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base repository: virtualcell/vcell
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base: 7.6.0.40
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head repository: virtualcell/vcell
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compare: master
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7 contributors
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Showing 852 changed files with 101,371 additions and 28,617 deletions.
32 changes: 10 additions & 22 deletions .github/workflows/CI-full.yml
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Original file line number Diff line number Diff line change
@@ -12,7 +12,7 @@ jobs:
build:
runs-on: ubuntu-22.04
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- name: Get the VCell version from tags
id: version
run: echo ::set-output name=tag::$(echo ${GITHUB_REF:10})
@@ -37,7 +37,7 @@ jobs:
sudo tar -xvf deploy/deploy_dir_2023_07_30.tar
sudo chmod 777 -R deploy
- name: Set up Python
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ env.python-version }}
cache: "pip"
@@ -88,40 +88,28 @@ jobs:
poetry run python -m pytest
- name: setup java 17 with maven cache
uses: actions/setup-java@v3
uses: actions/setup-java@v4
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 ${{ secrets.ACTION_TOKEN }} ghcr.io
echo "${{ secrets.GITHUB_TOKEN }}" | sudo docker login ghcr.io -u ${{ github.actor }} --password-stdin
echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
./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)
- name: tag as latest and push to registry
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;\
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
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