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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_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_${{ github.run_number }}"
# steps:
# - uses: actions/checkout@v2
# with:
# fetch-depth: 0
# - name: Get changed files
# id: changed-files
# uses: tj-actions/changed-files@v7
# - name: List all modified files
# run: |
# for file in "${{ 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 ${{ env.AI_PLATFORM_JOB_NAME }}"
# timeout-minutes: 180
# # -------------------------------------------------------------------------------------- #
# # BUILD/PUSH BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE CLASSIFICATION CONTAINER IMAGE #
# # -------------------------------------------------------------------------------------- #
# build_push-bl_chemical_to_disease_or_phenotypic_feature-predict:
# name: "build/push bl_chemical_to_disease_or_phenotypic_feature predict container"
# needs: "build_push_train-bl_chemical_to_disease_or_phenotypic_feature-train"
# runs-on: ubuntu-latest
# env:
# TASK_NAME: bl_chemical_to_disease_or_phenotypic_feature
# DOCKERFILE: predict.Dockerfile
# TRAIN_DOCKERFILE: train.Dockerfile
# TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh
# ENTRYPOINT_FILE: scripts/predict.entrypoint.sh
# BASE_DOCKERFILE: base.Dockerfile
# MODEL_VERSION_KEY: BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE
# CLASSIFICATION_LABELS: "treats false"
# DATA_FILE: data/bl_chemical_to_disease_or_phenotypic_feature/data.tsv
# steps:
# - uses: actions/checkout@v2
# with:
# fetch-depth: 0
# - name: Get changed files
# id: changed-files
# uses: tj-actions/changed-files@v7
# - name: List all modified files
# run: |
# for file in "${{ 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_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