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merge wfcommons_test
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‎.github/workflows/build.yml‎

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

‎.gitignore‎

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# Workflow Schema
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workflow-schema.json
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# Binaries
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bin/cpu-benchmark
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bin/cpu-benchmark.o
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# wfc-1.3_to_dask specifics
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/wfcommons/wfc-1.3_to_dask/__pycache__/
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/wfcommons/wfc-1.3_to_dask/.coverage

‎README.md‎

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## Installation
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WfCommons is available on [PyPI](https://pypi.org/project/wfcommons).
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WfCommons requires Python3.8+ and has been tested on Linux and macOS.
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WfCommons requires Python3.9+ and has been tested on Linux and macOS.
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### Installation using pip
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‎docs/source/quickstart_installation.rst‎

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

‎pyproject.toml‎

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[build-system]
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requires = ["setuptools>=65.5.1"] # PEP 518 specifications
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build-backend = "setuptools.build_meta"
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[project]
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name = "wfcommons"
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authors = [{name = "WfCommons team", email = "support@wfcommons.org"}]
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description = "A Framework for Enabling Scientific Workflow Research and Education"
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readme = "README.md"
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requires-python = ">=3.8"
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classifiers = [
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"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
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"Operating System :: OS Independent",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.9",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Intended Audience :: Developers",
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"Intended Audience :: Education",
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"Intended Audience :: Science/Research",
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"Natural Language :: English",
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"Topic :: Documentation :: Sphinx",
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"Topic :: System :: Distributed Computing"
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]
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license = {text = "GNU General Public License v3 (GPLv3)"}
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dependencies = [
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"jsonschema",
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"matplotlib",
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"networkx",
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"numpy",
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"python-dateutil",
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"requests",
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"scipy",
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"pyyaml",
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"pandas",
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"stringcase"
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]
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dynamic = ["version"]
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[project.urls]
42+
Homepage = "https://wfcommons.org"
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Source = "https://github.com/wfcommons/wfcommons"
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Documentation = "https://docs.wfcommons.org"
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Tracker = "https://github.com/wfcommons/WfCommons/issues"
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[project.optional-dependencies]
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test = ["pytest", "pytest-cov"]
49+
50+
[tool.setuptools.dynamic]
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version = {attr = "wfcommons.version.__version__"}
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[tool.pytest.ini_options]
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addopts="""
55+
--cov-context test \
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--cov-config pyproject.toml \
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--cov-report xml:coverage.xml \
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--cov-report term-missing \
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--cov ./wfcommons \
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--ignore wfcommons/wfbench/translator/templates \
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--no-cov-on-fail \
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-ra \
63+
-W ignore"""
64+
testpaths = [
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"tests"
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]
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markers = [
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"unit: Mark a test as a unit test"
69+
]

‎setup.py‎

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@@ -33,7 +33,7 @@ def run(self):
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setup(
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name='wfcommons',
36-
version=str(__version__),
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version="1.1",
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license='LGPLv3',
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author='WfCommons team',
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author_email='support@wfcommons.org',
@@ -75,7 +75,7 @@ def run(self):
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'Topic :: Documentation :: Sphinx',
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'Topic :: System :: Distributed Computing'
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],
78-
python_requires='>=3.8',
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python_requires='>=3.9',
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data_files=[
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('bin', ['bin/cpu-benchmark', 'bin/wfbench'])
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],

‎tests/unit/test_task.py‎

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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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#
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# Copyright (c) 2024 The WfCommons Team.
5+
#
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# This program is free software: you can redistribute it and/or modify
7+
# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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11+
import pytest
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13+
from wfcommons.common import Task, TaskType, File, FileLink, Machine, MachineSystem
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15+
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task_name = "Task Test"
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task_id = "task_test_1"
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input_files = [File(file_id="file_in_1", size=10, link=FileLink.INPUT), File(file_id="file_in_2", size=20, link=FileLink.INPUT)]
19+
output_files = [File(file_id="file_out_1", size=30, link=FileLink.OUTPUT), File(file_id="file_out_2", size=40, link=FileLink.OUTPUT)]
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class TestTask:
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@pytest.fixture
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def task(self) -> Task:
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return Task(
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name=task_name,
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task_id=task_id,
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runtime=123.45,
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input_files=input_files,
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output_files=output_files,
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category="task_test",
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machines=[Machine(name="machine_1", cpu = {"coreCount": 48, "speedInMHz": 1200, "vendor": "Vendor Name"})],
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program="program",
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args=["arg_1", "arg_2"],
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avg_cpu=0.5,
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bytes_read=12345,
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bytes_written=54321,
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memory=10,
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energy=100,
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avg_power=1.0,
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priority=100,
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executedAt="2024-09-15T08:59:33.699321-04:00",
44+
task_type=TaskType.COMPUTE,
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launch_dir="/tmp",
46+
)
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48+
@pytest.mark.unit
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def test_task_specification(self, task: Task) -> None:
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51+
task_specification = {
52+
"name": task_name,
53+
"id": task_id,
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"parents": [],
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"children": [],
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"inputFiles": [str(f) for f in input_files],
57+
"outputFiles": [str(f) for f in output_files]
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}
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assert(task_specification == task.specification_as_dict())

