Update stable to 24.04, unstable to 24.07. Add mopper and scores #19
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |