new_model #2
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| name: Add a new model | |
| # Trigger the workflow on pull request | |
| on: workflow_dispatch | |
| jobs: | |
| # create_new_branch: | |
| # if: ${{ startsWith(github.event.issue.title, 'New Model:') && github.event.label.name != 'failed' && github.event.label.name != 'new-model' && github.event.label.name != 'update-model' }} | |
| # runs-on: ubuntu-latest | |
| # outputs: | |
| # BRANCHNAME: ${{ steps.branch.outputs.branchName }} | |
| # # All the issue form data | |
| # MODELPATH: ${{ steps.get_path.outputs.path }} | |
| # WEIGHTS: ${{ steps.get_weights.outputs.weights }} | |
| # DOCKER: ${{ steps.get_docker.outputs.docker }} | |
| # PYTHON: ${{ steps.python_scripts.outputs.pythons }} | |
| # MODELINFO: ${{ env.model_info }} | |
| # SAMPLEDATA: ${{ steps.get_data.outputs.sample_data }} | |
| # PYTHONS: ${{ env.pythons }} | |
| # CONFIG: ${{ steps.get_model_config.outputs.model_config }} | |
| # TESTCOMMAND: ${{ steps.get_test_command.outputs.test_command }} | |
| # steps: | |
| # # This will automatically create a new branch from this issue, using custom config at /.github/issue-branch.yml 🟢 | |
| # - name: Create Issue Branch | |
| # id: branch | |
| # uses: robvanderleek/create-issue-branch@main | |
| # env: | |
| # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # # Set up Python 🟢 | |
| # - name: Set up Python | |
| # uses: actions/setup-python@v4 | |
| # with: | |
| # python-version: 3.11 | |
| # # Checkout the repository to the GitHub Actions runner 🟢 | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # ref: ${{ steps.branch.outputs.branchName }} | |
| # # Scrape the info from the issue 🟢 | |
| # - uses: stefanbuck/github-issue-parser@v3 | |
| # id: issue-parser | |
| # with: | |
| # template-path: .github/ISSUE_TEMPLATE/addModel.yml # optional but recommended | |
| # # Scrape info from the form 🟢 | |
| # - name: Get the Path | |
| # id: get_path | |
| # run: echo "path=${{ steps.issue-parser.outputs.issueparser_path }}" >> $GITHUB_OUTPUT | |
| # - name: Get the Weights | |
| # id: get_weights | |
| # run: echo "weights=${{ steps.issue-parser.outputs.issueparser_weights }}" >> $GITHUB_OUTPUT | |
| # - name: Get docker folder | |
| # id: get_docker | |
| # run: echo "docker=${{ steps.issue-parser.outputs.issueparser_docker }}" >> $GITHUB_OUTPUT | |
| # - name: Get Python Scripts | |
| # id: python_scripts | |
| # run: | | |
| # echo "pythons<<EOF" >> $GITHUB_ENV | |
| # echo "${{ steps.issue-parser.outputs.issueparser_python-scripts }}" >> $GITHUB_ENV | |
| # echo "EOF" >> $GITHUB_ENV | |
| # - name: Get Model Info | |
| # id: get_model_info | |
| # run: | | |
| # echo "model_info<<EOF" >> $GITHUB_ENV | |
| # echo "${{ steps.issue-parser.outputs.issueparser_model_info }}" >> $GITHUB_ENV | |
| # echo "EOF" >> $GITHUB_ENV | |
| # - name: Get Test Command | |
| # id: get_test_command | |
| # run: | | |
| # echo "test_command=${{ steps.issue-parser.outputs.issueparser_testCommand }}" >> $GITHUB_OUTPUT | |
| # - name: Get Sample Data | |
| # id: get_data | |
| # run: echo "sample_data=${{ steps.issue-parser.outputs.issueparser_sample-data }}" >> $GITHUB_OUTPUT | |
| # - name: Get Config | |
| # id: get_model_config | |
| # run: | | |
| # echo "model_config=${{ steps.issue-parser.outputs.issueparser_modelConfig }}" >> $GITHUB_OUTPUT | |
| # push-model: | |
| # needs: create_new_branch | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # # Checkout the repository to the GitHub Actions runner to the new branch created for the issue 🟢 | |
| # - uses: actions/checkout@v4 | |
| # if: needs.create_new_branch.outputs.BRANCHNAME == '' | |
| # with: | |
| # ref: issue-${{ github.event.issue.number }} | |
