Update bert-models-cicd.yaml

UCDenver-ccp · Dec 12, 2023 · 8c07771 · 8c07771
1 parent 7fcc599
commit 8c07771
Showing 1 changed file with 129 additions and 129 deletions.
diff --git a/.github/workflows/bert-models-cicd.yaml b/.github/workflows/bert-models-cicd.yaml
@@ -341,142 +341,142 @@ jobs:
 #         docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION"
 
 
-  # ----------------------------------------------------------------------------------- #
-  # ----------------------------------------------------------------------------------- #
-  # ----------------------------------------------------------------------------------- #
-  #              TRAIN BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE MODEL               #
-  # ----------------------------------------------------------------------------------- #
-  # ----------------------------------------------------------------------------------- #
-  # ----------------------------------------------------------------------------------- #
-
-  build_push_train-bl_chemical_to_disease_or_phenotypic_feature-train:
-    name: "build/push/train bl_chemical_to_disease_or_phenotypic_feature model"
-    # needs: "build_push-bert-base"
-    runs-on: ubuntu-latest
-    env:
-      TASK_NAME: bl_chemical_to_disease_or_phenotypic_feature
-      DOCKERFILE: train.Dockerfile
-      ENTRYPOINT_FILE: scripts/train.entrypoint.sh
-      BASE_DOCKERFILE: base.Dockerfile
-      DATA_FILE: data/bl_chemical_to_disease_or_phenotypic_feature/data.tsv
-      MODEL_VERSION_KEY: BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE
-      AI_PLATFORM_JOB_NAME: "bl_chemical_to_disease_or_phenotypic_feature_train_${{ github.run_number }}"
-    steps:
-    - uses: actions/checkout@v2
-      with:
-        fetch-depth: 0
-    # - name: Get changed files
-    #   id: changed-files
-    #   uses: tj-actions/changed-files@v7
-
-    # - name: List all modified files
-    #   run: |
-    #     for file in "${{ steps.changed-files.outputs.all_modified_files }}"; do
-    #       echo "$file was modified"
-    #     done
-
-    # - name: Run step when a file changes
-    #   if: |
-    #     contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) ||
-    #     contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) ||
-    #     contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) ||
-    #     contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
-    #   run: |
-    #     echo "A modified file has triggered a rebuild of the ${{ env.TASK_NAME }} model."
-
-    - name: Set up Cloud SDK
-      # if: |
-      #   contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
-      uses: google-github-actions/setup-gcloud@main
-      with:
-        project_id: ${{ secrets.GCE_PROJECT }}
-        service_account_key: ${{ secrets.GCE_SA_KEY }}
-        version: '290.0.1'
-
-    - name: Configure Docker Authentication
-      # if: |
-      #   contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
-      run: |
-        gcloud --quiet auth configure-docker
-
-    - name: Set MODEL_VERSION env
-      # if: |
-      #   contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
-      run: |
-        echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
-
-    - name: Set BASE_VERSION env
-      # if: |
-      #   contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
-      run: |
-        echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
-
-    - name: Build Docker Image
-      # if: |
-      #   contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
-      run: |
-        docker build --build-arg "PROJECT_ID=$PROJECT_ID" \
-                     --build-arg "TASK_NAME=$TASK_NAME" \
-                     --build-arg "BASE_VERSION=$BASE_VERSION" \
-                     --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \
-                     --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \
-                     -f ${{ env.DOCKERFILE }} .
-
-    - name: Publish Docker Image to Google Container Registry
-      # if: |
-      #   contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
-      run: |
-        docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION"
-
-    - name: Submit a training job to AI Plaform to train and cache the model
-      # if: |
-      #   contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
-      run: |
-        gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \
-        --scale-tier basic_gpu --region "$GCE_REGION" \
-        --master-image-uri "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \
-        -- \
-        NO_ARG \
-        "gs://$MODEL_STORAGE_BUCKET"
-
-    - name: Monitor the training job
-      # if: |
-      #   contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) ||
-      #   contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
-      run: |
-        sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}"
-      timeout-minutes: 500
+  # # ----------------------------------------------------------------------------------- #
+  # # ----------------------------------------------------------------------------------- #
