Dependency Dashboard #2543
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name: Validate and/or commit simulator | |
on: | |
issues: | |
types: [labeled, edited] | |
jobs: | |
validateCommit: | |
name: Validate and/or commit simulator | |
runs-on: ubuntu-20.04 # includes Docker | |
if: | | |
github.event.issue.state == 'open' | |
&& contains(github.event.issue.labels.*.name, 'Validate/submit simulator') | |
&& ( | |
github.event.action == 'edited' | |
|| ( | |
github.event.action == 'labeled' | |
&& github.event.label.name == 'Validate/submit simulator' | |
) | |
|| ( | |
github.event.action == 'labeled' | |
&& github.event.label.name == 'Approved' | |
&& github.event.sender.login != 'biosimulators-daemon' | |
) | |
) | |
steps: | |
- name: Install Python | |
uses: actions/setup-python@v3 | |
with: | |
python-version: '3.11' | |
#- name: Setup pip cache | |
# uses: actions/cache@v2 | |
# with: | |
# path: /opt/hostedtoolcache/Python | |
# key: ${{ runner.os }}-pip-${{ hashFiles('${GITHUB_WORKSPACE}/requirements.txt') }}-${{ hashFiles('${GITHUB_WORKSPACE}/requirements.optional.txt') }} | |
# restore-keys: | | |
# ${{ runner.os }}-pip- | |
- name: Install pip and setuptools | |
run: | | |
python -m pip install --upgrade setuptools | |
# wget https://bootstrap.pypa.io/get-pip.py | |
# python get-pip.py pip==20.3.4 | |
python -m pip install pip==20.3.4 | |
- name: Install Java # for pyNeuroML | |
uses: actions/setup-java@v3 | |
with: | |
distribution: 'adopt' | |
java-version: '15' | |
- name: Install Perl # for BioNetGen | |
run: | | |
sudo apt-get update -y | |
sudo apt-get install -y --no-install-recommends perl | |
- name: Install XPP | |
run: | | |
sudo apt-get install -y --no-install-recommends xppaut | |
- name: Install Go (for Singularity) | |
uses: actions/setup-go@v3 | |
with: | |
go-version: '^1.13.1' # The Go version to download (if necessary) and use. | |
- name: Install Singularity # to validate that the Docker image can be converted into a Singularity image | |
env: | |
GO_VERSION: 1.17.2 | |
SINGULARITY_VERSION: 3.9.5 | |
OS: linux | |
ARCH: amd64 | |
run: | | |
sudo apt-get install -y --no-install-recommends \ | |
build-essential \ | |
libseccomp-dev \ | |
pkg-config \ | |
squashfs-tools \ | |
cryptsetup | |
wget https://dl.google.com/go/go$GO_VERSION.$OS-$ARCH.tar.gz | |
sudo tar -C /usr/local -xzvf go$GO_VERSION.$OS-$ARCH.tar.gz | |
rm go$GO_VERSION.$OS-$ARCH.tar.gz | |
echo 'export PATH=/usr/local/go/bin:$PATH' >> ~/.bashrc | |
source ~/.bashrc | |
echo "/usr/local/go/bin" >> $GITHUB_PATH | |
wget https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz | |
tar -xzf singularity-ce-${SINGULARITY_VERSION}.tar.gz | |
cd singularity-ce-${SINGULARITY_VERSION} | |
./mconfig | |
make -C builddir | |
sudo make -C builddir install | |
- name: Checkout BioSimulators test suite | |
uses: actions/checkout@v3 | |
with: | |
repository: biosimulators/biosimulators_test_suite | |
fetch-depth: 1 | |
ref: depFixes | |
- name: Install simulator validation utilities | |
working-directory: ${{ github.workspace }} | |
run: | | |
# python -m pip cache purge | |
# python -m pip install --no-cache-dir "biosimulators_utils @ git+https://github.com/biosimulators/Biosimulators_utils@depFixes#egg=biosimulators_utils[containers,sbml]" | |
# python -m pip install git+https://github.com/biosimulators/RBApy.git#egg=rbapy | |
python -m pip install docker python-libsbml "urllib3<2.0" | |
python -m pip install -e .[all] | |
python --version | |
python -m pip freeze | |
- name: Login into Docker registries | |
run: | | |
# Docker Hub | |
docker login \ | |
--username ${{ secrets.DOCKER_HUB_USERNAME }} \ | |
--password ${{ secrets.DOCKER_HUB_TOKEN }} | |
# BioSimulators Docker registry (GHCR) | |
docker login ${{ secrets.DOCKER_REGISTRY_URL }} \ | |
--username ${{ secrets.DOCKER_REGISTRY_USERNAME }} \ | |
--password ${{ secrets.DOCKER_REGISTRY_TOKEN }} | |
- id: validateCommitSimulator | |
name: Validate and commit simulator | |
uses: GabrielBB/xvfb-action@v1 | |
env: | |
GH_REPO: ${{ github.repository }} | |
GH_ACTION_RUN_ID: ${{ github.run_id }} | |
GH_ISSUE_NUMBER: ${{ github.event.issue.number }} | |
GH_ISSUES_USER: ${{ secrets.GH_ISSUES_USER }} | |
GH_ISSUES_ACCESS_TOKEN: ${{ secrets.GH_ISSUES_ACCESS_TOKEN }} | |
DOCKER_HUB_USERNAME: ${{ secrets.DOCKER_HUB_USERNAME }} | |
DOCKER_HUB_TOKEN: ${{ secrets.DOCKER_HUB_TOKEN }} | |
DOCKER_REGISTRY_URL: ${{ secrets.DOCKER_REGISTRY_URL }} | |
DOCKER_REGISTRY_USERNAME: ${{ secrets.DOCKER_REGISTRY_USERNAME }} | |
DOCKER_REGISTRY_TOKEN: ${{ secrets.DOCKER_REGISTRY_TOKEN }} | |
BIOSIMULATORS_API_CLIENT_ID: ${{ secrets.BIOSIMULATORS_API_CLIENT_ID }} | |
BIOSIMULATORS_API_CLIENT_SECRET: ${{ secrets.BIOSIMULATORS_API_CLIENT_SECRET }} | |
# BIOSIMULATORS_API_ENDPOINT: https://api.biosimulators.dev/ # uncomment to use the dev deployment of the BioSimulators API | |
RUNBIOSIMULATIONS_API_CLIENT_ID: ${{ secrets.RUNBIOSIMULATIONS_API_CLIENT_ID }} | |
RUNBIOSIMULATIONS_API_CLIENT_SECRET: ${{ secrets.RUNBIOSIMULATIONS_API_CLIENT_SECRET }} | |
# RUNBIOSIMULATIONS_API_ENDPOINT: https://api.biosimulations.dev/ # uncomment to use the dev deployment of the BioSimulators API | |
with: | |
working-directory: ${{ github.workspace }} | |
run: | | |
python -m pip install --upgrade biosimulators_utils | |
python -c "from biosimulators_test_suite.exec_gh_action import ValidateCommitSimulatorGitHubAction; ValidateCommitSimulatorGitHubAction().run(); exit();" | |
# If tmate is useful for a particular debugging issue, comment this back in: | |
# - name: Setup tmate session 3 (if failed) | |
# uses: mxschmitt/action-tmate@v3 | |
# if: ${{ failure() }} | |
# timeout-minutes: 40 | |
- name: Save test results | |
uses: actions/upload-artifact@v2 | |
if: success() || failure() | |
with: | |
name: Validation test results | |
path: ${{ github.workspace }}/.biosimulators-test-suite-results.json | |
if-no-files-found: warn |