| # # If branchName is empty use issue number, else, use the branchName 🟢 | |
| # - uses: actions/checkout@v4 | |
| # if: needs.create_new_branch.outputs.BRANCHNAME != '' | |
| # with: | |
| # ref: ${{ needs.create_new_branch.outputs.BRANCHNAME }} | |
| # # Install svn to clone subdir of github repos 🟢 | |
| # - name: Install svn | |
| # run: sudo apt-get install subversion | |
| # # Get svn url for exporting docker 🟢 | |
| # - name: Clone docker folder | |
| # run: | | |
| # url="${{ needs.create_new_branch.outputs.DOCKER }}" | |
| # svn_url=$(echo "$url" | sed -E 's|/tree/[^/]+|/trunk|; s|/blob/[^/]+|/trunk|') | |
| # svn export --force $svn_url ./${{ needs.create_new_branch.outputs.MODELPATH }}/docker | |
| # # Get svn url for exporting 🟢 | |
| # - name: Generate Python SVN URLs | |
| # id: generate_urls | |
| # run: | | |
| # echo "pythons2<<EOF" >> $GITHUB_ENV | |
| # python ./.github/workflows/getPythonScripts.py >> $GITHUB_ENV | |
| # echo "EOF" >> $GITHUB_ENV | |
| # env: | |
| # pythons: ${{ needs.create_new_branch.outputs.PYTHONS }} | |
| # # Export the urls/clone the scripts 🟢 | |
| # - name: Clone python scripts | |
| # run: | | |
| # cd ./${{ needs.create_new_branch.outputs.MODELPATH }} | |
| # svn_urls="${{ env.pythons2 }}" | |
| # for svn_url in $svn_urls; do | |
| # svn export --force $svn_url | |
| # done | |
| # # Get svn urls for exporting card and spec urls 🟢 | |
| # - name: Generate Model Info SVN URLs | |
| # id: generate_model_info_urls | |
| # run: | | |
| # echo "model_info2<<EOF" >> $GITHUB_ENV | |
| # python ./.github/workflows/getModelInfo.py >> $GITHUB_ENV | |
| # echo "EOF" >> $GITHUB_ENV | |
| # env: | |
| # model_info: ${{ needs.create_new_branch.outputs.MODELINFO }} | |
| # # Export the urls/clone the model info 🟢 | |
| # - name: Clone model info | |
| # run: | | |
| # model_info="${{ env.model_info2 }}" | |
| # for svn_url in $model_info; do | |
| # svn export --force $svn_url ./${{ needs.create_new_branch.outputs.MODELPATH }} | |
| # done | |
| # # Clone config files | |
| # - name: Config file clone | |
| # # Only run if needs.create_new_branch.outputs.CONFIG is not empty | |
| # if: ${{ needs.create_new_branch.outputs.CONFIG != '' }} | |
| # run: | | |
| # mkdir ./${{ needs.create_new_branch.outputs.MODELPATH }}/config/ | |
| # url="${{ needs.create_new_branch.outputs.CONFIG }}" | |
| # svn_url=$(echo "$url" | sed -E 's|/tree/[^/]+|/trunk|; s|/blob/[^/]+|/trunk|') | |
| # svn export --force $svn_url ./${{ needs.create_new_branch.outputs.MODELPATH }}/config | |
| # # Commit the new created files and folders to the branch needs.create_new_branch.outputs.BRANCHNAME 🟢 | |
| # - name: Commit and Push the new files | |
| # run: | | |
| # git config --global user.name "trained_models" | |
| # git config --global user.email "trained_models" | |
| # git add ${{ needs.create_new_branch.outputs.MODELPATH }} | |
| # git commit -m "Added model files" | |
| # git push origin ${{ needs.create_new_branch.outputs.BRANCHNAME }} | |
| # build: | |
| # needs: [create_new_branch, push-model] | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # # Checkout the repository to the GitHub Actions runner 🟢 | |
| # - uses: actions/checkout@v3 | |
| # if: needs.create_new_branch.outputs.BRANCHNAME == '' | |
| # with: | |
| # ref: issue-${{ github.event.issue.number }} | |
| # # If branchName is empty use issue number, else, use the branchName 🟢 | |
| # - uses: actions/checkout@v3 | |
| # if: needs.create_new_branch.outputs.BRANCHNAME != '' | |
| # with: | |
| # ref: ${{ needs.create_new_branch.outputs.BRANCHNAME }} | |
| # # Set up Python | |
| # - name: Set up Python | |
| # uses: actions/setup-python@v4 | |
| # with: | |
| # python-version: 3.11 | |
