
+
+  # passthru
+  snakemake-interface-scheduler-plugins,
 }:
 
-let
+buildPythonPackage (finalAttrs: {
+  pname = "snakemake-interface-scheduler-plugins";
   version = "2.0.2";
+  pyproject = true;
+  __structuredAttrs = true;
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = "snakemake-interface-scheduler-plugins";
-    tag = "v${version}";
+    tag = "v${finalAttrs.version}";
     hash = "sha256-BowMwZllFR9IKYUMhISAbf606awTxfmS/nQxkGgb4y8=";
   };
-in
-buildPythonPackage {
-  pname = "snakemake-interface-scheduler-plugins";
-  inherit version src;
-  pyproject = true;
 
-  build-system = [ hatchling ];
+  build-system = [
+    hatchling
+  ];
 
-  dependencies = [ snakemake-interface-common ];
+  dependencies = [
+    snakemake-interface-common
+  ];
 
   pythonImportsCheck = [ "snakemake_interface_scheduler_plugins" ];
 
-  # test_scheduler: No module named 'snakemake'
-  # nativeCheckInputs = [ pytestCheckHook ];
+  nativeCheckInputs = [
+    pytestCheckHook
+    snakemake
+  ];
 
-  # enabledTestPaths = [ "tests/tests.py" ];
+  enabledTestPaths = [ "tests/tests.py" ];
+
+  # Circular dependency with snakemake
+  doCheck = false;
+  passthru.tests.pytest = snakemake-interface-scheduler-plugins.overridePythonAttrs {
+    doCheck = true;
+  };
 
   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/${src.rev}/CHANGELOG.md";
+    changelog = "https://github.com/snakemake/snakemake-interface-scheduler-plugins/blob/${finalAttrs.src.tag}/CHANGELOG.md";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ kyehn ];
   };
-}
+})

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

@@ -2,42 +2,77 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+
+  # build-system
   poetry-core,
+
+  # dependencies
   humanfriendly,
   reretry,
   snakemake-interface-common,
+  tenacity,
   throttler,
   wrapt,
+
+  # tests
+  pytestCheckHook,
+  snakemake,
+  snakemake-storage-plugin-http,
+
+  # passthru
+  snakemake-interface-storage-plugins,
 }:
 
-buildPythonPackage rec {
+buildPythonPackage (finalAttrs: {
   pname = "snakemake-interface-storage-plugins";
-  version = "4.3.2";
+  version = "4.4.1";
   pyproject = true;
+  __structuredAttrs = true;
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = "snakemake-interface-storage-plugins";
-    tag = "v${version}";
-    hash = "sha256-W2cUwc+9jng4IvBuN+m4WqpehA8qElTRb43w3QOIeN0=";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-tqSIJnU1+DPx/GI5/wzMkoxpLyM/k/SO8FtejRv9Zls=";
   };
 
-  nativeBuildInputs = [ poetry-core ];
+  build-system = [ poetry-core ];
 
-  propagatedBuildInputs = [
+  dependencies = [
     humanfriendly
     reretry
     snakemake-interface-common
+    tenacity
     throttler
     wrapt
   ];
 
   pythonImportsCheck = [ "snakemake_interface_storage_plugins" ];
 
+  nativeCheckInputs = [
+    pytestCheckHook
+    snakemake
+    snakemake-storage-plugin-http
+  ];
+
+  enabledTestPaths = [ "tests/tests.py" ];
+
+  disabledTests = [
+    # Requires internet access
+    "test_storage"
+  ];
+
+  # Circular dependency with snakemake
+  doCheck = false;
+  passthru.tests.pytest = snakemake-interface-storage-plugins.overridePythonAttrs {
+    doCheck = true;
+  };
+
   meta = {
-    description = "This package provides a stable interface for interactions between Snakemake and its storage plugins";
+    description = "Stable interface for interactions between Snakemake and its storage plugins";
+    changelog = "https://github.com/snakemake/snakemake-interface-storage-plugins/releases/tag/${finalAttrs.src.tag}";
     homepage = "https://github.com/snakemake/snakemake-interface-storage-plugins";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ veprbl ];
   };
-}
+})

