main changes

.github/workflows/build.yml

@@ -1,29 +1,39 @@
 name: Build
 
-on:
-  push:
-    branches:
-      - main
+on: push
 
 jobs:
   build:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
+        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
     steps:
       - uses: actions/checkout@v4
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+
       - name: Install dependencies
         run: |
           sudo apt-get install -y python3-sphinx sphinx-rtd-theme-common
-          pip install sphinx_rtd_theme recommonmark
+          pip install sphinx_rtd_theme recommonmark pytest pytest-cov
+
       - name: Check package install
         run: |
-          pip install .
+          pip install -e .
+
+      - name: Run tests
+        run: pytest -m unit --cov=wfcommons tests/
+
+      - name: Upload coverage
+        if: github.ref == 'refs/heads/main'
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Build documentation
         run: |
           cd docs

.gitignore

@@ -44,6 +44,10 @@ venv
 # Workflow Schema
 workflow-schema.json
 
+# Binaries
+bin/cpu-benchmark
+bin/cpu-benchmark.o
+
 # wfc-1.3_to_dask specifics
 /wfcommons/wfc-1.3_to_dask/__pycache__/
 /wfcommons/wfc-1.3_to_dask/.coverage

README.md

@@ -3,6 +3,7 @@
 [![License: LGPL v3][license-badge]](LICENSE)
 [![CodeFactor][codefactor-badge]][codefactor-link]
 [![Documentation Status][rtd-badge]][rtd-link]
+[![Codecov][cov-badge]][cov-link]
 [![Downloads](https://static.pepy.tech/personalized-badge/wfcommons?period=total&units=international_system&left_color=grey&right_color=yellowgreen&left_text=Downloads)](https://pepy.tech/project/wfcommons)
 
 <a href="https://wfcommons.org" target="_blank"><img src="https://wfcommons.org/images/wfcommons-horizontal.png" width="350" /></a>
@@ -20,7 +21,7 @@ This Python package provides a collection of tools for:
 ## Installation
 
 WfCommons is available on [PyPI](https://pypi.org/project/wfcommons).
-WfCommons requires Python3.8+ and has been tested on Linux and macOS.
+WfCommons requires Python3.9+ and has been tested on Linux and macOS.
 
 ### Installation using pip
 
@@ -114,3 +115,5 @@ that paper, as it provides a recent and general overview on the framework.
 [codefactor-link]:     https://www.codefactor.io/repository/github/wfcommons/wfcommons
 [rtd-badge]:           https://readthedocs.org/projects/wfcommons/badge/?version=latest
 [rtd-link]:            https://wfcommons.readthedocs.io/en/latest/?badge=latest
+[cov-badge]:           https://codecov.io/gh/wfcommons/WfCommons/graph/badge.svg?token=PJTXMLCIXD
+[cov-link]:            https://codecov.io/gh/wfcommons/WfCommons

bin/wfbench

@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
 # Copyright (c) 2021-2024 The WfCommons Team.
@@ -125,9 +125,10 @@ def cpu_mem_benchmark(cpu_threads: Optional[int] = 5,
             os.sched_setaffinity(cpu_proc.pid, {core})
         cpu_procs.append(cpu_proc)
 
-    mem_proc = subprocess.Popen(mem_prog)
-    if core:
-        os.sched_setaffinity(mem_proc.pid, {core})
+    if mem_threads > 0:
+        mem_proc = subprocess.Popen(mem_prog)
+        if core:
+            os.sched_setaffinity(mem_proc.pid, {core})
 
     return cpu_procs
 
@@ -261,8 +262,9 @@ def main():
         if core:
             print(f"[WfBench]  {args.name} acquired core {core}")
 
+        mem_threads=int(10 - 10 * args.percent_cpu)
         cpu_procs = cpu_mem_benchmark(cpu_threads=int(10 * args.percent_cpu),
-                                    mem_threads=int(10 - 10 * args.percent_cpu),
+                                    mem_threads=mem_threads,
                                     cpu_work=sys.maxsize if args.time else int(args.cpu_work),
                                     core=core,
                                     total_mem=args.mem)

docs/source/generating_workflow_benchmarks.rst

@@ -109,7 +109,7 @@ workflow benchmark for running with Nextflow::
 
     # generate a Nextflow workflow
     translator = NextflowTranslator(benchmark.workflow)
-    translator.translate(output_file_name=pathlib.Path("/tmp/benchmark-workflow.nf"))
+    translator.translate(output_file_path=pathlib.Path("/tmp/benchmark-workflow.nf"))
 
 .. warning::
 

docs/source/quickstart_installation.rst

@@ -2,7 +2,7 @@ Installation
 ============
 
 WfCommons is available on `PyPI <https://pypi.org/project/wfcommons>`_.
-WfCommons requires Python3.6+ and has been tested on Linux and macOS.
+WfCommons requires Python3.9+ and has been tested on Linux and macOS.
 
