new data for chemical-to-disease #345
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| name: CI/CD for BERT-based sentence classification models | |
| # ########################################################################### # | |
| # # | |
| # This workflow trains BERT-based models for sentence classification. # | |
| # Changes in training data files as well as relevant Docker-related files # | |
| # automatically trigger new builds/training for the appropriate model. # | |
| # # | |
| # --- Changes to base.Docker will trigger a rebuild of the base container # | |
| # and all downstream containers. # | |
| # # | |
| # --- Changes to train.Dockerfile will trigger a rebuild of all training # | |
| # containers and all downstream containers. # | |
| # # | |
| # --- Changes to predict.Dockerfile will trigger a rebuild of all prediction # | |
| # containers. # | |
| # # | |
| # --- Changes to the data.tsv file in the data/ directories will trigger # | |
| # rebuilds for the appropriate model-specific training and downstream # | |
| # containers. # | |
| # # | |
| # ########################################################################### # | |
| on: | |
| # Trigger the workflow on push or pull request, | |
| # but only for the main branch | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| env: | |
| PROJECT_ID: ${{ secrets.GCE_PROJECT }} | |
| GCS_SERVICE_ACCOUNT: ${{ secrets.GCE_SA_KEY }} | |
| GCE_REGION: ${{ secrets.GCE_REGION }} | |
| MODEL_STORAGE_BUCKET: ${{ secrets.MODEL_STORAGE_BUCKET }} | |
| jobs: | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # BUILD/PUSH BLUEBERT-BASE CONTAINER IMAGE # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # Note: when trying to run build_push-bert-base with other jobs below, an error is reported on line 90. | |
| # # However, when run on its own it works fine. | |
| # build_push-bert-base: | |
| # name: "build/push bluebert-base container image" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # IMAGE_NAME: bluebert-base | |
| # DOCKERFILE: base.Dockerfile | |
| # permissions: | |
| # contents: 'read' | |
| # id-token: 'write' | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: echo "MODEL_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: docker build --tag "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION" -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: docker push "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION" | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # TRAIN BL_DISEASE_TO_ANATOMY MODEL # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_disease_to_anatomy-train: | |
| # name: "build/push/train bl_disease_to_anatomy model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_disease_to_anatomy | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_disease_to_anatomy/data.tsv | |
| # MODEL_VERSION_KEY: BL_DISEASE_TO_ANATOMY | |
| # AI_PLATFORM_JOB_NAME: "bl_disease_to_anatomy_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_DISEASE_TO_ANATOMY CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_disease_to_anatomy-predict: | |
| # name: "build/push bl_disease_to_anatomy predict container" | |
| # needs: "build_push_train-bl_disease_to_anatomy-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_disease_to_anatomy | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_DISEASE_TO_ANATOMY | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "has_basis_in other" | |
| # DATA_FILE: data/bl_disease_to_anatomy/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # TRAIN BL_DISEASE_TO_CELL MODEL # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_disease_to_cell-train: | |
| # name: "build/push/train bl_disease_to_cell model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_disease_to_cell | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_disease_to_cell/data.tsv | |
| # MODEL_VERSION_KEY: BL_DISEASE_TO_CELL | |
| # AI_PLATFORM_JOB_NAME: "bl_disease_to_cell_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_DISEASE_TO_CELL CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_disease_to_cell-predict: | |
| # name: "build/push bl_disease_to_cell predict container" | |
| # needs: "build_push_train-bl_disease_to_cell-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_disease_to_cell | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_DISEASE_TO_CELL | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "has_basis_in other" | |
| # DATA_FILE: data/bl_disease_to_cell/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # TRAIN BL_DISEASE_TO_GENE MODEL # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_disease_to_gene-train: | |
| # name: "build/push/train bl_disease_to_gene model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_disease_to_gene | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_disease_to_gene/data.tsv | |
| # MODEL_VERSION_KEY: BL_DISEASE_TO_GENE | |
| # AI_PLATFORM_JOB_NAME: "bl_disease_to_gene_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_DISEASE_TO_GENE CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_disease_to_gene-predict: | |
| # name: "build/push bl_disease_to_gene predict container" | |
| # needs: "build_push_train-bl_disease_to_gene-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_disease_to_gene | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_DISEASE_TO_GENE | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "has_basis_in other" | |
| # DATA_FILE: data/bl_disease_to_gene/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # TRAIN BL_DISEASE_TO_PHENOTYPE MODEL # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_disease_to_phenotype-train: | |
| # name: "build/push/train bl_disease_to_phenotype model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_disease_to_phenotype | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_disease_to_phenotype/data.tsv | |
| # MODEL_VERSION_KEY: BL_DISEASE_TO_PHENOTYPE | |
| # AI_PLATFORM_JOB_NAME: "bl_disease_to_phenotype_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_DISEASE_TO_PHENOTYPE CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_disease_to_phenotype-predict: | |
| # name: "build/push bl_disease_to_phenotype predict container" | |
| # needs: "build_push_train-bl_disease_to_phenotype-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_disease_to_phenotype | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_DISEASE_TO_PHENOTYPE | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "has_phenotype other" | |
| # DATA_FILE: data/bl_disease_to_phenotype/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # TRAIN BL_DISEASE_TO_PROCESS MODEL # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_disease_to_process-train: | |