+  # # ----------------------------------------------------------------------------------- #
+  # #              TRAIN BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE MODEL               #
+  # # ----------------------------------------------------------------------------------- #
+  # # ----------------------------------------------------------------------------------- #
+  # # ----------------------------------------------------------------------------------- #
+
+  # build_push_train-bl_chemical_to_disease_or_phenotypic_feature-train:
+  #   name: "build/push/train bl_chemical_to_disease_or_phenotypic_feature model"
+  #   # needs: "build_push-bert-base"
+  #   runs-on: ubuntu-latest
+  #   env:
+  #     TASK_NAME: bl_chemical_to_disease_or_phenotypic_feature
+  #     DOCKERFILE: train.Dockerfile
+  #     ENTRYPOINT_FILE: scripts/train.entrypoint.sh
+  #     BASE_DOCKERFILE: base.Dockerfile
+  #     DATA_FILE: data/bl_chemical_to_disease_or_phenotypic_feature/data.tsv
+  #     MODEL_VERSION_KEY: BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE
+  #     AI_PLATFORM_JOB_NAME: "bl_chemical_to_disease_or_phenotypic_feature_train_${{ github.run_number }}"
+  #   steps:
+  #   - uses: actions/checkout@v2
+  #     with:
+  #       fetch-depth: 0
+  #   # - name: Get changed files
+  #   #   id: changed-files
+  #   #   uses: tj-actions/changed-files@v7
+
+  #   # - name: List all modified files
+  #   #   run: |
+  #   #     for file in "${{ steps.changed-files.outputs.all_modified_files }}"; do
+  #   #       echo "$file was modified"
+  #   #     done
+
+  #   # - name: Run step when a file changes
+  #   #   if: |
+  #   #     contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) ||
+  #   #     contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) ||
+  #   #     contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) ||
+  #   #     contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
+  #   #   run: |
+  #   #     echo "A modified file has triggered a rebuild of the ${{ env.TASK_NAME }} model."
+
+  #   - name: Set up Cloud SDK
+  #     # if: |
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
+  #     uses: google-github-actions/setup-gcloud@main
+  #     with:
+  #       project_id: ${{ secrets.GCE_PROJECT }}
+  #       service_account_key: ${{ secrets.GCE_SA_KEY }}
+  #       version: '290.0.1'
+
+  #   - name: Configure Docker Authentication
+  #     # if: |
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
+  #     run: |
+  #       gcloud --quiet auth configure-docker
+
+  #   - name: Set MODEL_VERSION env
+  #     # if: |
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
+  #     run: |
+  #       echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
+
+  #   - name: Set BASE_VERSION env
+  #     # if: |
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
+  #     run: |
+  #       echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
+
+  #   - name: Build Docker Image
+  #     # if: |
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
+  #     run: |
+  #       docker build --build-arg "PROJECT_ID=$PROJECT_ID" \
+  #                    --build-arg "TASK_NAME=$TASK_NAME" \
+  #                    --build-arg "BASE_VERSION=$BASE_VERSION" \
+  #                    --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \
+  #                    --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \
+  #                    -f ${{ env.DOCKERFILE }} .
+
+  #   - name: Publish Docker Image to Google Container Registry
+  #     # if: |
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
+  #     run: |
+  #       docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION"
+
+  #   - name: Submit a training job to AI Plaform to train and cache the model
+  #     # if: |
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
+  #     run: |
+  #       gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \
+  #       --scale-tier basic_gpu --region "$GCE_REGION" \
+  #       --master-image-uri "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \
+  #       -- \
+  #       NO_ARG \
+  #       "gs://$MODEL_STORAGE_BUCKET"
+
+  #   - name: Monitor the training job
+  #     # if: |
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) ||
+  #     #   contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE)
+  #     run: |
+  #       sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}"
+  #     timeout-minutes: 500
 
   # -------------------------------------------------------------------------------------- #
   # BUILD/PUSH BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE CLASSIFICATION CONTAINER IMAGE #
   # -------------------------------------------------------------------------------------- #
 
   build_push-bl_chemical_to_disease_or_phenotypic_feature-predict:
     name: "build/push bl_chemical_to_disease_or_phenotypic_feature predict container"
-    needs: "build_push_train-bl_chemical_to_disease_or_phenotypic_feature-train"
+    # needs: "build_push_train-bl_chemical_to_disease_or_phenotypic_feature-train"
     runs-on: ubuntu-latest
     env:
       TASK_NAME: bl_chemical_to_disease_or_phenotypic_feature