Merge branch 'main' into flowcept_improvements

Author: rafaelfsilva

tests/unit/test_utils.py

@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Copyright (c) 2025 The WfCommons Team.
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+
+import json
+import pathlib
+import pytest
+import wfcommons.utils
+
+from typing import Dict, List, Tuple
+
+
+class TestUtils:
+    
+    @pytest.mark.unit
+    @pytest.mark.parametrize(
+        "data,distribution",
+        [
+            pytest.param([1, 2, 3], ("rdist", (1.5504806356651624, 0.0013236200991527764, 0.0013236200991527767))),
+            pytest.param([1, 1, 1], ("pareto", (2.25803497307119, -7.535551383120264e-19, 4.806600020282434e-19))),
+        ],
+    )
+    def test_best_fit_distribution(self, data: List[float], distribution: Tuple) -> None:
+        assert(wfcommons.utils.best_fit_distribution(data) == distribution)
+
+    @pytest.mark.unit
+    @pytest.mark.parametrize(
+        "distribution,min_value,max_value",
+        [
+            pytest.param(None, 10, 100),
+            pytest.param({"name": "norm", "params": [0.08688656476267097, 0.2572832376513094]}, 10, 100),
+        ],
+    ) 
+    def test_generate_rvs(self, distribution: Dict, min_value: float, max_value: float) -> None:
+        assert(min_value <= wfcommons.utils.generate_rvs(distribution, min_value, max_value) <= max_value )
+
+    @pytest.mark.unit
+    @pytest.mark.parametrize(
+        "n,r,combinations",
+        [
+            pytest.param(2, 2, 1),
+            pytest.param(10, 2, 45),
+            pytest.param(10, 3, 120),
+        ],
+    )   
+    def test_ncr(self, n: int, r: int, combinations: int) -> None:
+        assert(wfcommons.utils.ncr(n, r) == combinations)

tests/unit/wfinstances/test_instance_analyzer.py

@@ -0,0 +1,85 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Copyright (c) 2025 The WfCommons Team.
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+
+import json
+import pathlib
+import pytest
+
+from wfcommons.wfinstances import Instance, InstanceAnalyzer
+
+
+class TestInstanceAnalyzer:
+
+    @pytest.fixture
+    def instance(self) -> pathlib.Path:
+        instance = {
+            "name": "workflow_test",
+            "description": "Instance generate for WfCommons Test",
+            "createdAt": "2020-12-30T02:19:01.238077",
+            "schemaVersion": "1.5",
+            "author": {
+                "name": "wfcommons",
+                "email": "support@wfcommons.org"
+            },
+            "workflow": {
+                "specification": {
+                    "tasks": [
+                        {
+                            "name": "task_01",
+                            "id": "task_01",
+                            "children": ["task_02", "task_03"],
+                            "inputFiles": ["input_01.txt", "input_02.txt"],
+                            "outputFiles": ["output_01.txt"],
+                            "parents": []
+                        }
+                    ],
+                    "files": [
+                        {"id": "input_01.txt", "sizeInBytes": 10}, {"id": "input_02.txt", "sizeInBytes": 20},
+                        {"id": "output_01.txt", "sizeInBytes": 15}
+                    ]
+                },
+                "execution": {
+                    "makespanInSeconds": 111.5,
+                    "executedAt": "2024-11-30T03:25:55+00:00",
+                    "tasks": [
+                        {
+                            "id": "task_01",
+                            "runtimeInSeconds": 0.052203,
+                            "command": {
+                                "program": "program_1",
+                                "arguments": ["a", "b"]
+                            },
+                            "coreCount": 1,
+                            "avgCPU": 90.123,
+                            "readBytes": 150,
+                            "writtenBytes": 200,
+                            "memoryInBytes": 300,
+                            "machines": ["worker-1"]
+                        }
+                    ],
+                    "machines": [
+                        {"nodeName": "worker-1", "cpu": {"coreCount": 24}}
+                    ]
+                }
+            },
+            "runtimeSystem": {"name": "wfcommons", "version": "1.0", "url": "https://wfcommons.org"}
+        }
+        instance_path = pathlib.Path("/tmp/wfcommons_test_workflow.json")
+        instance_path.write_text(json.dumps(instance))
+        return instance_path
+
+    @pytest.mark.unit
+    def test_instance_analyzer_summary(self, instance : pathlib.Path) -> None:
+        instance = Instance(instance)
+        analyzer = InstanceAnalyzer()
+        analyzer.append_instance(instance)
+        workflow_tasks = ['task_01']
+        summary = analyzer.build_summary(workflow_tasks, include_raw_data=False)
+        assert(summary == {'task_01': {'runtime': {'min': 0.052203, 'max': 0.052203, 'distribution': {'name': 'dweibull', 'params': [0.19451622991431783, 4.155260197271249e-34, 1.161132255170155]}}, 'input': {'.txt': {'distribution': {'name': 'rdist', 'params': [1.5504806356651624, 0.0013236200991527764, 0.0013236200991527767]}, 'min': 10, 'max': 20}}, 'output': {'.txt': {'distribution': None, 'min': 15, 'max': 15}}}})

wfcommons/wfbench/translator/cwl.py

@@ -132,7 +132,7 @@ def _parse_steps(self) -> None:
 
                 code = [
                     f"  {task.task_id}:",
-                    "    run: clt/bash.cwl",
+                    "    run: clt/shell.cwl",
                     "    in:",
                 ]
 
@@ -224,7 +224,7 @@ def _write_cwl_files(self, output_folder: pathlib.Path) -> None:
         clt_folder.mkdir(exist_ok=True)
         shutil.copy(this_dir.joinpath("templates/cwl_templates/wfbench.cwl"), clt_folder)
         shutil.copy(this_dir.joinpath("templates/cwl_templates/folder.cwl"), clt_folder)
-        shutil.copy(this_dir.joinpath("templates/cwl_templates/bash.cwl"), clt_folder)
+        shutil.copy(this_dir.joinpath("templates/cwl_templates/shell.cwl"), clt_folder)
 
         with open(cwl_folder.joinpath("main.cwl"), "w", encoding="utf-8") as f:
             f.write("\n".join(self.cwl_script))

wfcommons/wfbench/translator/templates/cwl_templates/shell.cwl

@@ -3,8 +3,8 @@ class: CommandLineTool
 requirements:
   InlineJavascriptRequirement: {}
   ShellCommandRequirement: {}
-stdout: $("logs/" + inputs.step_name + ".out")
-stderr: $("logs/" + inputs.step_name + ".err")
+stdout: $(inputs.step_name + ".out")
+stderr: $(inputs.step_name + ".err")
 
 arguments:
   - position: 1