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bert-models-cicd.yaml
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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