removing desc-head_T1w from brain_extraction #35
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| name: Launch regression test | |
| on: | |
| pull_request: | |
| branches: | |
| - develop | |
| types: | |
| - opened | |
| - ready_for_review | |
| - reopened | |
| workflow_call: | |
| inputs: | |
| test_mode: | |
| type: string | |
| required: true | |
| secrets: | |
| GH_CLI_BIN_PATH: | |
| description: 'path to directory containing GitHub CLI binary if not on default $PATH' | |
| required: false | |
| SSH_PRIVATE_KEY: | |
| required: true | |
| SSH_USER: | |
| required: true | |
| SSH_HOST: | |
| required: true | |
| SSH_WORK_DIR: | |
| required: true | |
| workflow_dispatch: | |
| inputs: | |
| test_mode: | |
| type: string | |
| required: true | |
| jobs: | |
| test: | |
| name: Regression Test - ${{ inputs.test_mode }} | |
| environment: ACCESS | |
| env: | |
| COMPARISON_PATH: ${{ secrets.COMPARISON_PATH }} | |
| DASHBOARD_REPO: ${{ vars.DASHBOARD_REPO}} | |
| DOCKER_TAG: | |
| GH_CLI_BIN_PATH: ${{ secrets.GH_CLI_BIN_PATH }} | |
| SLURM_TESTING_BRANCH: ${{ vars.SLURM_TESTING_BRANCH }} | |
| SLURM_TESTING_PACKAGE: ${{ vars.SLURM_TESTING_PACKAGE }} | |
| SLURM_TESTING_REPO: ${{ vars.SLURM_TESTING_REPO }} | |
| SSH_PRIVATE_KEY: ${{ secrets.SSH_PRIVATE_KEY }} | |
| SSH_HOST: ${{ secrets.SSH_HOST }} | |
| SSH_USER: ${{ secrets.SSH_USER }} | |
| SSH_WORK_DIR: ${{ secrets.SSH_WORK_DIR }} | |
| TOKEN_FILE: ${{ secrets.TOKEN_FILE }} | |
| if: | | |
| ${{ github.env.SSH_PRIVATE_KEY != '' && | |
| (github.event_name == 'workflow_dispatch' || | |
| (github.event_name == 'pull_request' && | |
| github.event.repository.fork == 'false')) }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Get C-PAC branch | |
| run: | | |
| if [[ ! $GITHUB_REF_NAME == 'main' ]] && [[ ! $GITHUB_REF_NAME == 'develop' ]] | |
| then | |
| TAG=${GITHUB_REF_NAME//\//_} | |
| elif [[ $GITHUB_REF_NAME == 'develop' ]] | |
| then | |
| TAG=nightly | |
| elif [[ $GITHUB_REF_NAME == 'main' ]] | |
| then | |
| TAG=latest | |
| fi | |
| TAG=$TAG$VARIANT | |
| echo DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}" | tr '[:upper:]' '[:lower:]'):$TAG >> $GITHUB_ENV | |
| cat $GITHUB_ENV | |
| - name: Install SSH Keys | |
| run: | | |
| mkdir -p ~/.ssh/ | |
| echo "${{ env.SSH_PRIVATE_KEY }}" > ~/.ssh/id_rsa | |
| chmod 600 ~/.ssh/id_rsa | |
| ssh-keyscan -H -t rsa "${{ env.SSH_HOST }}" > ~/.ssh/known_hosts | |
| - name: Connect and Run Regression Test ${{ inputs.test_mode }} | |
| uses: appleboy/[email protected] | |
| with: | |
| host: ${{ env.SSH_HOST }} | |
| username: ${{ env.SSH_USER }} | |
| key: ${{ env.SSH_PRIVATE_KEY }} | |
| command_timeout: 200m | |
| script: | | |
| set -x | |
| cd ${{ env.SSH_WORK_DIR }} | |
| if pip show "${{ env.SLURM_TESTING_PACKAGE }}" > /dev/null 2>&1; then | |
| # If the package is installed, upgrade it | |
| python3 -m pip install --user --upgrade --force-reinstall "https://github.com/${{ env.SLURM_TESTING_REPO }}/archive/${{ env.SLURM_TESTING_BRANCH }}.zip" | |
| else | |
| # If the package is not installed, install it | |
| python3 -m pip install --user "https://github.com/${{ env.SLURM_TESTING_REPO }}/archive/${{ env.SLURM_TESTING_BRANCH }}.zip" | |
| fi | |
| _CPAC_SLURM_TESTING_WD="${{ env.SSH_WORK_DIR }}/automatic_tests/${{ inputs.test_mode }}/${{ github.sha }}" | |
| mkdir -p "${_CPAC_SLURM_TESTING_WD}" | |
| sbatch cpac-slurm-status ${{ inputs.test_mode }} launch \ | |
| --wd="${_CPAC_SLURM_TESTING_WD}" \ | |
| --comparison-path="${{ env.COMPARISON_PATH }}" \ | |
| --dashboard-repo="${{ env.DASHBOARD_REPO}}" \ | |
| --home-dir="${{ env.SSH_WORK_DIR }}" \ | |
| --image="${{ env.DOCKER_TAG }}" \ | |
| --owner="${{ github.repository_owner }}" \ | |
| --path-extra="${{ env.GH_CLI_BIN_PATH }}" \ | |
| --repo="${{ github.repository }}" \ | |
| --sha="${{ github.sha }}" \ | |
| --slurm-testing-branch="${{ env.SLURM_TESTING_BRANCH }}" \ | |
| --slurm-testing-repo="${{ env.SLURM_TESTING_REPO }}" \ | |
| --token-file="${{ env.TOKEN_FILE }}" | |
| - name: Cleanup SSH | |
| run: | | |
| rm -rf ~/.ssh |