| # # Install yaml | |
| # - name: Install yaml and oyaml | |
| # run: | | |
| # pip install pyyaml | |
| # pip install oyaml | |
| # # Install linkml | |
| # - name: Install LinkML | |
| # run: pip install linkml | |
| # # Create model card and spec.yaml file | |
| # - name: Validate model card and spec files | |
| # run: | | |
| # echo "## Model Card and Spec Validation :white_check_mark:" >> $GITHUB_STEP_SUMMARY | |
| # echo "Model Card and spec yaml files are being validated here with LinkML Schema" >> $GITHUB_STEP_SUMMARY | |
| # python ./.github/workflows/create_model_card_and_spec.py | |
| # env: | |
| # model_path: ${{ needs.create_new_branch.outputs.MODELPATH }} | |
| # # Update the model's spec.yaml file | |
| # - name: Update yaml file | |
| # run: | | |
| # model_name=$(echo "${{ needs.create_new_branch.outputs.MODELPATH }}" | awk -F '/' '{print $(NF-1)}') | |
| # python ./.github/workflows/update_yaml_info.py ${{ needs.create_new_branch.outputs.MODELPATH }}/docker $model_name | |
| # # Commit the changes (spec.yaml file and model card) 🟢 | |
| # - name: Commit changes | |
| # run: | | |
| # git config --global user.name "trained_models" | |
| # git config --global user.email "trained_models" | |
| # git add ${{ needs.create_new_branch.outputs.MODELPATH }}/spec.yaml | |
| # git commit -m "Updated spec.yaml" | |
| # git push origin ${{ needs.create_new_branch.outputs.BRANCHNAME }} | |
| # build-docker: | |
| # needs: [create_new_branch, push-model, build] | |
| # runs-on: ubuntu-latest | |
| # outputs: | |
| # IMAGENAME: ${{ steps.set_image_name.outputs.image_name }} | |
| # MODELNAME: ${{ steps.set_image_name.outputs.model_name }} | |
| # steps: | |
| # # Cleanup steps to free up disk space | |
| # #- name: Cleanup disk space for large docker images | |
| # #run: | | |
| # #sudo rm -rf /usr/share/dotnet | |
| # #sudo rm -rf /opt/ghc | |
| # #sudo rm -rf "/usr/local/share/boost" | |
| # #sudo rm -rf /opt/hostedtoolcache | |
| # #sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| # #- name: Free Disk Space (Ubuntu) | |
| # #uses: jlumbroso/free-disk-space@main | |
| # #with: | |
| # # this might remove tools that are actually needed, | |
| # # if set to "true" but frees about 6 GB | |
| # #tool-cache: false | |
| # # all of these default to true, but feel free to set to | |
| # # "false" if necessary for your workflow | |
| # #android: true | |
| # #dotnet: true | |
| # #haskell: true | |
| # #large-packages: true | |
| # #docker-images: false | |
| # # Checkout the repository to the GitHub Actions runner 🟢 | |
| # - uses: actions/checkout@v3 | |
| # if: needs.create_new_branch.outputs.BRANCHNAME == '' | |
| # with: | |
| # ref: issue-${{ github.event.issue.number }} | |
| # # If branchName is empty use issue number, else, use the branchName 🟢 | |
| # - uses: actions/checkout@v3 | |
| # if: needs.create_new_branch.outputs.BRANCHNAME != '' | |
| # with: | |
| # ref: ${{ needs.create_new_branch.outputs.BRANCHNAME }} | |
| # # Get image name 🟢 | |
| # - name: Set docker image name | |
| # id: set_image_name | |
| # run: | | |
| # full_path="${{ needs.create_new_branch.outputs.MODELPATH }}" | |
| # model_name=$(echo "$full_path" | awk -F '/' '{print $(NF-1)}') | |
| # echo "image_name=neuronets/$model_name" >> $GITHUB_OUTPUT | |
| # echo "model_name=$model_name" >> $GITHUB_OUTPUT | |
| # push-weights: | |
| # needs: [create_new_branch, push-model, build, build-docker] | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # # Checkout the repository to the GitHub Actions runner to the new branch created for the issue 🟢 | |
| # - uses: actions/checkout@v3 | |
| # if: needs.create_new_branch.outputs.BRANCHNAME == '' | |
| # with: | |