pkgs/development/python-modules/snakemake-logger-plugin-rich/default.nix

@@ -0,0 +1,60 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+
+  # build-system
+  hatchling,
+
+  # dependencies
+  pydantic,
+  rich,
+  snakemake-interface-executor-plugins,
+  snakemake-interface-logger-plugins,
+
+  # tests
+  pytestCheckHook,
+  snakemake,
+  writableTmpDirAsHomeHook,
+}:
+
+buildPythonPackage (finalAttrs: {
+  pname = "snakemake-logger-plugin-rich";
+  version = "0.4.1";
+  pyproject = true;
+  __structuredAttrs = true;
+
+  src = fetchFromGitHub {
+    owner = "cademirch";
+    repo = "snakemake-logger-plugin-rich";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-kMjzagM95Td529JU+qIxGStgJGctS08glrFo3CF+Ih8=";
+  };
+
+  build-system = [
+    hatchling
+  ];
+
+  dependencies = [
+    pydantic
+    rich
+    snakemake-interface-executor-plugins
+    snakemake-interface-logger-plugins
+  ];
+
+  pythonImportsCheck = [ "snakemake_logger_plugin_rich" ];
+
+  nativeCheckInputs = [
+    pytestCheckHook
+    snakemake
+    writableTmpDirAsHomeHook
+  ];
+
+  meta = {
+    description = "Snakemake logger plugin using Rich";
+    homepage = "https://github.com/cademirch/snakemake-logger-plugin-rich";
+    changelog = "https://github.com/cademirch/snakemake-logger-plugin-rich/blob/${finalAttrs.src.tag}/CHANGELOG.md";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ GaetanLepage ];
+  };
+})

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

@@ -2,42 +2,59 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+
+  # build-system
   poetry-core,
-  snakemake-interface-storage-plugins,
+
+  # dependencies
   snakemake-interface-common,
+  snakemake-interface-storage-plugins,
   sysrsync,
+
+  # tests
+  pytestCheckHook,
+  snakemake,
+  writableTmpDirAsHomeHook,
 }:
 
-buildPythonPackage rec {
+buildPythonPackage (finalAttrs: {
   pname = "snakemake-storage-plugin-fs";
   version = "1.1.3";
   pyproject = true;
+  __structuredAttrs = true;
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = "snakemake-storage-plugin-fs";
-    tag = "v${version}";
+    tag = "v${finalAttrs.version}";
     hash = "sha256-UdK0yhl7ljLh57CXAvH/OYiVyw+BjhPwGjSBXX8sbZk=";
   };
 
-  build-system = [ poetry-core ];
+  build-system = [
+    poetry-core
+  ];
 
   dependencies = [
-    snakemake-interface-storage-plugins
     snakemake-interface-common
+    snakemake-interface-storage-plugins
     sysrsync
   ];
 
-  # The current tests are not worth dealing with cyclic dependency on snakemake
-  doCheck = false;
+  pythonImportsCheck = [ "snakemake_storage_plugin_fs" ];
 
-  # Use nothing due to a cyclic dependency on snakemake
-  pythonImportsCheck = [ ];
+  nativeCheckInputs = [
+    pytestCheckHook
+    snakemake
+    writableTmpDirAsHomeHook
+  ];
+
+  enabledTestPaths = [ "tests/tests.py" ];
 
   meta = {
     description = "Snakemake storage plugin that reads and writes from a locally mounted filesystem using rsync";
     homepage = "https://github.com/snakemake/snakemake-storage-plugin-fs";
+    changelog = "https://github.com/snakemake/snakemake-storage-plugin-fs/blob/${finalAttrs.src.tag}/CHANGELOG.md";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ veprbl ];
   };
-}
+})

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

@@ -0,0 +1,68 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+
+  # build-system
+  poetry-core,
+
+  # dependencies
+  requests,
+  requests-oauthlib,
+  snakemake-interface-common,
+  snakemake-interface-storage-plugins,
+
+  # tests
+  pytestCheckHook,
+  snakemake,
+}:
+
+buildPythonPackage (finalAttrs: {
+  pname = "snakemake-storage-plugin-http";
+  version = "0.3.1";
+  pyproject = true;
+  __structuredAttrs = true;
+
+  src = fetchFromGitHub {
+    owner = "snakemake";
+    repo = "snakemake-storage-plugin-http";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-ad4IOjU761CaZ+o0//I8/xW+e+4UJG0+VAbQ9KcNjFY=";
+  };
+
+  build-system = [
+    poetry-core
+  ];
+
+  pythonRelaxDeps = [
+    "requests-oauthlib"
+  ];
+  dependencies = [
+    requests
+    requests-oauthlib
+    snakemake-interface-common
+    snakemake-interface-storage-plugins
+  ];
+
+  pythonImportsCheck = [ "snakemake_storage_plugin_http" ];
+
+  nativeCheckInputs = [
+    pytestCheckHook
+    snakemake
+  ];
+
+  enabledTestPaths = [ "tests/tests.py" ];
+
+  disabledTests = [
+    # Requires internet access
+    "test_storage"
+  ];
+
+  meta = {
+    description = "Snakemake storage plugin for donwloading input files from HTTP(s)";
+    homepage = "https://github.com/snakemake/snakemake-storage-plugin-http";
+    changelog = "https://github.com/snakemake/snakemake-storage-plugin-http/blob/${finalAttrs.src.tag}/CHANGELOG.md";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ GaetanLepage ];
+  };
+})

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

@@ -2,24 +2,33 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+
+  # build-system
+  poetry-core,
+
+  # dependencies
   boto3,
   botocore,
-  poetry-core,
-  snakemake,
-  snakemake-interface-storage-plugins,
   snakemake-interface-common,
+  snakemake-interface-storage-plugins,
   urllib3,
+
+  # tests
+  pytestCheckHook,
+  snakemake,
+  writableTmpDirAsHomeHook,
 }:
 