| # name: "build/push/train bl_disease_to_process model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_disease_to_process | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_disease_to_process/data.tsv | |
| # MODEL_VERSION_KEY: BL_DISEASE_TO_PROCESS | |
| # AI_PLATFORM_JOB_NAME: "bl_disease_to_process_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_DISEASE_TO_PROCESS CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_disease_to_process-predict: | |
| # name: "build/push bl_disease_to_process predict container" | |
| # needs: "build_push_train-bl_disease_to_process-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_disease_to_process | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_DISEASE_TO_PROCESS | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "has_basis_in other" | |
| # DATA_FILE: data/bl_disease_to_process/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # TRAIN BL_GENE_TO_LOCATION MODEL # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_gene_to_location-train: | |
| # name: "build/push/train bl_gene_to_location model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_to_location | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_gene_to_location/data.tsv | |
| # MODEL_VERSION_KEY: BL_GENE_TO_LOCATION | |
| # AI_PLATFORM_JOB_NAME: "bl_gene_to_location_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_GENE_TO_LOCATION CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_gene_to_location-predict: | |
| # name: "build/push bl_gene_to_location predict container" | |
| # needs: "build_push_train-bl_gene_to_location-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_to_location | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_GENE_TO_LOCATION | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "located_in other" | |
| # DATA_FILE: data/bl_gene_to_location/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # TRAIN BL_GENE_TO_ANATOMY MODEL # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_gene_to_anatomy-train: | |
| # name: "build/push/train bl_gene_to_anatomy model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_to_anatomy | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_gene_to_anatomy/data.tsv | |
| # MODEL_VERSION_KEY: BL_GENE_TO_ANATOMY | |
| # AI_PLATFORM_JOB_NAME: "bl_gene_to_anatomy_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_GENE_TO_ANATOMY CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_gene_to_anatomy-predict: | |
| # name: "build/push bl_gene_to_anatomy predict container" | |
| # needs: "build_push_train-bl_gene_to_anatomy-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_to_anatomy | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_GENE_TO_ANATOMY | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "located_in other" | |
| # DATA_FILE: data/bl_gene_to_anatomy/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # TRAIN BL_GENE_TO_CELL_COMPONENT MODEL # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_gene_to_cell_component-train: | |
| # name: "build/push/train bl_gene_to_cell_component model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_to_cell_component | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_gene_to_cell_component/data.tsv | |
| # MODEL_VERSION_KEY: BL_GENE_TO_COMPONENT_CELL | |
| # AI_PLATFORM_JOB_NAME: "bl_gene_to_cell_component_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_GENE_TO_CELL_COMPONENT CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_gene_to_cell_component-predict: | |
| # name: "build/push bl_gene_to_cell_component predict container" | |
| # needs: "build_push_train-bl_gene_to_cell_component-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_to_cell_component | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_GENE_TO_COMPONENT_CELL | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "located_in other" | |
| # DATA_FILE: data/bl_gene_to_cell_component/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # TRAIN BL_GENE_TO_CELL MODEL # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_gene_to_cell-train: | |
| # name: "build/push/train bl_gene_to_cell model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_to_cell | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_gene_to_cell/data.tsv | |
| # MODEL_VERSION_KEY: BL_GENE_TO_CELL | |
| # AI_PLATFORM_JOB_NAME: "bl_gene_to_cell_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_GENE_TO_CELL CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_gene_to_cell-predict: | |
| # name: "build/push bl_gene_to_cell predict container" | |
| # needs: "build_push_train-bl_gene_to_cell-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_to_cell | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_GENE_TO_CELL | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "located_in other" | |
| # DATA_FILE: data/bl_gene_to_cell/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # TRAIN BL_PROCESS_TO_LOCATION MODEL # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_process_to_location-train: | |
| # name: "build/push/train bl_process_to_location model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_process_to_location | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_process_to_location/data.tsv | |
| # MODEL_VERSION_KEY: BL_PROCESS_TO_LOCATION | |
| # AI_PLATFORM_JOB_NAME: "bl_process_to_location_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_PROCESS_TO_LOCATION CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_process_to_location-predict: | |
| # name: "build/push bl_process_to_location predict container" | |
| # needs: "build_push_train-bl_process_to_location-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_process_to_location | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_PROCESS_TO_LOCATION | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "occurs_in other" | |
| # DATA_FILE: data/bl_process_to_location/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # TRAIN BL_PROCESS_TO_ANATOMY MODEL # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_process_to_anatomy-train: | |
| # name: "build/push/train bl_process_to_anatomy model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_process_to_anatomy | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_process_to_anatomy/data.tsv | |
| # MODEL_VERSION_KEY: BL_PROCESS_TO_ANATOMY | |
| # AI_PLATFORM_JOB_NAME: "bl_process_to_anatomy_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_PROCESS_TO_ANATOMY CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_process_to_anatomy-predict: | |