| # ref: issue-${{ github.event.issue.number }} | |
| # # If branchName is empty use issue number, else, use the branchName 🟢 | |
| # - uses: actions/checkout@v3 | |
| # if: needs.create_new_branch.outputs.BRANCHNAME != '' | |
| # with: | |
| # ref: ${{ needs.create_new_branch.outputs.BRANCHNAME }} | |
| # # Set up Python | |
| # - name: Set up Python | |
| # uses: actions/setup-python@v4 | |
| # with: | |
| # python-version: 3.11 | |
| # # Install datalad 🟢 | |
| # - name: Install Datalad | |
| # id: testing | |
| # run: | | |
| # sudo apt-get install datalad | |
| # python3 -m pip install datalad-osf | |
| # pip install requests | |
| # git config --global user.name "trained_models" | |
| # git config --global user.email "trained_models" | |
| # # Get file extensions for the weights and sample data | |
| # # - name: Get extensions for weights | |
| # # id: get_extensions_weights | |
| # # run: | | |
| # # echo "weights_ext<<EOF" >> $GITHUB_OUTPUT | |
| # # python ./.github/workflows/getFileExtension.py "${{ needs.create_new_branch.outputs.WEIGHTS }}" >> $GITHUB_OUTPUT | |
| # # echo "EOF" >> $GITHUB_OUTPUT | |
| # # - name: Get extensions for sample data | |
| # # id: get_extensions_sample_data | |
| # # run: | | |
| # # echo "sample_ext<<EOF" >> $GITHUB_OUTPUT | |
| # # python ./.github/workflows/getFileExtension.py "${{ needs.create_new_branch.outputs.SAMPLEDATA }}" >> $GITHUB_OUTPUT | |
| # # echo "EOF" >> $GITHUB_OUTPUT | |
| # #Git annex addurl the weights | |
| # - name: Git-annex/Datalad add the weights | |
| # env: | |
| # OSF_TOKEN: ${{ secrets.OSF_TOKEN }} | |
| # run: | | |
| # # datalad siblings | |
| # mkdir ./${{ needs.create_new_branch.outputs.MODELPATH }}/weights | |
| # cd ./${{ needs.create_new_branch.outputs.MODELPATH }}/weights | |
| # # datalad download-url --overwrite -m "Added Weights" -O ./${{ needs.create_new_branch.outputs.MODELPATH }}/weights/best_model.${{ steps.get_extensions_weights.outputs.weights_ext }} "${{ needs.create_new_branch.outputs.WEIGHTS }}" | |
| # datalad download-url --overwrite -m "Added Sample Dataset" "${{ needs.create_new_branch.outputs.WEIGHTS }}" | |
| # datalad save . -m "Added model weights" | |
| # #datalad push --to osf-annex2-storage | |
| # datalad push --to origin | |
| # - name: Git-annex/Datalad add the sample datasets | |
| # env: | |
| # OSF_TOKEN: ${{ secrets.OSF_TOKEN }} | |
| # run: | | |
| # mkdir ./${{ needs.create_new_branch.outputs.MODELPATH }}/example-data | |
| # cd ./${{ needs.create_new_branch.outputs.MODELPATH }}/example-data | |
| # # datalad download-url --overwrite -m "Added Sample Dataset" -O ./${{needs.create_new_branch.outputs.MODELPATH}}/example-data/sample.${{ steps.get_extensions_sample_data.outputs.sample_ext }} "${{needs.create_new_branch.outputs.SAMPLEDATA}}" | |
| # datalad download-url --overwrite -m "Added Sample Dataset" "${{ needs.create_new_branch.outputs.SAMPLEDATA }}" | |
| # datalad save . -m "Added sample data" | |
| # #datalad push --to osf-annex2-storage | |
| # datalad push --to origin | |
| start-runner: | |
| # needs: [create_new_branch, push-model, build, build-docker, push-weights] | |
| runs-on: ubuntu-latest | |
| outputs: | |
| label: ${{ steps.start-ec2-runner.outputs.label }} | |
| ec2-instance-id: ${{ steps.start-ec2-runner.outputs.ec2-instance-id }} | |
| steps: | |
| - name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v1 | |
| with: | |
| aws-access-key-id: ${{ secrets.AWS_KEY_ID }} | |
| aws-secret-access-key: ${{ secrets.AWS_KEY_SECRET }} | |
| aws-region: ${{ vars.AWS_REGION }} | |
| - name: Start EC2 runner | |
| id: start-ec2-runner | |
| uses: machulav/ec2-github-runner@v2 | |
| with: | |
| mode: start | |
| github-token: ${{ secrets.GH_TOKEN }} | |
