Coding fix (#32) #48
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| name: Conda Env Workflow | |
| on: | |
| push: | |
| branches: | |
| - master | |
| permissions: | |
| id-token: write | |
| contents: read | |
| jobs: | |
| create-conda-env: | |
| runs-on: ubuntu-latest | |
| 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: 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" |