| # name: "build/push bl_process_to_anatomy predict container" | |
| # needs: "build_push_train-bl_process_to_anatomy-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_process_to_anatomy | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_PROCESS_TO_ANATOMY | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "occurs_in other" | |
| # DATA_FILE: data/bl_process_to_anatomy/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # TRAIN BL_PROCESS_TO_CELL_COMPONENT MODEL # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_process_to_cell_component-train: | |
| # name: "build/push/train bl_process_to_cell_component model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_process_to_cell_component | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_process_to_cell_component/data.tsv | |
| # MODEL_VERSION_KEY: BL_PROCESS_TO_COMPONENT_CELL | |
| # AI_PLATFORM_JOB_NAME: "bl_process_to_cell_component_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_PROCESS_TO_CELL_COMPONENT CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_process_to_cell_component-predict: | |
| # name: "build/push bl_process_to_cell_component predict container" | |
| # needs: "build_push_train-bl_process_to_cell_component-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_process_to_cell_component | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_PROCESS_TO_COMPONENT_CELL | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "occurs_in other" | |
| # DATA_FILE: data/bl_process_to_cell_component/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # TRAIN BL_PROCESS_TO_CELL MODEL # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_process_to_cell-train: | |
| # name: "build/push/train bl_process_to_cell model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_process_to_cell | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_process_to_cell/data.tsv | |
| # MODEL_VERSION_KEY: BL_PROCESS_TO_CELL | |
| # AI_PLATFORM_JOB_NAME: "bl_process_to_cell_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_PROCESS_TO_CELL CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_process_to_cell-predict: | |
| # name: "build/push bl_process_to_cell predict container" | |
| # needs: "build_push_train-bl_process_to_cell-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_process_to_cell | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_PROCESS_TO_CELL | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "occurs_in other" | |
| # DATA_FILE: data/bl_process_to_cell/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # TRAIN BL_GENE_TO_PROCESS MODEL # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_gene_to_process-train: | |
| # name: "build/push/train bl_gene_to_process model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_to_process | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_gene_to_process/data.tsv | |
| # MODEL_VERSION_KEY: BL_GENE_TO_PROCESS | |
| # AI_PLATFORM_JOB_NAME: "bl_gene_to_process_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_GENE_TO_PROCESS CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_gene_to_process-predict: | |
| # name: "build/push bl_gene_to_process predict container" | |
| # needs: "build_push_train-bl_gene_to_process-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_to_process | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_GENE_TO_PROCESS | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "participates_in enhances inhibits other" | |
| # DATA_FILE: data/bl_gene_to_process/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # TRAIN BL_GENE_TO_GENE MODEL # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_gene_to_gene-train: | |
| # name: "build/push/train bl_gene_to_gene model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_to_gene | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_gene_to_gene/data.tsv | |
| # MODEL_VERSION_KEY: BL_GENE_TO_GENE | |
| # AI_PLATFORM_JOB_NAME: "bl_gene_to_gene_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_GENE_TO_GENE CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_gene_to_gene-predict: | |
| # name: "build/push bl_gene_to_gene predict container" | |
| # needs: "build_push_train-bl_gene_to_gene-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_to_gene | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_GENE_TO_GENE | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "modulates activates deactivates physically_interacts_with other" | |
| # DATA_FILE: data/bl_gene_to_gene/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # ----------------------------------------------------------------------------------- # | |
| # # # # ----------------------------------------------------------------------------------- # | |
| # # # # ----------------------------------------------------------------------------------- # | |
| # # # # TRAIN BL_CHEMICAL_TO_CELL MODEL # | |
| # # # # ----------------------------------------------------------------------------------- # | |
| # # # # ----------------------------------------------------------------------------------- # | |
| # # # # ----------------------------------------------------------------------------------- # | |
| build_push_train-bl_chemical_to_cell-train: | |
| name: "build/push/train bl_chemical_to_cell model" | |
| # needs: "build_push-bert-base" | |
| runs-on: ubuntu-latest | |
| env: | |
| TASK_NAME: bl_chemical_to_cell | |
| DOCKERFILE: train.Dockerfile | |
| ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| BASE_DOCKERFILE: base.Dockerfile | |
| DATA_FILE: data/bl_chemical_to_cell/data.tsv | |
| MODEL_VERSION_KEY: BL_CHEMICAL_TO_CELL | |
| AI_PLATFORM_JOB_NAME: "bl_chemical_to_cell_train_${{ github.run_number }}" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - id: 'auth' | |
| uses: 'google-github-actions/auth@v2' | |
| with: | |
| project_id: ${{ secrets.GCE_PROJECT }} | |
| service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| - name: 'Set up Cloud SDK' | |
| uses: 'google-github-actions/setup-gcloud@v2' | |
| with: | |
| version: '>= 363.0.0' | |
| - name: Setup Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.7 | |
| - name: Configure Docker Authentication | |
| run: | | |
| gcloud --quiet auth configure-docker | |
| - name: Set MODEL_VERSION env | |
| run: | | |
| echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| - name: Set BASE_VERSION env | |
| run: | | |
| echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| - name: Set NUM_EPOCHS env | |
| run: | | |
| echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| - name: Build Docker Image | |