| ec2-image-id: ${{ vars.AWS_IMAGE_ID }} | |
| ec2-instance-type: ${{ vars.AWS_INSTANCE_TYPE }} | |
| subnet-id: ${{ vars.AWS_SUBNET }} | |
| security-group-id: ${{ vars.AWS_SECURITY_GROUP }} | |
| test-model: | |
| name: Do the job on the runner | |
| # needs: [create_new_branch, push-model, build, build-docker, push-weights, start-runner] # required to start the main job when the runner is ready | |
| needs: [start-runner] | |
| runs-on: ${{ needs.start-runner.outputs.label }} # run the job on the newly created runner | |
| steps: | |
| # Setups singularity to the job to make it accessible to other steps | |
| # Cleanup steps to free up disk space | |
| # - name: Cleanup disk space for large docker images | |
| # run: | | |
| # sudo rm -rf /usr/share/dotnet | |
| # sudo rm -rf /opt/ghc | |
| # sudo rm -rf "/usr/local/share/boost" | |
| # sudo rm -rf /opt/hostedtoolcache | |
| # sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| # - name: Free Disk Space (Ubuntu) | |
| # uses: jlumbroso/free-disk-space@main | |
| # with: | |
| # # this might remove tools that are actually needed, | |
| # # if set to "true" but frees about 6 GB | |
| # tool-cache: false | |
| # # all of these default to true, but feel free to set to | |
| # # "false" if necessary for your workflow | |
| # android: true | |
| # dotnet: true | |
| # haskell: true | |
| # large-packages: true | |
| # docker-images: false | |
| # - uses: actions/checkout@v3 | |
| # if: needs.create_new_branch.outputs.BRANCHNAME == '' | |
| # with: | |
| # ref: issue-${{ github.event.issue.number }} | |
| # # If branchName is empty use issue number, else, use the branchName 🟢 | |
| - uses: actions/checkout@v3 | |
| # if: needs.create_new_branch.outputs.BRANCHNAME != '' | |
| # with: | |
| # ref: ${{ needs.create_new_branch.outputs.BRANCHNAME }} | |
| - name: Install singularity | |
| run: | | |
| wget https://github.com/sylabs/singularity/releases/download/v4.0.0/singularity-ce_4.0.0-focal_amd64.deb | |
| sudo apt install ./singularity-ce_4.0.0-focal_amd64.deb -y | |
| singularity version | |
| # Build the Docker image 🟢 | |
| #- name: Build Docker image | |
| #run: | | |
| #docker build -t ${{ needs.build-docker.outputs.MODELNAME }} ./${{ needs.create_new_branch.outputs.MODELPATH }}/docker | |
| #docker save --output ./${{ needs.create_new_branch.outputs.MODELPATH }}/docker/${{ needs.build-docker.outputs.MODELNAME }}.tar ${{ needs.build-docker.outputs.MODELNAME }} | |
| # Convert the docker image to a singularity image | |
| #- name: Convert docker image to singularity image | |
| #run: | | |
| #singularity build ./${{ needs.create_new_branch.outputs.MODELPATH }}/docker/${{ needs.build-docker.outputs.MODELNAME }}.sif docker-archive://./${{ needs.create_new_branch.outputs.MODELPATH }}/docker/${{ needs.build-docker.outputs.MODELNAME }}.tar | |
| # Datalad get the sample dataset | |
| #- name: Get sample dataset | |
| #run: | | |
| #sudo apt install python3-pip -y | |
| #pip install datalad | |
| #git config --global user.name "trained_models" | |
| #git config --global user.email "trained_models" | |
| #datalad get ./${{ needs.create_new_branch.outputs.MODELPATH }}/weights/ | |
| #datalad get ./${{ needs.create_new_branch.outputs.MODELPATH }}/example-data/ | |
| #sudo apt install unzip | |
| #cd ./${{ needs.create_new_branch.outputs.MODELPATH }}/example-data/ | |
| #find . -name "*.zip" -exec unzip {} \; | |
| # Push the dataset to the repo | |
| #datalad save . -m "Added sample data" | |
| #datalad push --to osf-annex2-storage | |
| #datalad push --to origin | |
| #- name: Get the weights | |
| #run: | | |
| #cd ./${{ needs.create_new_branch.outputs.MODELPATH }}/weights/ | |
| #find . -name "*.zip" -exec unzip {} \; | |
