Updates required for full rebuild of analysis3-24.04 #9
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| name: Build and test conda env | |
| on: pull_request | |
| jobs: | |
| generate_matrix: | |
| uses: ./.github/workflows/get_changed_env.yml | |
| setup: | |
| 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 | |
| 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@v41 | |
| 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: Sync repository to Gadi | |
| ### Latest at time of writing | |
| uses: up9cloud/[email protected] | |
| env: | |
| HOST: gadi.nci.org.au | |
| TARGET: ${{secrets.GADI_REPO_PATH}} | |
| KEY: ${{secrets.DEPLOY_KEY}} | |
| USER: ${{secrets.GADI_USER}} | |
| - name: Create Admin dirs on Gadi | |
| uses: appleboy/[email protected] | |
| with: | |
| host: gadi.nci.org.au | |
| username: ${{secrets.GADI_USER}} | |
| key: ${{secrets.DEPLOY_KEY}} | |
| script: | | |
| source ${{secrets.GADI_REPO_PATH}}/scripts/install_config.sh | |
| source ${{secrets.GADI_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 | |
| 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 |