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bsts_local.yml
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name: BSTS local
# derived from https://raw.githubusercontent.com/biosimulators/Biosimulators/dev/.github/workflows/validateCommitSimulator.yml
on:
workflow_dispatch:
inputs:
biosimulators_vcell_tag:
description: 'version.major.minor.patch'
required: true
default: '7.5.0.127'
# vcell_build:
# description: 'build number'
# required: true
# default: '23'
# vcell_site:
# description: 'rel or alpha'
# required: true
# default: 'alpha'
# server_only:
# description: 'Deploy only the server components?'
# required: true
# default: 'false'
jobs:
validateCommit:
name: Validate and/or commit simulator
runs-on: ubuntu-20.04 # includes Docker
steps:
- name: Install Python
uses: actions/setup-python@v3
with:
python-version: '3.11'
- 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 vcell
uses: actions/checkout@v3
- name: Login into Docker registries
run: |
# VCell Docker registry (GHCR)
echo ${{ secrets.ACTION_TOKEN }} | docker login ghcr.io -u ${{ secrets.ACTION_USER }} --password-stdin
- name: configure biosimulations.json
working-directory: ${{ github.workspace }}
run: |
docker pull ghcr.io/virtualcell/biosimulators_vcell:${{ github.event.inputs.biosimulators_vcell_tag }}
export IMAGE_DIGEST=$(docker image inspect ghcr.io/virtualcell/biosimulators_vcell:${{ github.event.inputs.biosimulators_vcell_tag }} | jq -r '.[0].RepoDigests[0]' | cut -d "@" -f 2-)
sed -i 's/_VC_VERSION_TAG_/${{github.event.inputs.biosimulators_vcell_tag}}/g' biosimulators.json
sed -i 's/_VC_DIGEST_TAG_/${IMAGE_DIGEST}/g' biosimulators.json
- name: save updated biosimulators.json
uses: actions/upload-artifact@v2
with:
name: biosimulators.json
path: ${{ github.workspace }}/biosimulators.json
overwrite: true
- name: Checkout BioSimulators test suite
uses: actions/checkout@v3
with:
repository: biosimulators/biosimulators_test_suite
fetch-depth: 1
ref: depFixes
- name: retrieve updated biosimulators.json
uses: actions/download-artifact@v2
with:
name: biosimulators.json
path: ${{ github.workspace }}
- 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
- 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
biosimulators-test-suite --verbose biosimulators.json
- 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