‎tests/unit/test_workflow.py‎

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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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#
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# Copyright (c) 2024 The WfCommons Team.
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#
6+
# This program is free software: you can redistribute it and/or modify
7+
# it under the terms of the GNU General Public License as published by
8+
# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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11+
import pathlib
12+
import pytest
13+
14+
from wfcommons.common import Task, Workflow
15+
from wfcommons.version import __version__, __schema_version__
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17+
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tasks_list = [
19+
([Task(name="task_1", task_id="task_1", runtime=15.0)]),
20+
([Task(name="task_1", task_id="task_1", runtime=15.0), Task(name="task_2", task_id="task_2", runtime=30.0)]),
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([Task(name="task_1", task_id="task_1", runtime=15.0), Task(name="task_2", task_id="task_2", runtime=30.0), Task(name="task_3", task_id="task_3", runtime=60.0)]),
22+
]
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25+
class TestWorkflow:
26+
27+
@pytest.fixture
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def workflow(self) -> Workflow:
29+
return Workflow(
30+
name="Workflow Test",
31+
makespan=100.0
32+
)
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@pytest.mark.unit
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def test_workflow_creation(self, workflow: Workflow) -> None:
36+
workflow.write_json(pathlib.Path("/tmp/workflow_test.json"))
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38+
workflow_json = {
39+
"name": "Workflow Test",
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"description": "Instance generated with WfCommons - https://wfcommons.org",
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"createdAt": workflow.created_at,
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"schemaVersion": f"{__schema_version__}",
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"author": {
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"name": f"{workflow.author_name}",
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"email": "support@wfcommons.org"
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},
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"workflow": {
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"specification": {
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"tasks": [],
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"files": []
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},
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"execution": {
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"makespanInSeconds": 100.0,
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"executedAt": workflow.executed_at,
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"tasks": []
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}
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},
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"runtimeSystem": {
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"name": "WfCommons",
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"version": f"{__version__}",
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"url": "https://docs.wfcommons.org/en/v1.1.dev/"
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}
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}
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assert(workflow.workflow_json == workflow_json)
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@pytest.mark.unit
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def test_workflow_empty_tasks(self, workflow: Workflow) -> None:
69+
assert(not workflow.tasks)
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@pytest.mark.parametrize(("tasks"), tasks_list)
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@pytest.mark.unit
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def test_workflow_add_tasks(self, workflow: Workflow, tasks: list[Task]) -> None:
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tasks_list = []
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for task in tasks:
76+
workflow.add_task(task)
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tasks_list.append(task.task_id)
78+
assert(workflow.leaves() == tasks_list)
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@pytest.mark.parametrize(("tasks"), tasks_list)
81+
@pytest.mark.unit
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def test_workflow_add_dependencies_roots(self, workflow: Workflow, tasks: list[Task]) -> None:
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previous_task = None
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for task in tasks:
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workflow.add_task(task)
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if previous_task:
87+
workflow.add_dependency(previous_task.task_id, task.task_id)
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previous_task = task
89+
assert(workflow.roots() == [tasks[0].task_id])
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@pytest.mark.parametrize(("tasks"), tasks_list)
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@pytest.mark.unit
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def test_workflow_add_dependencies_leaves(self, workflow: Workflow, tasks: list[Task]) -> None:
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previous_task = None
95+
for task in tasks:
96+
workflow.add_task(task)
97+
if previous_task:
98+
workflow.add_dependency(previous_task.task_id, task.task_id)
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previous_task = task
100+
assert(workflow.leaves() == [previous_task.task_id])

‎wfcommons/common/__init__.py‎

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# (at your option) any later version.
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from .workflow import Workflow
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from .file import File
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from .file import FileLink
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from .task import Task
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from .task import TaskType
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from .file import File, FileLink
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from .task import Task, TaskType
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from .machine import Machine, MachineSystem

‎wfcommons/common/file.py‎

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'id': self.file_id,
5454
'sizeInBytes': self.size
5555
}
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def __str__(self) -> str:
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return self.file_id

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