| # Push the weights to the repo | |
| #datalad save . -m "Added model weights" | |
| #datalad push --to osf-annex2-storage | |
| #datalad push --to origin | |
| #- name: Collect Workflow Telemetry | |
| #uses: runforesight/workflow-telemetry-action@v1 | |
| #with: | |
| #job_summary: true | |
| #proc_trace_sys_enable: true | |
| #proc_trace_table_show: true | |
| # Run in singularity the test command saved under needs.create_new_branch.outputs.DEEPCSR | |
| - name: Run test command in Singularity | |
| run: | | |
| # Parent directory as a bind path in a env variable | |
| #singularity exec --nv --bind /actions-runner,/actions-runner/_work/,/actions-runner/_work/${{ github.event.repository.name }}/${{ github.event.repository.name }}/${{ needs.create_new_branch.outputs.MODELPATH }}/,/actions-runner/_work/${{ github.event.repository.name }}/${{ github.event.repository.name }}/${{ needs.create_new_branch.outputs.MODELPATH }}/docker,/actions-runner/_work/${{ github.event.repository.name }}/${{ github.event.repository.name }}/${{ needs.create_new_branch.outputs.MODELPATH }}/weights,/actions-runner/_work/${{ github.event.repository.name }}/${{ github.event.repository.name }}/${{ needs.create_new_branch.outputs.MODELPATH }}/example-data:/output ./${{ needs.create_new_branch.outputs.MODELPATH }}/docker/${{ needs.build-docker.outputs.MODELNAME }}.sif ${{ needs.create_new_branch.outputs.TESTCOMMAND }} | |
| docker login -u hvgazula -p dckr_pat_VpAuZs0gh1vNrzENg1b1wsAyWYk | |
| # singularity build ./${{ needs.create_new_branch.outputs.MODELPATH }}/docker/${{ needs.build-docker.outputs.MODELNAME }}.sif docker://hvgazula/test:tm-sim | |
| # singularity exec --nv --bind /actions-runner/_work/${{ github.event.repository.name }}/${{ github.event.repository.name }}:/output ./${{ needs.create_new_branch.outputs.MODELPATH }}/docker/${{ needs.build-docker.outputs.MODELNAME }}.sif ls | |
| singularity build tm-sim.sif docker://hvgazula/test:tm-sim | |
| singularity exec --bind /actions-runner/_work/:/output test:tm-sim.sif echo $PWD | |
| singularity exec --bind /actions-runner/_work/:/output test:tm-sim.sif ls | |
| # Load the Docker image 🟢 | |
| #- name: Load Docker image | |
| #run: | | |
| #docker load --input "./${{ needs.create_new_branch.outputs.MODELPATH }}/docker/${{ needs.build-docker.outputs.MODELNAME }}.tar" | |
| #- name: Collect Workflow Telemetry | |
| #uses: runforesight/workflow-telemetry-action@v1 | |
| #with: | |
| #job_summary: true | |
| #proc_trace_sys_enable: true | |
| #proc_trace_table_show: true | |
| # Test model with docker image as well | |
| #- name: Run test command in Docker | |
| #run: | | |
| #docker run --gpus all -v /actions-runner/_work/${{ github.event.repository.name }}/${{ github.event.repository.name }}:/output ${{ needs.build-docker.outputs.MODELNAME }} "cd /output; ${{ needs.create_new_branch.outputs.TESTCOMMAND }}" | |
| # Get model's version from model's path | |
| #- name: Get model's version | |
| #id: modelVersion | |
| #run: | | |
| # Get the version | |
| #model_version=$(echo "${{ needs.create_new_branch.outputs.MODELPATH }}" | awk -F '/' '{print $(NF)}') | |
| # Set the version as an output | |
| #echo "model_version=$model_version" >> $GITHUB_OUTPUT | |
| # Push the Docker image to Docker Hub (only if the PR is merged) 🟢 | |
| #- name: Push Docker image | |
| #run: | | |
| #docker login -u ${{ secrets.DOCKER_USERNAME }} -p ${{ secrets.DOCKER_PASSWORD }} | |
| #docker tag ${{ needs.build-docker.outputs.MODELNAME }} ${{ needs.build-docker.outputs.IMAGENAME }}:${{ steps.modelVersion.outputs.model_version }} | |
| #docker push ${{ needs.build-docker.outputs.IMAGENAME }} | |
| stop-runner: | |
| name: Stop self-hosted EC2 runner | |