| run: | | |
| docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| --build-arg "TASK_NAME=$TASK_NAME" \ | |
| --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| -f ${{ env.DOCKERFILE }} . | |
| - name: Publish Docker Image to Google Container Registry | |
| run: | | |
| docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| - name: Submit a training job to AI Plaform to train and cache the model | |
| run: | | |
| gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| --scale-tier=CUSTOM \ | |
| --master-machine-type=n1-standard-8 \ | |
| --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| --region "$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 | |
| run: | | |
| sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| timeout-minutes: 500 | |
| # # -------------------------------------------------------------------------------------- # | |
| # # BUILD/PUSH BL_CHEMICAL_TO_CELL CLASSIFICATION CONTAINER IMAGE # | |
| # # -------------------------------------------------------------------------------------- # | |
| build_push-bl_chemical_to_cell-predict: | |
| name: "build/push bl_chemical_to_cell predict container" | |
| needs: "build_push_train-bl_chemical_to_cell-train" | |
| runs-on: ubuntu-latest | |
| env: | |
| TASK_NAME: bl_chemical_to_cell | |
| DOCKERFILE: predict.Dockerfile | |
| TRAIN_DOCKERFILE: train.Dockerfile | |
| TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| BASE_DOCKERFILE: base.Dockerfile | |
| MODEL_VERSION_KEY: BL_CHEMICAL_TO_CELL | |
| # Don't forget to change labels | |
| CLASSIFICATION_LABELS: "secretes stores responds_to metabolizes other" | |
| DATA_FILE: data/bl_chemical_to_cell/data.tsv | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - id: 'auth' | |
| uses: 'google-github-actions/auth@v2' | |
| with: | |
| project_id: ${{ secrets.GCE_PROJECT }} | |
| service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| - name: 'Set up Cloud SDK' | |
| uses: 'google-github-actions/setup-gcloud@v2' | |
| with: | |
| version: '>= 363.0.0' | |
| - name: Setup Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.7 | |
| - name: Configure Docker Authentication | |
| run: | | |
| gcloud --quiet auth configure-docker | |
| - name: Set MODEL_VERSION env | |
| run: | | |
| echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| - name: Set IMAGE_VERSION env | |
| run: | | |
| echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| - name: Set BASE_VERSION env | |
| run: | | |
| echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| - name: Build Docker Image | |
| run: | | |
| docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| --build-arg "TASK_NAME=$TASK_NAME" \ | |
| --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| -f ${{ env.DOCKERFILE }} . | |
| - name: Publish Docker Image to Google Container Registry | |
| run: | | |
| docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_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@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # 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" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_chemical_to_disease_or_phenotypic_feature | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "has_unintended_effect_of resistance_is_associated_with is_contraindicated_in exacerbates increases_risk_for decreases_risk_for is_used_to_treat other" | |
| # DATA_FILE: data/bl_chemical_to_disease_or_phenotypic_feature/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # TRAIN BL_CHEMICAL_TO_PROCESS MODEL # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_chemical_to_process-train: | |
| # name: "build/push/train bl_chemical_to_process model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_chemical_to_process | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_chemical_to_process/data.tsv | |
| # MODEL_VERSION_KEY: BL_CHEMICAL_TO_PROCESS | |
| # AI_PLATFORM_JOB_NAME: "bl_chemical_to_process_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_CHEMICAL_TO_PROCESS CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_chemical_to_process-predict: | |
| # name: "build/push bl_chemical_to_process predict container" | |
| # needs: "build_push_train-bl_chemical_to_process-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_chemical_to_process | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_CHEMICAL_TO_PROCESS | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "participates_in enhances inhibits is_produced_by other" | |
| # DATA_FILE: data/bl_chemical_to_process/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # TRAIN BL_CHEMICAL_TO_GENE MODEL # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_chemical_to_gene-train: | |
| # name: "build/push/train bl_chemical_to_gene model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_chemical_to_gene | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_chemical_to_gene/data.tsv | |
| # MODEL_VERSION_KEY: BL_CHEMICAL_TO_GENE | |
| # AI_PLATFORM_JOB_NAME: "bl_chemical_to_gene_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_CHEMICAL_TO_GENE CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_chemical_to_gene-predict: | |
| # name: "build/push bl_chemical_to_gene predict container" | |
| # needs: "build_push_train-bl_chemical_to_gene-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_chemical_to_gene | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_CHEMICAL_TO_GENE | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "activates modulates deactivates metabolized_by transported_by other" | |
| # DATA_FILE: data/bl_chemical_to_gene/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # TRAIN BL_CHEMICAL_TO_CHEMICAL MODEL # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_chemical_to_chemical-train: | |
| # name: "build/push/train bl_chemical_to_chemical model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_chemical_to_chemical | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_chemical_to_chemical/data.tsv | |
| # MODEL_VERSION_KEY: BL_CHEMICAL_TO_CHEMICAL | |
| # AI_PLATFORM_JOB_NAME: "bl_chemical_to_chemical_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_CHEMICAL_TO_CHEMICAL CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_chemical_to_chemical-predict: | |
| # name: "build/push bl_chemical_to_chemical predict container" | |
| # needs: "build_push_train-bl_chemical_to_chemical-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_chemical_to_chemical | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_CHEMICAL_TO_CHEMICAL | |
| # # Don't forget to change labels | |
