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starting Python package for test suite code
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‎.flake8

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[flake8]
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max-line-length = 150
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exclude =
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tests/*
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docs/*

‎.github/workflows/ci.yml

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name: Continuous integration
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on:
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- push
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jobs:
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getVersionNumber:
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name: Get version number
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if: startsWith(github.ref, 'refs/tags/')
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runs-on: ubuntu-latest
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outputs:
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version: ${{ steps.get-version-number.outputs.version }}
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steps:
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- id: get-version-number
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name: Get version number
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env:
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TAG: ${{ github.ref }}
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run: |
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version="${TAG/refs\/tags\//}"
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echo "::set-output name=version::$version"
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build:
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name: Lint, test, and compile documentation
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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with:
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fetch-depth: 1
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- name: Install Python
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uses: actions/setup-python@v2
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with:
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python-version: '3.7'
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- name: Setup pip cache
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uses: actions/cache@v2
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with:
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path: /opt/hostedtoolcache/Python
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key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements.optional.txt') }}
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restore-keys: |
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${{ runner.os }}-pip-
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- name: Install pip and setuptools
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run: |
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python -m pip install --upgrade pip
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python -m pip install --upgrade setuptools
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# install package
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- name: Install the package
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run: python -m pip install .[all]
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# lint
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- name: Install flake8
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run: python -m pip install flake8
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- name: Lint the package
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run: python -m flake8
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# test and upload coverage report to Codecov
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- name: Install pytest
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run: python -m pip install pytest pytest-cov
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- name: Install the requirements for the tests
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run: python -m pip install .[tests]
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- name: Run the tests
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run: python -m pytest tests/ --cov=./biosimulators_test_suite --cov-report=xml
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- name: Upload the coverage report to Codecov
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uses: codecov/[email protected]
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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flags: unittests
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file: ./coverage.xml
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# compile documentation
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- name: Install the requirements for compiling the documentation
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run: python -m pip install -r docs-src/requirements.txt
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- name: Compile the documentation
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run: |
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sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
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mkdir -p docs-src/_static
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sphinx-build docs-src docs
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release:
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name: Release a new version
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needs: [getVersionNumber, build]
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runs-on: ubuntu-latest
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outputs:
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docsChanged: ${{ steps.commit-docs.outputs.docsChanged }}
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steps:
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- name: Checkout code
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uses: actions/checkout@v2
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with:
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fetch-depth: 1
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ref: dev
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- name: Install Python
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uses: actions/setup-python@v2
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with:
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python-version: '3.7'
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- name: Setup pip cache
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uses: actions/cache@v2
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with:
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path: /opt/hostedtoolcache/Python
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key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements.optional.txt') }}
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restore-keys: |
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${{ runner.os }}-pip-
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- name: Install pip and setuptools
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run: |
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python -m pip install --upgrade pip
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python -m pip install --upgrade setuptools
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# install package
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- name: Install the package
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run: python -m pip install .[all]
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# compile and push documentation
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- name: Install the requirements for compiling the documentation
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run: python -m pip install -r docs-src/requirements.txt
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- name: Compile the documentation
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run: |
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sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
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mkdir -p docs-src/_static
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sphinx-build docs-src docs
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- id: commit-docs
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name: Commit the compiled documentation
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run: |
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git config --local user.email "[email protected]"
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git config --local user.name "biosimulatorsdaemon"
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git config pull.rebase false
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git stash
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git pull
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git stash pop
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git add docs
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set +e
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git commit -m "Updating compiled documentation"
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if [[ $? = 0 ]]; then
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docsChanged=1
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else
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docsChanged=0
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fi
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echo "::set-output name=docsChanged::$docsChanged"
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- name: Push the compiled documentation
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if: steps.commit-docs.outputs.docsChanged == '1'
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uses: ad-m/github-push-action@master
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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branch: dev
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# Create GitHub release
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- name: Create GitHub release
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uses: actions/create-release@v1
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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tag_name: ${{ needs.getVersionNumber.outputs.version }}
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release_name: Release ${{ needs.getVersionNumber.outputs.version }}
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# Create PyPI release
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- name: Install pandoc
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run: |
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sudo apt-get update -y
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sudo apt-get install -y --no-install-recommends wget
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wget https://github.com/jgm/pandoc/releases -O /tmp/pandocVersions.html
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urlPart=`grep "\.deb" /tmp/pandocVersions.html | head -n 1 | cut -d'/' -f2-7 | cut -d'"' -f1`
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wget "https://github.com/$urlPart" -O /tmp/pandoc.deb
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sudo dpkg -i /tmp/pandoc.deb
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rm /tmp/pandocVersions.html
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rm /tmp/pandoc.deb
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- name: Convert README to .rst format
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run: pandoc --from=gfm --output=README.rst --to=rst README.md
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- name: Install twine
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run: |
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python -m pip install wheel twine
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- name: Create packages to upload to PyPI
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run: |
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python setup.py sdist
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python setup.py bdist_wheel
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- name: Upload packages to PyPI
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env:
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TWINE_USERNAME: __token__
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TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
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run: |
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twine upload dist/*

