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Guarding deploy and fixing output organization
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
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@@ -114,20 +114,6 @@ jobs: | |
| else | ||
| echo "needDeploy=false" >> "$GITHUB_OUTPUT" | ||
| fi | ||
| sed -i -e 's/__COPASI_VERSION__/${copasiVersion}/g' biosimulators.json | ||
| sed -i -E \ | ||
| "s/ARG SIMULATOR_VERSION=([^ \n]+|\".*?\")/ARG SIMULATOR_VERSION=\"${copasiVersion}\"/" \ | ||
| Dockerfile | ||
| sed -i -E \ | ||
| "s/ARG VERSION=([^ \n]+|\".*?\")/ARG VERSION=\"${bioSimVersion}\"/" \ | ||
| Dockerfile | ||
| echo "::set-output name=biosimulatorsVersion::$bioSimVersion" | ||
| echo "::set-output name=simulatorVersion::$copasiVersion" | ||
| echo | ||
| ############################################# | ||
| ## Check for Deploy, Stop if not Deploying | ||
|
|
@@ -140,9 +126,12 @@ jobs: | |
| #* Release *# | ||
| #*******************************************# | ||
|
|
||
| ############################################# | ||
| # If new tag, commit and push documentation | ||
| ############################################# | ||
| - id: commit-docs | ||
| name: Commit the compiled documentation | ||
| if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| run: | | ||
| git config --local user.email "[email protected]" | ||
| git config --local user.name "biosimulatorsdaemon" | ||
|
|
@@ -175,6 +164,7 @@ jobs: | |
| ############################################# | ||
| - name: Create GitHub release | ||
| uses: actions/create-release@v1 | ||
| if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| with: | ||
|
|
@@ -185,6 +175,7 @@ jobs: | |
| # Create PyPI release | ||
| ############################################# | ||
| - name: Create PyPI release | ||
| if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| env: | ||
| POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }} | ||
| run: | | ||
|
|
@@ -205,13 +196,35 @@ jobs: | |
| # Build and Publish | ||
| poetry build | ||
| poetry publish --no-interaction --username __token__ --password $POETRY_PYPI_TOKEN_PYPI | ||
| ############################################# | ||
| ## Build Docker image | ||
| ## Form-fill the versions to the container and to `biosimulators.json` | ||
| ############################################# | ||
| - name: Update the version of the simulator | ||
| if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| run: | | ||
| containerLabel=${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }} | ||
| docker pull $containerLabel | ||
| imageId=docker image ls | grep ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }} \ | ||
| grep ${{ steps.get-docker-image-tag.outputs.simulatorVersion }} | awk '{ print $3; ]' | ||
| dockerDigest=docker inspect --format='{{index .RepoDigests 0}}' $imageId | cut -d '@' -f 2 | ||
| copasiVersion=${{ steps.update-simulator-version.outputs.copasiVersion }} | ||
| bioSimVersion=${{ steps.update-simulator-version.outputs.bioSimVersion }} | ||
| sed -i -e 's/__CONTAINER_DIGEST__/${dockerDigest}/g' biosimulators.json | ||
| sed -i -e 's/__COPASI_VERSION__/${copasiVersion}/g' biosimulators.json | ||
| sed -i -E "s/ARG SIMULATOR_VERSION=([^ \n]+|\".*?\")/ARG SIMULATOR_VERSION=\"${copasiVersion}\"/" Dockerfile | ||
| sed -i -E "s/ARG VERSION=([^ \n]+|\".*?\")/ARG VERSION=\"${bioSimVersion}\"/" Dockerfile | ||
| ############################################# | ||
| ## Build and Push Docker image | ||
| ############################################# | ||
| - id: get-docker-image-tag | ||
| name: Determine Docker image tag | ||
| if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| run: | | ||
| sudo apt-get update -y | ||
| sudo apt-get install -y --no-install-recommends jq | ||
|
|
@@ -229,6 +242,7 @@ jobs: | |
| echo "::set-output name=dockerRegistry::${DOCKER_REGISTRY}" | ||
| - name: Build Docker image | ||
| if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| run: | | ||
| REVISION=$(git rev-parse HEAD) | ||
| CREATED=$(date --rfc-3339=seconds | sed 's/ /T/') | ||
|
|
@@ -242,22 +256,8 @@ jobs: | |
| --tag ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:latest \ | ||
| . | ||
| ############################################# | ||
| ## Apply the digest of the container to `biosimulators.json` | ||
| ############################################# | ||
| - name: Update the version of the simulator | ||
| run: | | ||
| containerLabel=${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }} | ||
| docker pull $containerLabel | ||
| imageId=docker image ls | grep ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }} \ | ||
| grep ${{ steps.get-docker-image-tag.outputs.simulatorVersion }} | awk '{ print $3; ]' | ||
| dockerDigest=docker inspect --format='{{index .RepoDigests 0}}' $imageId | cut -d '@' -f 2 | ||
| sed -i -e 's/__CONTAINER_DIGEST__/${dockerDigest}/g' biosimulators.json | ||
| ############################################# | ||
| # Push Docker image to GitHub Container Registry | ||
| ############################################# | ||
| - name: Push Docker image | ||
| if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| run: | | ||
| docker login ${{ steps.get-docker-image-tag.outputs.dockerRegistry }} \ | ||
| --username ${{ secrets.DOCKER_REGISTRY_USERNAME }} \ | ||
|
|
@@ -272,6 +272,7 @@ jobs: | |
| # Submit to BioSimulators registry | ||
| ############################################# | ||
| - name: Submit to BioSimulators registry | ||
| if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| run: | | ||
| REVISION=$(git rev-parse HEAD) | ||
| IMAGE_DIGEST=$(docker image inspect ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }} | jq -r '.[0].RepoDigests[0]' | cut -d "@" -f 2-) | ||
|
|
@@ -288,6 +289,7 @@ jobs: | |
| ############################################# | ||
| # # If new version of simulator, commit and push the new version | ||
| # - name: Commit the revised version of the simulator | ||
| # if: steps.update-simulator-version.outputs.needDeploy == 'true' | ||
| # run: | | ||
| # git config --local user.email "[email protected]" | ||
| # git config --local user.name "biosimulatorsdaemon" | ||
|
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