| # CLASSIFICATION_LABELS: "co-treat ddi other" | |
| # DATA_FILE: data/bl_chemical_to_chemical/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| ### ========== Below is older stuff =============== | |
| ### ========== Below is older stuff =============== | |
| ### ========== Below is older stuff =============== | |
| ### ========== Below is older stuff =============== | |
| ### ========== Below is older stuff =============== | |
| ### ========== Below is older stuff =============== | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # BUILD/PUSH CAT_SENTENCES CONTAINER IMAGE # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # build_push-cat-sentences: | |
| # name: "build/push cat-sentences container image" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # IMAGE_NAME: cat-sentences | |
| # DOCKERFILE: cat_sentences.Dockerfile | |
| # permissions: | |
| # contents: 'read' | |
| # id-token: 'write' | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: echo "MODEL_VERSION=$(grep 'CAT_SENTENCES' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --tag "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: docker push "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION" | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # BUILD/PUSH CAT_BERT_OUTPUT CONTAINER IMAGE # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # build_push-cat-bert-output: | |
| # name: "build/push cat-bert-output container image" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # IMAGE_NAME: cat-bert-output | |
| # DOCKERFILE: cat_bert_output.Dockerfile | |
| # permissions: | |
| # contents: 'read' | |
| # id-token: 'write' | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: echo "MODEL_VERSION=$(grep 'CAT_BERT_OUTPUT' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --tag "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: docker push "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION" | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # TRAIN BL_CELL_TO_DISEASE MODEL # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_cell_to_disease-train: | |
| # name: "build/push/train bl_cell_to_disease model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_cell_to_disease | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_cell_to_disease/data.tsv | |
| # MODEL_VERSION_KEY: BL_CELL_TO_DISEASE | |
| # AI_PLATFORM_JOB_NAME: "bl_cell_to_disease_train_${{ github.run_number }}" | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # run: | | |
| # gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \ | |
| # --scale-tier=CUSTOM \ | |
| # --master-machine-type=n1-standard-8 \ | |
| # --master-accelerator=count=1,type=nvidia-tesla-v100 \ | |
| # --region "$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 | |
| # run: | | |
| # sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 500 | |
| # # # -------------------------------------------------------------------------------------- # | |
| # # # BUILD/PUSH BL_CELL_TO_DISEASE CLASSIFICATION CONTAINER IMAGE # | |
| # # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_cell_to_disease-predict: | |
| # name: "build/push bl_cell_to_disease predict container" | |
| # needs: "build_push_train-bl_cell_to_disease-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_cell_to_disease | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_CELL_TO_DISEASE | |
| # CLASSIFICATION_LABELS: "dysfunction hyperactivity other proliferation" | |
| # DATA_FILE: data/bl_cell_to_disease/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # TRAIN BL_GENE_LOSS_GAIN_OF_FUNCTION_TO_DISEASE MODEL # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_gene_loss_gain_of_function_to_disease-train: | |
| # name: "build/push/train bl_gene_loss_gain_of_function_to_disease model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_loss_gain_of_function_to_disease | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_gene_loss_gain_of_function_to_disease/data.tsv | |
| # MODEL_VERSION_KEY: BL_GENE_LOSS_GAIN_OF_FUNCTION_TO_DISEASE | |
| # AI_PLATFORM_JOB_NAME: "bl_gene_loss_gain_of_function_to_disease_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 ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 1800 | |
| # # -------------------------------------------------------------------------------------- # | |
| # # BUILD/PUSH BL_GENE_LOSS_GAIN_OF_FUNCTION_TO_DISEASE CLASSIFICATION CONTAINER IMAGE # | |
| # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_gene_loss_gain_of_function_to_disease-predict: | |
| # name: "build/push bl_gene_loss_gain_of_function_to_disease predict container" | |
| # needs: "build_push_train-bl_gene_loss_gain_of_function_to_disease-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_loss_gain_of_function_to_disease | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_GENE_LOSS_GAIN_OF_FUNCTION_TO_DISEASE | |
| # CLASSIFICATION_LABELS: "contributes_to_via_loss_of_function contributes_to_via_gain_of_function false" | |
| # DATA_FILE: data/bl_gene_loss_gain_of_function_to_disease/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v2 | |
| # with: | |
| # fetch-depth: 0 | |
| # - name: Get changed files | |
| # id: changed-files | |
| # uses: tj-actions/changed-files@v7 | |
| # - name: List all modified files | |
| # run: | | |
| # for file in "${{ 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.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # 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 }} predict container." | |
| # - 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.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # 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: ${{ secrets.GCE_SA_KEY }} | |
| # version: '290.0.1' | |
| # - name: Configure Docker Authentication | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$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@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set NUM_EPOCHS env | |
| # run: | | |
| # echo "NUM_EPOCHS=5.0" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "EPOCHS=$NUM_EPOCHS" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # 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 | |
| # 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" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_chemical_to_disease_or_phenotypic_feature | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE | |
| # #CLASSIFICATION_LABELS: "treats causes_or_contributes_to false" | |
| # CLASSIFICATION_LABELS: "associated_with_resistance_to decreases_risk_for exacerbates exposure_is_origin_of has_excessive_amount_in increases_risk_for is_biomarker_for is_contraindicated_for is_deficient_in prevents results_in_side_effect treats other" | |