| # needs: [create_new_branch, push-model, build, build-docker, push-weights, start-runner, test-model] # required to wait when the main job is done | |
| needs: [start-runner, test-model] | |
| runs-on: ubuntu-latest | |
| if: ${{ always() }} | |
| # required to stop the runner even if the error happened in the previous jobs | |
| steps: | |
| - name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v1 | |
| with: | |
| aws-access-key-id: ${{ secrets.AWS_KEY_ID }} | |
| aws-secret-access-key: ${{ secrets.AWS_KEY_SECRET }} | |
| aws-region: ${{ vars.AWS_REGION }} | |
| - name: Stop EC2 runner | |
| uses: machulav/ec2-github-runner@v2 | |
| with: | |
| mode: stop | |
| github-token: ${{ secrets.GH_TOKEN }} | |
| label: ${{ needs.start-runner.outputs.label }} | |
| ec2-instance-id: ${{ needs.start-runner.outputs.ec2-instance-id }} | |
| # failed: | |
| # runs-on: ubuntu-latest | |
| # needs: [create_new_branch, push-model, build, build-docker, push-weights, start-runner, test-model] | |
| # if: ${{ failure() }} | |
| # steps: | |
| # - name: Set labels | |
| # uses: actions-cool/issues-helper@v3 | |
| # with: | |
| # actions: 'set-labels' | |
| # token: ${{ secrets.GITHUB_TOKEN }} | |
| # issue-number: ${{ github.event.issue.number }} | |
| # labels: 'failed' | |
| # - name: Create comment | |
| # uses: actions-cool/issues-helper@v3 | |
| # with: | |
| # actions: 'create-comment' | |
| # token: ${{ secrets.GITHUB_TOKEN }} | |
| # issue-number: ${{ github.event.issue.number }} | |
| # body: | | |
| # [This is an automated message] Hello @${{ github.event.issue.user.login }}, | |
| # 🔴 The folders/scripts you provided did not pass our tests. Please review the Action, and modify this issue's urls accordingly. | |
| # When ready, just change the label of this issue to "Ready for testing". | |
| # emoji: '+1,eyes' | |
| # success: | |
| # needs: [create_new_branch, push-model, build, build-docker, push-weights, start-runner, test-model, stop-runner] | |
| # runs-on: ubuntu-latest | |
| # steps: | |
| # - name: Set labels | |
| # uses: actions-cool/issues-helper@v3 | |
| # with: | |
| # actions: 'set-labels' | |
| # token: ${{ secrets.GITHUB_TOKEN }} | |
| # issue-number: ${{ github.event.issue.number }} | |
| # labels: 'success' | |
| # - name: Create comment | |
| # uses: actions-cool/issues-helper@v3 | |
| # with: | |
| # actions: 'create-comment' | |
| # token: ${{ secrets.GITHUB_TOKEN }} | |
| # issue-number: ${{ github.event.issue.number }} | |
| # body: | | |
| # [This is an automated message] Hello @${{ github.event.issue.user.login }}. The workflow linked to adding your model finished successfully! Please double check that this issue's tag is "success." | |
| # 🟢 A Draft PR should be linked to this issue. Now that your model passed the checks, feel free to change the status of the PR to "ready for review." | |
| # ⭐ Thank you for adding a model to Nobrainer-Zoo! | |
| # emoji: '+1,hooray,rocket' | |
| ########################################## | |
| # This workflow will add a new model to the zoo | |
| # The flow of the workflow is as follows: | |
| # 1. Create a new branch from the issue | |
| # 2. Scrape the info from the issue | |
| # 3. Scrape info from the form | |
| # 4. Push the new created files and folders to the branch | |
| # 5. Build the model card and spec.yaml file | |
| # 6. Update the model's spec.yaml file | |
| # 7. Build the docker image | |
| # 8. Push the weights and sample data to the datalad repo | |
| # 9. Start the self-hosted runner | |
| # 10. Test the model/Push docker image to dockerhub | |
| # 11. Stop the self-hosted runner | |
| # 12. If the model fails, add the failed label and comment | |
| # 13. If the model succeeds, add the success label and comment |