 Installation using pip
 ----------------------

pyproject.toml

@@ -0,0 +1,70 @@
+[build-system]
+requires = ["setuptools>=65.5.1"]  # PEP 518 specifications
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "wfcommons"
+authors = [{name = "WfCommons team", email = "[email protected]"}]
+description = "A Framework for Enabling Scientific Workflow Research and Education"
+readme = "README.md"
+requires-python = ">=3.9"
+classifiers = [
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Education",
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
+    "Topic :: Documentation :: Sphinx",
+    "Topic :: System :: Distributed Computing"
+]
+license = {text = "GNU General Public License v3 (GPLv3)"}
+dependencies = [
+    "jsonschema",
+    "matplotlib",
+    "networkx",
+    "numpy",
+    "pandas",
+    "python-dateutil",
+    "requests",
+    "scipy",
+    "pyyaml",
+    "pandas",
+    "stringcase"
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://wfcommons.org"
+Source = "https://github.com/wfcommons/wfcommons"
+Documentation = "https://docs.wfcommons.org"
+Tracker = "https://github.com/wfcommons/WfCommons/issues"
+
+[project.optional-dependencies]
+test = ["pytest", "pytest-cov"]
+
+[tool.setuptools.dynamic]
+version = {attr = "wfcommons.version.__version__"}
+
+[tool.pytest.ini_options]
+addopts="""
+--cov-context test  \
+--cov-config pyproject.toml \
+--cov-report xml:coverage.xml \
+--cov-report term-missing \
+--cov ./wfcommons \
+--ignore wfcommons/wfbench/translator/templates \
+--no-cov-on-fail \
+-ra \
+-W ignore"""
+testpaths = [
+  "tests"
+]
+markers = [
+  "unit: Mark a test as a unit test"
+]

setup.py

@@ -25,59 +25,13 @@ def run(self):
             sys.exit(-1) 
         super().run()
 
-
-with open('README.md', 'r') as fh:
-    long_description = fh.read()
-
-# Fetch the version
-exec(open('wfcommons/version.py').read())
-
 setup(
-    name='wfcommons',
-    version=str(__version__),
-    license='LGPLv3',
-    author='WfCommons team',
-    author_email='[email protected]',
-    description='A Framework for Enabling Scientific Workflow Research and Education',
-    long_description=long_description,
-    long_description_content_type='text/markdown',
-    url='https://github.com/wfcommons/wfcommons',
     packages=find_packages(),
     include_package_data=True,
     has_ext_modules=lambda: True,
     cmdclass={
         'build_ext': Build,
     },
-    install_requires=[
-        'jsonschema',
-        'matplotlib',
-        'networkx',
-        'numpy',
-        'python-dateutil',
-        'requests',
-        'scipy',
-        'setuptools',
-        'pyyaml',
-        'pandas',
-        'stringcase'
-    ],
-    classifiers=[
-        'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
-        'Operating System :: OS Independent',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.8',
-        'Programming Language :: Python :: 3.9',
-        'Programming Language :: Python :: 3.10',
-        'Programming Language :: Python :: 3.11',
-        'Programming Language :: Python :: 3.12',
-        'Intended Audience :: Developers',
-        'Intended Audience :: Education',
-        'Intended Audience :: Science/Research',
-        'Natural Language :: English',
-        'Topic :: Documentation :: Sphinx',
-        'Topic :: System :: Distributed Computing'
-    ],
-    python_requires='>=3.8',
     data_files=[
         ('bin', ['bin/cpu-benchmark', 'bin/wfbench'])
     ],

tests/unit/test_task.py

@@ -0,0 +1,60 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Copyright (c) 2024 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 pytest
+
+from wfcommons.common import Task, TaskType, File, FileLink, Machine, MachineSystem
+
+
+task_name = "Task Test"
+task_id = "task_test_1"
+input_files = [File(file_id="file_in_1", size=10, link=FileLink.INPUT), File(file_id="file_in_2", size=20, link=FileLink.INPUT)]
+output_files = [File(file_id="file_out_1", size=30, link=FileLink.OUTPUT), File(file_id="file_out_2", size=40, link=FileLink.OUTPUT)]
+
+
+class TestTask:
+
+    @pytest.fixture
+    def task(self) -> Task:
+        return Task(
+            name=task_name,
+            task_id=task_id,
+            runtime=123.45,
+            input_files=input_files,
+            output_files=output_files,
+            category="task_test",
+            machines=[Machine(name="machine_1", cpu = {"coreCount": 48, "speedInMHz": 1200, "vendor": "Vendor Name"})],
+            program="program",
+            args=["arg_1", "arg_2"],
+            avg_cpu=0.5,
+            bytes_read=12345,
+            bytes_written=54321,
+            memory=10,
+            energy=100,
+            avg_power=1.0,
+            priority=100,
+            executedAt="2024-09-15T08:59:33.699321-04:00",
+            task_type=TaskType.COMPUTE,
+            launch_dir="/tmp",
+        )
+
+    @pytest.mark.unit
+    def test_task_specification(self, task: Task) -> None:
+
+        task_specification = {
+            "name": task_name,
+            "id": task_id,
+            "parents": [],
+            "children": [],
+            "inputFiles": [str(f) for f in input_files],
+            "outputFiles": [str(f) for f in output_files]
+        }
+
+        assert(task_specification == task.specification_as_dict())