| # DATA_FILE: data/bl_chemical_to_disease_or_phenotypic_feature/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # # # ----------------------------------------------------------------------------------- # | |
| # # # # ----------------------------------------------------------------------------------- # | |
| # # # # ----------------------------------------------------------------------------------- # | |
| # # # # TRAIN BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE_GPT MODEL # | |
| # # # # ----------------------------------------------------------------------------------- # | |
| # # # # ----------------------------------------------------------------------------------- # | |
| # # # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_chemical_to_disease_or_phenotypic_feature_gpt-train: | |
| # name: "build/push/train bl_chemical_to_disease_or_phenotypic_feature_gpt model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_chemical_to_disease_or_phenotypic_feature_gpt | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_chemical_to_disease_or_phenotypic_feature_gpt/data.tsv | |
| # MODEL_VERSION_KEY: BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE_GPT | |
| # AI_PLATFORM_JOB_NAME: "bl_chemical_to_disease_or_phenotypic_feature_gpt_train_${{ github.run_number }}" | |
| # steps: | |
| # # - uses: actions/checkout@v3 | |
| # # with: | |
| # # fetch-depth: 0 | |
| # # - name: Setup Python | |
| # # uses: actions/setup-python@v2 | |
| # # with: | |
| # # python-version: 3.7 | |
| # # - name: Set up Cloud SDK | |
| # # uses: google-github-actions/setup-gcloud@main | |
| # # with: | |
| # # project_id: ${{ secrets.GCE_PROJECT }} | |
| # # service_account_key: ${{ secrets.GCE_SA_KEY }} | |
| # # version: '290.0.1' | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$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 ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" | |
| # - name: Submit a training job to AI Plaform to train and cache the model | |
| # 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 | |
| # 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_GPT CLASSIFICATION CONTAINER IMAGE # | |
| # # -------------------------------------------------------------------------------------- # | |
| # build_push-bl_chemical_to_disease_or_phenotypic_feature_gpt-predict: | |
| # name: "build/push bl_chemical_to_disease_or_phenotypic_feature_gpt predict container" | |
| # # needs: "build_push_train-bl_chemical_to_disease_or_phenotypic_feature_gpt-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_chemical_to_disease_or_phenotypic_feature_gpt | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE_GPT | |
| # CLASSIFICATION_LABELS: "treats causes_or_contributes_to false" | |
| # DATA_FILE: data/bl_chemical_to_disease_or_phenotypic_feature_gpt/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # - id: 'auth' | |
| # uses: 'google-github-actions/auth@v2' | |
| # with: | |
| # project_id: ${{ secrets.GCE_PROJECT }} | |
| # service_account: ${{ secrets.SERVICE_ACCOUNT }} | |
| # credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }} | |
| # - name: 'Set up Cloud SDK' | |
| # uses: 'google-github-actions/setup-gcloud@v2' | |
| # with: | |
| # version: '>= 363.0.0' | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.7 | |
| # - name: Configure Docker Authentication | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set IMAGE_VERSION env | |
| # run: | | |
| # echo "IMAGE_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} IMAGE_VERSIONS_PREDICT | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$IMAGE_VERSION" | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # TRAIN BL_CHEMICAL_TO_GENE MODEL # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_chemical_to_gene-train: | |
| # name: "build/push/train bl_chemical_to_gene model" | |
| # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_chemical_to_gene | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_chemical_to_gene/data.tsv | |
| # MODEL_VERSION_KEY: BL_CHEMICAL_TO_GENE | |
| # AI_PLATFORM_JOB_NAME: "bl_chemical_to_gene_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 '=')" >> $GITHUB_ENV | |
| # - name: Build ChemProt Corpus container image | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # docker build --tag chemprot -f data/bl_chemical_to_gene/chemprot.Dockerfile data/bl_chemical_to_gene | |
| # - name: Process ChemProt Corpus and append to data/bl_chemical_to_gene/data.tsv | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # docker run --rm -v "$PWD/data/bl_chemical_to_gene:/home/dev/output" chemprot | |
| # - 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 ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 17280 | |
| # # Initial training of the chemical_to_gene model required 250 minutes | |
| # # using the basic_gpu tier (Tesla K80), so we set the timeout to 360 minutes | |
| # # here to be sure to allow enough time to finish. Note: 360 minutes might be the | |
| # # default timeout, so setting a timeout might not be necessary. | |
| # # ----------------------------------------------------------------------------------- # | |
| # # BUILD/PUSH BL_CHEMICAL_TO_GENE CLASSIFICATION CONTAINER IMAGE # | |
| # # ----------------------------------------------------------------------------------- # | |
| # build_push-bl_chemical_to_gene-predict: | |
| # name: "build/push bl_chemical_to_gene predict container" | |
| # needs: "build_push_train-bl_chemical_to_gene-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_chemical_to_gene | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_CHEMICAL_TO_GENE | |
| # CLASSIFICATION_LABELS: "positively_regulates negatively_regulates false" | |
| # DATA_FILE: data/bl_chemical_to_gene/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v2 | |
| # with: | |
| # fetch-depth: 0 | |
| # - name: Get changed files | |
| # id: changed-files | |
| # uses: tj-actions/changed-files@v7 | |
| # - name: List all modified files | |
| # run: | | |
| # for file in "${{ 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.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # 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 }} predict container." | |
| # - 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.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # 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: ${{ secrets.GCE_SA_KEY }} | |
| # version: '290.0.1' | |
