HealthSystem. Convert Excel files to CSV #1578
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| # Runs a pyinstrument profiling session on the scale_run profiling model, | |
| # capturing the profiling result and sending it to the TLOmodel-profiling | |
| # repository for processing and display. | |
| # | |
| # Profiling script executed is src/scripts/profiling/run-profiling.py. | |
| # Output is the .pyisession file from the profiler, placed into results/ | |
| # results/ folder is then pushed to the TLOmodel-profiling repo, results branch. | |
| name: Run profiling | |
| on: | |
| workflow_dispatch: | |
| # Allow profiling to be triggered by comments on pull requests | |
| # Trigger is /run profiling | |
| issue_comment: | |
| types: | |
| - created | |
| # Profile the model every Saturday at 00:00, | |
| # on the HEAD of master | |
| schedule: | |
| - cron: 0 0 * * 6 | |
| concurrency: | |
| # Prevent multiple profiling runs from happening on the same | |
| # commit simultaneously. | |
| # This ensures we don't overwrite the artifact to be uploaded | |
| # with another run that uses the same name, before the results | |
| # can be processed. | |
| group: profiling-${{ github.workflow }}-${{ github.ref }} | |
| jobs: | |
| set-variables: | |
| name: Create unique output file identifier and artifact name | |
| runs-on: ubuntu-latest | |
| if: (github.event_name != 'issue_comment') || ((github.event_name == 'issue_comment') && (github.event.comment.body == '/run profiling')) | |
| outputs: | |
| profiling-output-dir: profiling_results/ | |
| profiling-filename: ${{ steps.set-profiling-filename.outputs.name }} | |
| artifact-name: ${{ steps.set-artifact-name.outputs.name }} | |
| profiling-on-sha: ${{ steps.determine-correct-sha.outputs.result }} | |
| profiling-event-trigger: ${{ steps.set-github-info.outputs.event }} | |
| steps: | |
| - id: determine-if-pr-comment | |
| name: Determine if this is a PR comment | |
| run: | | |
| if ! [ -z "${{ github.event.issue.pull_request }}" ]; then echo "is-pr=true" >> "${GITHUB_OUTPUT}"; else echo "is-pr=false" >> "${GITHUB_OUTPUT}"; fi | |
| - id: determine-correct-sha | |
| name: Determine the SHA to run profiling on | |
| uses: actions/github-script@v7 | |
| with: | |
| result-encoding: string | |
| script: | | |
| if ("${{ steps.determine-if-pr-comment.outputs.is-pr }}" === "true") { | |
| const { data: pr } = await github.rest.pulls.get({ | |
| owner: context.issue.owner, | |
| repo: context.issue.repo, | |
| pull_number: context.issue.number, | |
| }); | |
| return pr.head.sha; | |
| }; | |
| return context.sha; | |
| - id: set-profiling-filename | |
| name: Set profiling output file name | |
| run: | | |
| echo "name=${GITHUB_EVENT_NAME}_${GITHUB_RUN_NUMBER}_${{ steps.determine-correct-sha.outputs.result }}" >> "${GITHUB_OUTPUT}" | |
| - id: set-artifact-name | |
| name: Set artifact name | |
| run: | | |
| echo "name=profiling_results_${GITHUB_RUN_NUMBER}" >> "${GITHUB_OUTPUT}" | |
| - id: set-github-info | |
| name: Fix Git and GitHub information when passing between workflows | |
| run: | | |
| echo "sha=${{ steps.determine-correct-sha.outputs.result }}" >> "${GITHUB_OUTPUT}" | |
| echo "event=${GITHUB_EVENT_NAME}" >> "${GITHUB_OUTPUT}" | |
| profile-on-comment: | |
| name: Comment triggered profiling | |
| if: github.event_name == 'issue_comment' | |
| needs: set-variables | |
| uses: ./.github/workflows/run-on-comment.yml | |
| with: | |
| runs-on: '["self-hosted", "profiling"]' | |
| keyword: profiling | |
| commands: | | |
| tox -vv -e profile -- \ | |
| --html \ | |
| --flat-html \ | |
| --root-output-dir ${{ needs.set-variables.outputs.profiling-output-dir }} \ | |
| --output-name ${{ needs.set-variables.outputs.profiling-filename }} \ | |
| --additional-stats \ | |
