Initial setup of Payu environment #8
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| name: Build and test conda env | |
| on: pull_request | |
| jobs: | |
| generate_matrix: | |
| uses: ./.github/workflows/get_changed_env.yml | |
| build_base_image: | |
| runs-on: ubuntu-latest | |
| needs: generate_matrix | |
| if: ${{ needs.generate_matrix.outputs.matrix != '{"include":[]}' }} | |
| container: | |
| image: quay.io/singularity/singularity:v3.11.4 | |
| options: --privileged | |
| outputs: | |
| built-container: ${{ steps.changed-container-def.outputs.containerdef_any_changed }} | |
| steps: | |
| - name: Checkout repository | |
| ### Latest at time of writing | |
| uses: actions/checkout@v4 | |
| - name: Check if container definition has changed | |
| id: changed-container-def | |
| uses: tj-actions/changed-files@48d8f15b2aaa3d255ca5af3eba4870f807ce6b3c # v43.0.2 | |
| with: | |
| files_yaml: | | |
| containerdef: | |
| - container/container.def | |
| - name: Build container if definition has changed | |
| if: steps.changed-container-def.outputs.containerdef_any_changed == 'true' | |
| run: | | |
| echo ${{ needs.generate_matrix.outputs.matrix }} | |
| sudo -E singularity build container/base.sif container/container.def | |
| - name: Upload base container | |
| if: steps.changed-container-def.outputs.containerdef_any_changed == 'true' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: base-container | |
| path: container/base.sif | |
| setup: | |
| runs-on: ubuntu-latest | |
| needs: [ generate_matrix, build_base_image ] | |
| if: ${{ needs.generate_matrix.outputs.matrix != '{"include":[]}' }} | |
| environment: Gadi | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Download base container | |
| if: needs.build_base_image.outputs.built-container == 'true' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: base-container | |
| path: container | |
| - name: Setup SSH | |
| uses: access-nri/actions/.github/actions/setup-ssh@main | |
| id: ssh | |
| with: | |
| hosts: | | |
| ${{ secrets.HOST }} | |
| ${{ secrets.HOST_DATA }} | |
| private-key: ${{ secrets.SSH_KEY }} | |
| - name: Create parent repository directories | |
| run: | | |
| ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT' | |
| mkdir -p ${{ secrets.REPO_PATH }} | |
| EOT | |
| - name: Sync repository to Gadi | |
| run: | | |
| rsync -e 'ssh -i ${{ steps.ssh.outputs.private-key-path }}' \ | |
| -avz --delete --exclude=/.git/ --exclude=/.github/ \ | |
| ./ \ | |
| ${{ secrets.USER }}@${{ secrets.HOST_DATA }}:${{ secrets.REPO_PATH }} | |
| - name: Create Admin dirs on Gadi | |
| run: | | |
| ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT' | |
| source ${{ secrets.REPO_PATH }}/scripts/install_config.sh | |
| source ${{ secrets.REPO_PATH }}/scripts/functions.sh | |
| mkdir -p $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR | |
| set_admin_perms $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR | |
| EOT | |
| build: | |
| needs: [ generate_matrix, setup ] | |
| uses: ./.github/workflows/build.yml | |
| with: | |
| environment: ${{ matrix.environment }} | |
| secrets: inherit | |
| if: ${{ needs.generate_matrix.outputs.matrix != '{"include":[]}' }} | |
| strategy: | |
| matrix: ${{fromJson(needs.generate_matrix.outputs.matrix)}} | |
| max-parallel: 1 | |
| fail-fast: false | |
| test: | |
| needs: [ generate_matrix, build ] | |
| uses: ./.github/workflows/test.yml | |
| with: | |
| environment: ${{ matrix.environment }} | |
| secrets: inherit | |
| if: ${{ needs.generate_matrix.outputs.matrix != '{"include":[]}' }} | |
| strategy: | |
| matrix: ${{fromJson(needs.generate_matrix.outputs.matrix)}} | |
| max-parallel: 1 | |
| fail-fast: false |