fix parameter estimation authentication, cleanup deprecated code #367
Workflow file for this run
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| name: CI-application-containers | |
| on: | |
| workflow_dispatch: | |
| release: | |
| types: [published] | |
| env: | |
| python-version: "3.9" | |
| jobs: | |
| build: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Get the VCell version from tags | |
| id: version | |
| run: echo ::set-output name=tag::$(echo ${GITHUB_REF:10}) | |
| - name: set global environment variables | |
| run: | | |
| echo "VCELL_TAG=`git rev-parse --short HEAD`" >> $GITHUB_ENV | |
| echo "VCELL_REPO_NAMESPACE=ghcr.io/virtualcell" >> $GITHUB_ENV | |
| echo "VCELL_DEPLOY_REMOTE_DIR=/share/apps/vcell3/deployed_github" >> $GITHUB_ENV | |
| echo "VCELL_MANAGER_NODE=vcellapi-beta.cam.uchc.edu" >> $GITHUB_ENV | |
| - name: setup ssh-agent | |
| uses: webfactory/[email protected] | |
| with: | |
| ssh-private-key: ${{ secrets.VC_KEY }} | |
| - name: get installer secrets | |
| run: | | |
| ssh-keyscan vcellapi-beta.cam.uchc.edu >> ~/.ssh/known_hosts | |
| sudo mkdir /usr/local/deploy | |
| sudo chmod 777 /usr/local/deploy | |
| cd /usr/local/deploy | |
| scp ${{ secrets.CD_FULL_USER }}@${VCELL_MANAGER_NODE}:${VCELL_DEPLOY_REMOTE_DIR}/deploy_dir_2023_07_30.tar . | |
| cd .. | |
| sudo tar -xvf deploy/deploy_dir_2023_07_30.tar | |
| sudo chmod 777 -R deploy | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.python-version }} | |
| cache: "pip" | |
| - name: Install Dependencies | |
| run: pip install -r requirements.txt | |
| - name: build vcell-cli-utils package | |
| run: | | |
| cd vcell-cli-utils | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build vcell-admin package | |
| run: | | |
| cd docker/swarm/vcell-admin | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build pythonCopasiOpt package | |
| run: | | |
| cd pythonCopasiOpt/vcell-opt | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build pythonVtk package | |
| run: | | |
| cd pythonVtk | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build vcutils package | |
| run: | | |
| cd python-utils | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build python-restclient package | |
| run: | | |
| cd python-restclient | |
| poetry install | |
| poetry run python -m pytest | |
| - name: build vcelldata package | |
| run: | | |
| cd pythonData | |
| poetry install | |
| poetry run python -m pytest | |
| - name: setup java 17 with maven cache | |
| uses: actions/setup-java@v3 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '17' | |
| cache: 'maven' | |
| - name: Install Singularity # to make singularity image for cluster | |
| uses: eWaterCycle/setup-singularity@v6 | |
| with: | |
| singularity-version: 3.7.1 | |
| - name: build and publish all images | |
| shell: bash | |
| run: | | |
| cd docker/build | |
| sudo docker login -u ${{ secrets.ACTION_USER }} -p ${{ secrets.ACTION_TOKEN }} ghcr.io | |
| docker login -u ${{ secrets.ACTION_USER }} -p ${{ secrets.ACTION_TOKEN }} ghcr.io | |
| ./build.sh all ${{ env.VCELL_REPO_NAMESPACE }} ${{ env.VCELL_TAG }} | |
| cd singularity-vm | |
| singularity remote login -u ${{ secrets.ACTION_USER }} -p ${{ secrets.ACTION_TOKEN }} oras://ghcr.io | |
| - name: tag as latest and push to registry # (jcs) are explicit singularity push commands redundant? (see ./build.sh) | |
| shell: bash | |
| run: | | |
| for CONTAINER in vcell-api vcell-rest vcell-webapp-prod vcell-webapp-dev vcell-webapp-stage vcell-webapp-island vcell-batch vcell-opt vcell-clientgen vcell-data vcell-db vcell-mongo vcell-sched vcell-submit vcell-admin;\ | |
| do docker tag ${VCELL_REPO_NAMESPACE}/$CONTAINER:${VCELL_TAG} ${VCELL_REPO_NAMESPACE}/$CONTAINER:latest;\ | |
| docker tag ${VCELL_REPO_NAMESPACE}/$CONTAINER:${VCELL_TAG} ${VCELL_REPO_NAMESPACE}/$CONTAINER:${{ steps.version.outputs.tag }};\ | |
| docker push --all-tags ${VCELL_REPO_NAMESPACE}/$CONTAINER;\ | |
| done | |
| cd docker/build/singularity-vm | |
| singularity push -U $(ls *batch*img) oras://${VCELL_REPO_NAMESPACE}/vcell-batch-singularity:${VCELL_TAG} | |
| singularity push -U $(ls *batch*img) oras://${VCELL_REPO_NAMESPACE}/vcell-batch-singularity:${{ steps.version.outputs.tag }} | |
| singularity push -U $(ls *batch*img) oras://${VCELL_REPO_NAMESPACE}/vcell-batch-singularity:latest | |
| singularity push -U $(ls *opt*img) oras://${VCELL_REPO_NAMESPACE}/vcell-opt-singularity:${VCELL_TAG} | |
| singularity push -U $(ls *opt*img) oras://${VCELL_REPO_NAMESPACE}/vcell-opt-singularity:${{ steps.version.outputs.tag }} | |
| singularity push -U $(ls *opt*img) oras://${VCELL_REPO_NAMESPACE}/vcell-opt-singularity:latest | |
| - name: Setup tmate session | |
| uses: mxschmitt/action-tmate@v3 | |
| if: ${{ failure() }} |