build-conda.yml

name: Build and Upload Conda Environments

on:
  push:
    branches:
      - main
    paths:
      - 'environments/*.yml'
  workflow_dispatch:

jobs:
  build-and-upload:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@v4

      - name: Set up Conda
        uses: conda-incubator/setup-miniconda@v2
        with:
          auto-update-conda: true
          python-version: "3.10" # Specify the Python version
          activate-environment: true
      - name: Install AWS CLI and Conda-Pack
        run: |
          conda install -c conda-forge awscli conda-pack=0.7.1
      - name: Discover Environments
        id: discover
        run: |
          echo "envs=$(ls environments/*.yml | xargs -n 1 basename | tr '\n' ' ')" >> $GITHUB_ENV

      - name: Create, Pack, and Upload Environments
        env:
          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
          AWS_S3_BUCKET_NAME: "bioimage.io"
          AWS_S3_ENDPOINT: "https://uk1s3.embassy.ebi.ac.uk"
          AWS_EC2_METADATA_DISABLED: "true" # https://github.com/aws/aws-cli/issues/5262#issuecomment-705832151
          PYTHONNOUSERSITE: "True"
        run: |
          # copy manifest to s3
          # aws s3 --endpoint-url $AWS_S3_ENDPOINT cp hypha-services-manifest.yaml s3://$AWS_S3_BUCKET_NAME/hypha-services-manifest.yaml
          # copy the apps folder to s3
          aws s3 --endpoint-url $AWS_S3_ENDPOINT cp --recursive apps s3://$AWS_S3_BUCKET_NAME/apps
          for env_file in $envs; do
            env_name="${env_file%.*}"
            echo "Processing $env_name"
            conda env create -f ./environments/$env_file -n $env_name
            conda pack -n $env_name -o $env_name.tar.gz
            aws s3 --endpoint-url $AWS_S3_ENDPOINT cp $env_name.tar.gz s3://$AWS_S3_BUCKET_NAME/environments/$env_name.tar.gz
            echo "Uploaded $env_name.tar.gz to S3"
            # remove the environment
            conda env remove -n $env_name
            rm $env_name.tar.gz
          done