| # - name: Configure Docker Authentication | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # TRAIN BL_DISEASE_TO_PHENOTYPIC_FEATURE MODEL # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_disease_to_phenotypic_feature-train: | |
| # name: "build/push/train bl_disease_to_phenotypic_feature model" | |
| # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_disease_to_phenotypic_feature | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_disease_to_phenotypic_feature/data.tsv | |
| # MODEL_VERSION_KEY: BL_DISEASE_TO_PHENOTYPIC_FEATURE | |
| # AI_PLATFORM_JOB_NAME: "bl_disease_to_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 ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 180 | |
| # # ----------------------------------------------------------------------------------- # | |
| # # BUILD/PUSH BL_DISEASE_TO_PHENOTYPIC_FEATURE CLASSIFICATION CONTAINER IMAGE # | |
| # # ----------------------------------------------------------------------------------- # | |
| # build_push-bl_disease_to_phenotypic_feature-predict: | |
| # name: "build/push bl_disease_to_phenotypic_feature predict container" | |
| # needs: "build_push_train-bl_disease_to_phenotypic_feature-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_disease_to_phenotypic_feature | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_DISEASE_TO_PHENOTYPIC_FEATURE | |
| # CLASSIFICATION_LABELS: "has_symptom false" | |
| # DATA_FILE: data/bl_disease_to_phenotypic_feature/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v2 | |
| # with: | |
| # fetch-depth: 0 | |
| # - name: Get changed files | |
| # id: changed-files | |
| # uses: tj-actions/changed-files@v7 | |
| # - name: List all modified files | |
| # run: | | |
| # for file in "${{ 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.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # 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 }} predict container." | |
| # - 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.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # 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: ${{ secrets.GCE_SA_KEY }} | |
| # version: '290.0.1' | |
| # - name: Configure Docker Authentication | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # TRAIN BL_GENE_REGULATORY_RELATIONSHIP MODEL # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_gene_regulatory_relationship-train: | |
| # name: "build/push/train bl_gene_regulatory_relationship model" | |
| # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_regulatory_relationship | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_gene_regulatory_relationship/data.tsv | |
| # MODEL_VERSION_KEY: BL_GENE_REGULATORY_RELATIONSHIP | |
| # AI_PLATFORM_JOB_NAME: "bl_gene_regulatory_relationship_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 '=')" >> $GITHUB_ENV | |
| # - name: Build GeneReg Corpus container image | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # docker build --tag genereg -f data/bl_gene_regulatory_relationship/genereg.Dockerfile data/bl_gene_regulatory_relationship | |
| # - name: Process GeneReg Corpus and append to data/bl_gene_regulator_relationship/data.tsv | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # docker run --rm -v "$PWD/data/bl_gene_regulatory_relationship:/home/dev/output" genereg | |
| # - 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 ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 180 | |
| # # ----------------------------------------------------------------------------------- # | |
| # # BUILD/PUSH BL_GENE_REGULATORY_RELATIONSHIP CLASSIFICATION CONTAINER IMAGE # | |
| # # ----------------------------------------------------------------------------------- # | |
| # build_push-bl_gene_regulatory_relationship-predict: | |
| # name: "build/push bl_gene_regulatory_relationship predict container" | |
| # needs: "build_push_train-bl_gene_regulatory_relationship-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_regulatory_relationship | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_GENE_REGULATORY_RELATIONSHIP | |
| # CLASSIFICATION_LABELS: "positively_regulates negatively_regulates false" | |
| # DATA_FILE: data/bl_gene_regulatory_relationship/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v2 | |
| # with: | |
| # fetch-depth: 0 | |
| # - name: Get changed files | |
| # id: changed-files | |
| # uses: tj-actions/changed-files@v7 | |
| # - name: List all modified files | |
| # run: | | |
| # for file in "${{ 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.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # 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 }} predict container." | |
| # - 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.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # 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: ${{ secrets.GCE_SA_KEY }} | |
| # version: '290.0.1' | |
| # - name: Configure Docker Authentication | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # TRAIN BL_GENE_TO_DISEASE MODEL # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_gene_to_disease-train: | |
| # name: "build/push/train bl_gene_to_disease model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_to_disease | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_gene_to_disease/data.tsv | |
| # MODEL_VERSION_KEY: BL_GENE_TO_DISEASE | |
| # AI_PLATFORM_JOB_NAME: "bl_gene_to_disease_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 ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 1800 | |
| # # ----------------------------------------------------------------------------------- # | |
| # # BUILD/PUSH BL_GENE_TO_DISEASE CLASSIFICATION CONTAINER IMAGE # | |
| # # ----------------------------------------------------------------------------------- # | |
| # build_push-bl_gene_to_disease-predict: | |
| # name: "build/push bl_gene_to_disease predict container" | |
| # needs: "build_push_train-bl_gene_to_disease-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_to_disease | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_GENE_TO_DISEASE | |
| # CLASSIFICATION_LABELS: "contributes_to false" | |
| # DATA_FILE: data/bl_gene_to_disease/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v2 | |
| # with: | |
| # fetch-depth: 0 | |
| # - name: Get changed files | |
| # id: changed-files | |
| # uses: tj-actions/changed-files@v7 | |
| # - name: List all modified files | |
| # run: | | |
| # for file in "${{ 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.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # 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 }} predict container." | |