‎.gitignore

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# compiled Python files
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*.egg-info/
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__pycache__/
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*.pyc
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dist/
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build/
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# coverage files
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htmlcov/
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.coverage
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coverage.xml
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# compiled documentation
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README.rst
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docs/objects.inv
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docs/.buildinfo
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docs/.doctrees/
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docs/_raw_sources/
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docs/_sources/

‎CONTRIBUTING.md

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# Contributing to the BioSimulations COMBINE archive test suite
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# Contributing to the BioSimulators test suite
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We enthusiastically welcome contributions to the BioSimulations COMBINE archive test suite!
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We enthusiastically welcome contributions to the BioSimulators test suite!
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## Coordinating contributions
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Before getting started, please contact the lead developers at [[email protected]](mailto:[email protected]) to coordinate your planned contributions with other ongoing efforts. Please also use GitHub issues to announce your plans to the community so that other developers can provide input into your plans and coordinate their own work. As the development community grows, we will institute additional infrastructure as needed such as a leadership committee and regular online meetings.
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## Repository organization
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* `README.md`: Overview of the test suite
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* `biosimulators_test_suite/`: collection of COMBINE/OMEX archives (`.omex` files) and metadata about each archive (one JSON file per archive)
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* `LICENSE`: License
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* `CONTRIBUTING.md`: Guide to contributing to the test suite (this document)
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* `CODE_OF_CONDUCT.md`: Code of conduct for developers
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This repository follows standard Python conventions:
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* `README.md`: Overview of this repository
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* `biosimulators_test_suite/`: Source code for this package
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* `examples`: Example modeling projects that the source code uses to test biosimulation software tools
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* `examples-ouputs`: Example outputs (reports and plots) of executing the example modeling projects
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* `tests/`: Unit tests for the code for this package
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* `setup.py`: pip installation script for this package
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* `setup.cfg`: Configuration for the pip installation script
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* `requirements.txt`: Dependencies of this package
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* `requirements.optional.txt`: Optional dependencies of this package
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* `MANIFEST.in`: List of files to include when the BioSimulators test suite is packaged for distribution through PyPI
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* `LICENSE`: License for the sofware of this package
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* `LICENSE-DATA`: License for the example modeling projects in this package
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* `CONTRIBUTING.md`: Guide to contributing to this package (this document)
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* `CODE_OF_CONDUCT.md`: Code of conduct for developers of this package
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## Coding convention
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The code in this repository follows standard Python style conventions:
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* Class names: `UpperCamelCase`
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* Function names: `lower_snake_case`
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* Variable names: `lower_snake_case`
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## Documentation convention
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The code in the BioSimulators test suite is documented using [reStructuredText](https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html) and the [napoleon Sphinx plugin](https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html). The documentation can be compiled with [Sphinx](https://www.sphinx-doc.org/) by running the following commands:
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```
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python -m pip install -r docs-src/requirements.txt
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sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
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sphinx-build docs-src docs
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```
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## Submitting changes
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‎MANIFEST.in

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# description
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include README.rst
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# license
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include LICENSE
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# requirements
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include requirements.txt
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include requirements.optional.txt