-buildPythonPackage rec {
+buildPythonPackage (finalAttrs: {
   pname = "snakemake-storage-plugin-s3";
   version = "0.3.6";
   pyproject = true;
+  __structuredAttrs = true;
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = "snakemake-storage-plugin-s3";
-    tag = "v${version}";
+    tag = "v${finalAttrs.version}";
     hash = "sha256-hvyQ6V6POUBWTCWt9moQlH0RgSM4J36kjbXK4TtO8Bo=";
   };
 
@@ -33,15 +42,31 @@ buildPythonPackage rec {
     urllib3
   ];
 
-  nativeCheckInputs = [ snakemake ];
-
   pythonImportsCheck = [ "snakemake_storage_plugin_s3" ];
 
+  nativeCheckInputs = [
+    pytestCheckHook
+    snakemake
+    writableTmpDirAsHomeHook
+  ];
+
+  enabledTestPaths = [ "tests/tests.py" ];
+
+  disabledTests = [
+    # Requires internet access
+    "test_storage"
+
+    # snakemake_interface_common.exceptions.WorkflowError: Failed to create local storage prefix .snakemake/storage/s3
+    # PermissionError: [Errno 13] Permission denied: '.snakemake'
+    "test_group_workflow"
+    "test_simple_workflow"
+  ];
+
   meta = {
     description = "Snakemake storage plugin for S3 API storage (AWS S3, MinIO, etc.)";
     homepage = "https://github.com/snakemake/snakemake-storage-plugin-s3";
-    changelog = "https://github.com/snakemake/snakemake-storage-plugin-s3/releases/tag/${src.tag}";
+    changelog = "https://github.com/snakemake/snakemake-storage-plugin-s3/releases/tag/${finalAttrs.src.tag}";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ veprbl ];
   };
-}
+})

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

@@ -1,29 +1,43 @@
 {
   lib,
+  pkgs,
   buildPythonPackage,
   fetchFromGitHub,
+
+  # build-system
   hatch-vcs,
   hatchling,
-  snakemake,
-  snakemake-interface-storage-plugins,
+
+  # dependencies
+  reretry,
   snakemake-interface-common,
+  snakemake-interface-storage-plugins,
   xrootd,
+
+  # tests
+  pytestCheckHook,
+  snakemake,
 }:
 
-buildPythonPackage rec {
+buildPythonPackage (finalAttrs: {
   pname = "snakemake-storage-plugin-xrootd";
-  version = "1.0.0";
+  version = "1.1.0";
   pyproject = true;
+  __structuredAttrs = true;
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = "snakemake-storage-plugin-xrootd";
-    tag = "v${version}";
-    hash = "sha256-QYG/BE7y3h/Mz1PrVVxmfBBLBLoirrEx9unSEaflUds=";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-vL9JD9h0ywsKpUPoXhgg6b+vwi7kxK8CF3L6HnAEidE=";
   };
 
-  # xrootd<6.0.0,>=5.6.4 not satisfied by version 5.7rc20240303
-  pythonRelaxDeps = [ "xrootd" ];
+  postPatch = ''
+    substituteInPlace tests/tests.py \
+      --replace-fail \
+        'subprocess.Popen(["xrootd",' \
+        'subprocess.Popen(["${lib.getExe pkgs.xrootd}",'
+  '';
 
   build-system = [
     hatch-vcs
@@ -33,17 +47,24 @@ buildPythonPackage rec {
   dependencies = [
     snakemake-interface-storage-plugins
     snakemake-interface-common
+    reretry
     xrootd
   ];
 
-  nativeCheckInputs = [ snakemake ];
-
   pythonImportsCheck = [ "snakemake_storage_plugin_xrootd" ];
 
+  nativeCheckInputs = [
+    pytestCheckHook
+    snakemake
+  ];
+
+  enabledTestPaths = [ "tests/tests.py" ];
+
   meta = {
     description = "Snakemake storage plugin for handling input and output via XRootD";
     homepage = "https://github.com/snakemake/snakemake-storage-plugin-xrootd";
+    changelog = "https://github.com/snakemake/snakemake-storage-plugin-xrootd/releases/tag/${finalAttrs.src.tag}";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ veprbl ];
   };
-}
+})

pkgs/top-level/python-packages.nix

@@ -18194,10 +18194,18 @@ self: super: with self; {
     callPackage ../development/python-modules/snakemake-interface-storage-plugins
       { };
 
+  snakemake-logger-plugin-rich =
+    callPackage ../development/python-modules/snakemake-logger-plugin-rich
+      { };
+
   snakemake-storage-plugin-fs =
     callPackage ../development/python-modules/snakemake-storage-plugin-fs
       { };
 
+  snakemake-storage-plugin-http =
+    callPackage ../development/python-modules/snakemake-storage-plugin-http
+      { };
+
   snakemake-storage-plugin-s3 =
     callPackage ../development/python-modules/snakemake-storage-plugin-s3
       { };