Create and publish a Docker image #31
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| # This workflow uses actions that are not certified by GitHub. | |
| # They are provided by a third-party and are governed by | |
| # separate terms of service, privacy policy, and support | |
| # documentation. | |
| # GitHub recommends pinning actions to a commit SHA. | |
| # To get a newer version, you will need to update the SHA. | |
| # You can also reference a tag or branch, but the action may change without warning. | |
| name: Create and publish a Docker image | |
| on: | |
| push: | |
| branches: | |
| - feat/improve_docker_building | |
| workflow_dispatch: | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| REGISTRY: ghcr.io | |
| IMAGE_NAME: choderalab/perses | |
| jobs: | |
| build-and-push-image: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Free disk space | |
| run: | | |
| run: | | |
| sudo docker rmi $(docker image ls -aq) >/dev/null 2>&1 || true | |
| sudo rm -rf \ | |
| /usr/share/dotnet /usr/local/lib/android /opt/ghc \ | |
| /usr/local/share/powershell /usr/share/swift /usr/local/.ghcup \ | |
| /usr/lib/jvm || true | |
| echo "some directories deleted" | |
| sudo apt install aptitude -y >/dev/null 2>&1 | |
| sudo aptitude purge aria2 ansible azure-cli shellcheck rpm xorriso zsync \ | |
| esl-erlang firefox gfortran-8 gfortran-9 google-chrome-stable \ | |
| google-cloud-sdk imagemagick \ | |
| libmagickcore-dev libmagickwand-dev libmagic-dev ant ant-optional kubectl \ | |
| mercurial apt-transport-https mono-complete libmysqlclient \ | |
| unixodbc-dev yarn chrpath libssl-dev libxft-dev \ | |
| libfreetype6 libfreetype6-dev libfontconfig1 libfontconfig1-dev \ | |
| snmp pollinate libpq-dev postgresql-client powershell ruby-full \ | |
| sphinxsearch subversion mongodb-org azure-cli microsoft-edge-stable \ | |
| -y -f >/dev/null 2>&1 | |
| sudo aptitude purge google-cloud-sdk -f -y >/dev/null 2>&1 | |
| sudo aptitude purge microsoft-edge-stable -f -y >/dev/null 2>&1 || true | |
| sudo apt purge microsoft-edge-stable -f -y >/dev/null 2>&1 || true | |
| sudo aptitude purge '~n ^mysql' -f -y >/dev/null 2>&1 | |
| sudo aptitude purge '~n ^php' -f -y >/dev/null 2>&1 | |
| sudo aptitude purge '~n ^dotnet' -f -y >/dev/null 2>&1 | |
| sudo apt-get autoremove -y >/dev/null 2>&1 | |
| sudo apt-get autoclean -y >/dev/null 2>&1 | |
| echo "some packages purged" | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Get Latest Version | |
| id: latest-version | |
| run: | | |
| LATEST_TAG=$(git describe --tags $(git rev-list --tags --max-count=1)) | |
| echo $LATEST_TAG | |
| echo "LATEST_TAG=$LATEST_TAG" >> $GITHUB_OUTPUT | |
| # In this case the version is the same as the latest_tag | |
| VERSION=$LATEST_TAG | |
| echo $VERSION | |
| echo "VERSION=$VERSION" >> $GITHUB_OUTPUT | |
| - name: Print Latest Version | |
| run: echo ${{ steps.latest-version.outputs.VERSION }} | |
| - name: Create fully qualified image registry path | |
| id: fqirp | |
| run: | | |
| FQIRP=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.latest-version.outputs.VERSION }} | |
| echo "FQIRP=$FQIRP" >> $GITHUB_OUTPUT | |
| - name: Print FQIRP | |
| run: echo ${{ steps.fqirp.outputs.FQIRP }} | |
| - name: Log in to the Container registry | |
| uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Extract metadata (tags, labels) for Docker | |
| id: meta | |
| uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 | |
| with: | |
| images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} | |
| tags: | | |
| type=schedule,pattern=nightly,enable=true,priority=1000 | |
| type=ref,event=branch,enable=true,priority=600 | |
| type=ref,event=tag,enable=true,priority=600 | |
| type=ref,event=pr,prefix=pr-,enable=true,priority=600 | |
| type=semver,pattern={{major}}.{{minor}} | |
| type=semver,pattern={{version}} | |
| type=sha | |
| ${{ steps.latest-version.outputs.VERSION }} | |
| latest | |
| - name: Build and export to Docker | |
| uses: docker/build-push-action@v4 | |
| with: | |
| context: . | |
| file: docker/Dockerfile | |
| load: true | |
| push: false | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| build-args: | | |
| VERSION=${{ steps.latest-version.outputs.VERSION }} | |
| - name: Test image | |
| run: | | |
| mkdir oe_license_dir | |
| # Write out license to a file | |
| echo "${{ secrets.OE_LICENSE }}" > oe_license_dir/oe_license.txt | |
| docker run --rm ${{ steps.fqirp.outputs.FQIRP }} perses-cli --help | |
| # Mount oe_license_dir (which should have the license file) to /openeye on container for testing | |
| #docker run -e GITHUB_ACTIONS=true --mount type=bind,source=$PWD/oe_license_dir/,target=/openeye/,readonly --rm ${{ steps.fqirp.outputs.FQIRP }} pytest --pyargs perses -a "not advanced" -n auto -m "not gpu_needed" -v | |
| - name: Push Docker image | |
| uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc | |
| with: | |
| context: . | |
| file: docker/Dockerfile | |
| push: true | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| build-args: | | |
| VERSION=${{ steps.latest-version.outputs.VERSION }} | |
| - name: Setup Apptainer | |
| uses: eWaterCycle/setup-apptainer@v2 | |
| with: | |
| apptainer-version: 1.1.2 | |
| - name: Build Apptainer Image | |
| run: singularity build perses_${{ steps.latest-version.outputs.VERSION }}.sif docker-daemon:${{ steps.fqirp.outputs.FQIRP }} | |
| - name: Test & Push Apptainer Image | |
| run: | | |
| set -e | |
| mkdir test_apptainer | |
| cd test_apptainer | |
| singularity run ../perses_${{ steps.latest-version.outputs.VERSION }}.sif perses-cli --help | |
| #singularity run --bind ../oe_license_dir/:/openeye/ --env "GITHUB_ACTIONS=true" ../perses_${{ steps.latest-version.outputs.VERSION }}.sif pytest --pyargs perses -a "not advanced" -n auto -m "not gpu_needed" -v | |
| echo ${{ secrets.GITHUB_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io | |
| singularity push ../perses_${{ steps.latest-version.outputs.VERSION }}.sif oras://${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.latest-version.outputs.VERSION }}-apptainer | |
| singularity push ../perses_${{ steps.latest-version.outputs.VERSION }}.sif oras://${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest-apptainer |