‎README.md

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[![Latest release](https://img.shields.io/github/v/release/biosimulators/Biosimulators_test_suite)](https://github.com/biosimulators/Biosimulators_test_suite/releases)
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[![PyPI](https://img.shields.io/pypi/v/Biosimulators-test-suite)](https://pypi.org/project/Biosimulators-test-suite/)
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[![CI status](https://github.com/biosimulators/Biosimulators_test_suite/workflows/Continuous%20integration/badge.svg)](https://github.com/biosimulators/Biosimulators_test_suite/actions?query=workflow%3A%22Continuous+integration%22)
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[![Test coverage](https://codecov.io/gh/biosimulators/Biosimulators_test_suite/branch/dev/graph/badge.svg)](https://codecov.io/gh/biosimulators/Biosimulators_test_suite)
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# BioSimulators test suite
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This package contains two related resources:
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The BioSimulators test suite is a tool for validating that biosimulation software tools implement the [BioSimulators standards for biosimulation tools](https://biosimulators.org/standards).
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The test suite is composed of two parts:
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* A collection of example modeling projects. Each project is represented by a single [COMBINE/OMEX archive](https://combinearchive.org/) that contains one or more simulation experiments described using the [Simulation Experiment Description Markup Language (SED-ML)](https://sed-ml.org) and one or more models described using a format such as the [BioNetGen Language (BNGL)](https://bionetgen.org) or the [Systems Biology Markup Language (SBML)](http://sbml.org).
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* Software for checking that biosimulation tools execute these projects according to the BioSimulators standards.
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* Simulation tools support the [BioSimulators standard command-line arguments](https://biosimulators.org/standards/simulator-interfaces).
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* Simulation tools support the [BioSimulators conventions for Docker images](https://biosimulators.org/standards/simulator-images).
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* Simulation tools follow the [BioSimulators conventions for executing simulations described by SED-ML files in COMBINE/OMEX archives](https://biosimulators.org/standards/simulation-experiments).
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* Simulation tools support the [BioSimulators conventions for the outputs of SED-ML files in COMBINE/OMEX archives](https://biosimulators.org/standards/simulation-reports).
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* **Collection of example [COMBINE/OMEX](http://co.mbine.org/standards/omex) archives**: This collection is a reference for the community. The collection is also the test suite that [BioSimulators](https://biosimulators.org) uses to validate the capabilities of simulation tools.
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* **Software for validating simulation tools**: This package also contains software for testing that simulation tools are compatible with the [BioSimulators standards for simulation software tools](https://biosimulators.org).
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## Contents
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* [Installation instructions, tutorial, and API documentation](#installation-instructions,-tutorial,-and-API-documentation)
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* [License](#license)
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* [Development team](#development-team)
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* [Contributing to the test suite](#contributing-to-the-test-suite)
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* [Acknowledgements](#acknowledgements)
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* [Questions and comments](#questions-and-comments)
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## Installation instructions, tutorial, and API documentation
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Installation instructions, tutorial, and API documentation are available [here](https://biosimulators.github.io/Biosimulators_test_suite/).
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## License
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The COMBINE/OMEX archives in this package are released under the [Creative Commons CC0 license](LICENSE-DATA). The software in this package is released under the [MIT License](LICENSE).
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The software in this package is released under the [MIT License](LICENSE). The modeling projects in this package are released under the [Creative Commons 1.0 Universal (CC0) license](LICENSE-DATA).
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## Development team
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This package was developed by the [Karr Lab](https://www.karrlab.org) at the Icahn School of Medicine at Mount Sinai in New York and the [Center for Reproducible Biomedical Modeling](http://reproduciblebiomodels.org).
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This package was developed by the [Karr Lab](https://www.karrlab.org) at the Icahn School of Medicine at Mount Sinai in New York, the [https://health.uconn.edu/cell-analysis-modeling/](https://health.uconn.edu/cell-analysis-modeling/) at the University of Connecticut, and the [Center for Reproducible Biomedical Modeling](http://reproduciblebiomodels.org).
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## Contributing to the test suite
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We enthusiastically welcome contributions to the test suite! Please see the [guide to contributing](CONTRIBUTING.md) and the [developer's code of conduct](CODE_OF_CONDUCT.md).
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## Acknowledgements
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This work was supported by National Institutes of Health awards P41EB023912 and R35GM119771 and the Icahn Institute for Data Science and Genomic Technology.
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This work was supported by National Institutes of Health award P41EB023912.
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## Questions and comments
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Please contact the [BioSimulators Team](mailto:[email protected]) with any questions or comments.

‎docs-src/about.rst

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About the BioSimulators test suite
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==================================
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License
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-------
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The software for the test suite is released under the `MIT License <https://github.com/biosimulators/Biosimulators_test_suite/blob/dev/LICENSE>`_. The example modeling projects in the test suite are released under the `Creative Commons 1.0 Universal (CCO) License <https://github.com/biosimulators/Biosimulators_test_suite/blob/dev/LICENSE-DATA>`_.
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Development team
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----------------
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This package was developed by the `Karr Lab <https://www.karrlab.org>`_ at the Icahn School of Medicine at Mount Sinai, the `Center for Cell Analysis & Modeling <https://health.uconn.edu/cell-analysis-modeling/>`_ at the University of Connecticut, and the `Center for Reproducible Biomedical Modeling <https://reproduciblebiomodels.org/>`_.
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Contributing to the BioSimulators test suite
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--------------------------------------------
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We enthusiastically welcome contributions to the BioSimulators test suite! Please see the `guide to contributing <https://github.com/biosimulators/Biosimulators_test_suite/blob/dev/CONTRIBUTING.md>`_ and the `developer's code of conduct <https://github.com/biosimulators/Biosimulators_test_suite/blob/dev/CODE_OF_CONDUCT.md>`_.
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Acknowledgements
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----------------
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This work was supported by National Institutes of Health award P41EB023912.
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Questions and comments
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-------------------------
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Please contact the `BioSimulators Team <mailto:[email protected]>`_ with any questions or comments.

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