| sha=${{ needs.set-variables.outputs.profiling-on-sha }} \ | |
| trigger=${{ needs.set-variables.outputs.profiling-event-trigger }} \ | |
| --disable-log-output-to-stdout | |
| description: Profiled run of the model | |
| timeout-minutes: 8640 | |
| application-organization: UCL | |
| artifact-path: ${{ needs.set-variables.outputs.profiling-output-dir }} | |
| artifact-name: ${{ needs.set-variables.outputs.artifact-name }} | |
| artifact-retention-days: 1 | |
| secrets: | |
| application-id: ${{ secrets.COMMENT_BOT_APP_ID }} | |
| application-private-key: ${{ secrets.COMMENT_BOT_APP_PRIVATE_KEY }} | |
| profile-on-dispatch: | |
| name: Scheduled / dispatch triggered profiling | |
| if: ${{ github.event_name != 'issue_comment' }} | |
| needs: set-variables | |
| runs-on: [self-hosted, profiling] | |
| timeout-minutes: 8640 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.sha }} | |
| lfs: true | |
| ## The profile environment produces outputs in the /results directory | |
| - name: Run profiling in dev environment | |
| run: | | |
| tox -vv -e profile -- \ | |
| --html \ | |
| --flat-html \ | |
| --root-output-dir ${{ needs.set-variables.outputs.profiling-output-dir }} \ | |
| --output-name ${{ needs.set-variables.outputs.profiling-filename }} \ | |
| --additional-stats \ | |
| sha=${{ needs.set-variables.outputs.profiling-on-sha }} \ | |
| trigger=${{ needs.set-variables.outputs.profiling-event-trigger }} \ | |
| --disable-log-output-to-stdout | |
| ## Upload the output as an artifact so we can push it to the profiling repository | |
| - name: Save results as artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ needs.set-variables.outputs.artifact-name }} | |
| path: ${{ needs.set-variables.outputs.profiling-output-dir }} | |
| retention-days: 1 | |
| upload-profiling-results: | |
| name: Upload profiling results | |
| # Run on GH runners to free up self-hosted machines; | |
| # because we need Docker for the workflow call below, | |
| # and because we're now just pushing results files to another repo | |
| runs-on: ubuntu-latest | |
| # Only run this step if exactly one of the previous two jobs ran successfully | |
| # see https://stackoverflow.com/a/68952093 for more details | |
| # NOTE: We need to explicitly depend on set-variables to access the artifact name | |
| needs: [set-variables, profile-on-comment, profile-on-dispatch] | |
| if: | | |
| always() && ( | |
| (needs.profile-on-comment.result == 'success' && needs.profile-on-dispatch.result == 'skipped') || | |
| (needs.profile-on-comment.result == 'skipped' && needs.profile-on-dispatch.result == 'success') | |
| ) | |
| steps: | |
| - name: Download the profiling results | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: ${{ needs.set-variables.outputs.artifact-name }} | |
| path: ${{ needs.set-variables.outputs.profiling-output-dir }} | |
| ## The token provided needs contents and pages access to the target repo | |
| ## Token can be (re)generated by a member of the UCL organisation, | |
| ## the current member is the rc-softdev-admin. | |
| ## [17-07-2024] New token generated, will expire 10-07-2025 | |
| - name: Push results to profiling repository | |
| uses: dmnemec/copy_file_to_another_repo_action@v1.1.1 | |
| env: | |
| API_TOKEN_GITHUB: ${{ secrets.PROFILING_REPO_ACCESS }} | |
| with: | |
| source_file: ${{ needs.set-variables.outputs.profiling-output-dir }} | |
| destination_repo: UCL/TLOmodel-profiling | |
| destination_folder: . | |
| destination_branch: results | |
| user_email: rsd-notifications@ucl.ac.uk | |
| user_name: rc-softdev-admin | |
| - name: Trigger website rebuild | |
| uses: peter-evans/repository-dispatch@v3 | |
| with: | |
| token: ${{ secrets.PROFILING_REPO_ACCESS }} | |
| repository: UCL/TLOmodel-profiling | |
| event-type: new-profiling-results |