conda_env.yml

name: Conda Env Workflow

on:
  push:
    branches:
      - master
      - fix_ci_cd

permissions:
  id-token: write
  contents: read

jobs:
  create-conda-env:
    runs-on: ubuntu-22.04
    env:
      AWS_DEFAULT_REGION: eu-west-1
    container:
      image: amazonlinux:2
    steps:
    - name: Install tar (for code checkout)
      run: yum install -y tar gzip

    - name: Checkout Code
      uses: actions/checkout@v3  # Checks out the repository under $GITHUB_WORKSPACE.
    
    - name: Set up Node.js
      uses: actions/setup-node@v3
      with:
        node-version: '16' # Use a stable, compatible version
    - name: Setup conda
      uses: conda-incubator/setup-miniconda@v2
      with:
        miniconda-version: "latest"
        activate-environment: pheno
        python-version: 3.11
        environment-file: environment.yml

    - name: Install pheno-utils
      shell: bash -el {0}
      run: |
        cd $GITHUB_WORKSPACE
        pip install . # Install pheno-utils from the current directory
        conda list

    - name: Pack Conda
      shell: bash -el {0}
      run: |
        # Enable adding the kernel to JupyterLab 
        pip install -q ipykernel
        python -m ipykernel install --user --name pheno --display-name "Pheno"
        pip install -q conda-pack
        conda pack --quiet -n pheno -o $HOME/pheno.tar.gz

    - name: Configure AWS Credentials
      uses: aws-actions/configure-aws-credentials@v3
      with:
        role-to-assume: arn:aws:iam::081569964966:role/github_cicd
        aws-region: ${{ env.AWS_DEFAULT_REGION }}

    - name: Setup AWS CLI
      run: |
        yum install -y unzip > /dev/null
        echo "Installing AWS CLI"
        curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
        unzip awscliv2.zip
        ./aws/install
        aws --version

    - name: Upload to S3
      run: |
        echo "Uploading artifact to S3"
        DATE=$(date +%Y-%m-%d-%H-%S)
        BRANCH=${GITHUB_REF#refs/heads/}
        BRANCH=${BRANCH//\//_} # Replace / with _ in branch name
        aws s3 cp $HOME/pheno.tar.gz "s3://pheno-ds-github-cicd-${{ env.AWS_DEFAULT_REGION }}/conda_envs/${BRANCH}_${DATE}.tar.gz"