| # - 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.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # 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: ${{ secrets.GCE_SA_KEY }} | |
| # version: '290.0.1' | |
| # - name: Configure Docker Authentication | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # TRAIN BL_GENE_TO_EXPRESSION_SITE MODEL # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-bl_gene_to_expression_site-train: | |
| # name: "build/push/train bl_gene_to_expression_site model" | |
| # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_to_expression_site | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/bl_gene_to_expression_site/data.tsv | |
| # MODEL_VERSION_KEY: BL_GENE_TO_EXPRESSION_SITE | |
| # AI_PLATFORM_JOB_NAME: "bl_gene_to_expression_site_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 ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 180 | |
| # # ----------------------------------------------------------------------------------- # | |
| # # BUILD/PUSH BL_GENE_TO_EXPRESSION_SITE CLASSIFICATION CONTAINER IMAGE # | |
| # # ----------------------------------------------------------------------------------- # | |
| # build_push-bl_gene_to_expression_site-predict: | |
| # name: "build/push bl_gene_to_expression_site predict container" | |
| # needs: "build_push_train-bl_gene_to_expression_site-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: bl_gene_to_expression_site | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: BL_GENE_TO_EXPRESSION_SITE | |
| # CLASSIFICATION_LABELS: "expressed_in false" | |
| # DATA_FILE: data/bl_gene_to_expression_site/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v2 | |
| # with: | |
| # fetch-depth: 0 | |
| # - name: Get changed files | |
| # id: changed-files | |
| # uses: tj-actions/changed-files@v7 | |
| # - name: List all modified files | |
| # run: | | |
| # for file in "${{ 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.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # 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 }} predict container." | |
| # - 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.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # 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: ${{ secrets.GCE_SA_KEY }} | |
| # version: '290.0.1' | |
| # - name: Configure Docker Authentication | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # if: | | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # TRAIN CRAFT_RELATIONS MODEL # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # # ----------------------------------------------------------------------------------- # | |
| # build_push_train-craft_relations-train: | |
| # name: "build/push/train craft_relations model" | |
| # # needs: "build_push-bert-base" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: craft_relations | |
| # DOCKERFILE: train.Dockerfile | |
| # ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # DATA_FILE: data/craft_relations/data.tsv | |
| # MODEL_VERSION_KEY: CRAFT_RELATIONS | |
| # AI_PLATFORM_JOB_NAME: "craft_relations_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 ${{ env.AI_PLATFORM_JOB_NAME }}" | |
| # timeout-minutes: 180 | |
| # # ----------------------------------------------------------------------------------- # | |
| # # BUILD/PUSH CRAFT_RELATIONS CLASSIFICATION CONTAINER IMAGE # | |
| # # ----------------------------------------------------------------------------------- # | |
| # build_push-craft_relations-predict: | |
| # name: "build/push craft_relations predict container" | |
| # # needs: "build_push_train-craft_relations-train" | |
| # runs-on: ubuntu-latest | |
| # env: | |
| # TASK_NAME: craft_relations | |
| # DOCKERFILE: predict.Dockerfile | |
| # TRAIN_DOCKERFILE: train.Dockerfile | |
| # TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh | |
| # ENTRYPOINT_FILE: scripts/predict.entrypoint.sh | |
| # BASE_DOCKERFILE: base.Dockerfile | |
| # MODEL_VERSION_KEY: CRAFT_RELATIONS | |
| # CLASSIFICATION_LABELS: "bears_constitution_of_or_situatedness_at_or_possession_by_or_derivation_from coexists_as realizes_or_attribute_or_bearer_of_occurrence_in_or_possession_by realizes_or_bears_or_is_attribute_of_derivation_or_situatedness_or_possession_from false" | |
| # DATA_FILE: data/craft_relations/data.tsv | |
| # steps: | |
| # - uses: actions/checkout@v2 | |
| # with: | |
| # fetch-depth: 0 | |
| # # - name: Get changed files | |
| # # id: changed-files | |
| # # uses: tj-actions/changed-files@v7 | |
| # # - name: List all modified files | |
| # # run: | | |
| # # for file in "${{ 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.TRAIN_DOCKERFILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # # 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 }} predict container." | |
| # - 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.TRAIN_DOCKERFILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # # 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: ${{ secrets.GCE_SA_KEY }} | |
| # version: '290.0.1' | |
| # - name: Configure Docker Authentication | |
| # # if: | | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # gcloud --quiet auth configure-docker | |
| # - name: Set MODEL_VERSION env | |
| # # if: | | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Set BASE_VERSION env | |
| # # if: | | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV | |
| # - name: Build Docker Image | |
| # # if: | | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # docker build --build-arg "PROJECT_ID=$PROJECT_ID" \ | |
| # --build-arg "TASK_NAME=$TASK_NAME" \ | |
| # --build-arg "BASE_VERSION=$BASE_VERSION" \ | |
| # --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \ | |
| # --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \ | |
| # --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \ | |
| # --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" \ | |
| # -f ${{ env.DOCKERFILE }} . | |
| # - name: Publish Docker Image to Google Container Registry | |
| # # if: | | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.DOCKERFILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_DOCKERFILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.TRAIN_ENTRYPOINT_FILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.BASE_DOCKERFILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.DATA_FILE) || | |
| # # contains(steps.changed-files.outputs.all_modified_files, env.ENTRYPOINT_FILE) | |
| # run: | | |
| # docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" |