Scoring #9
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| name: Scoring | |
| on: | |
| workflow_dispatch: | |
| # scheduled submission every Thursday at 01.15 CET | |
| schedule: | |
| - cron: "15 00 * * 4" | |
| jobs: | |
| scoring_job: | |
| if: ${{ github.repository_owner == 'european-modelling-hubs' }} | |
| runs-on: ubuntu-latest | |
| outputs: | |
| changed_files: ${{ steps.format_scoring_output.outputs.scoring_file_latest }} ${{ steps.format_scoring_output.outputs.scoring_file_snapshot }} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| # Checkout the tools repo | |
| # ------------------------------------------- | |
| - name: checkout tools repo | |
| uses: actions/checkout@v3 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| repository: 'european-modelling-hubs/hub-tools' | |
| ref: 'main' | |
| path: './tools/' | |
| # Checkout the data repository | |
| # ------------------------------------------- | |
| - name: checkout data repo | |
| uses: actions/checkout@v3 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| repository: 'european-modelling-hubs/flu-forecast-hub' | |
| ref: 'main' | |
| path: './repo/' | |
| # Setup R env | |
| # ------------------------- | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| install-r: false | |
| use-public-rspm: true | |
| # Eventually install R dependencies | |
| - name: Installing dependencies | |
| run: | | |
| install.packages("remotes") | |
| install.packages("arrow", repos = c("https://apache.r-universe.dev", "https://cran.r-project.org")) | |
| remotes::install_github("Infectious-Disease-Modeling-Hubs/hubData") | |
| install.packages("dplyr") | |
| install.packages('jsonlite') | |
| install.packages("optparse") | |
| install.packages("scoringutils") | |
| shell: Rscript {0} | |
| # Setup Python | |
| # ------------------------- | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| # eventually install additional packages | |
| - name: Installing python additional packages | |
| run: pip install pandas==1.2.5 numpy==1.22.4 | |
| # Run R code to compute scoring and produce an output file (scoring_outfile) | |
| # ---------------------------------------------------------------------------- | |
| - name: Generate Scoring | |
| id: generate_scoring | |
| run: | | |
| # call R script from tools | |
| Rscript ./tools/R-code/forecast_evaluation.R --hub_path "./repo" --truth_file_name "latest-ILI_incidence.csv" --subfolders "ERVISS,FluID" | |
| # Do the python manipulations and produce an output file (scoring_file) | |
| # ------------------------------------------------------------------------ | |
| - name: format scoreing output | |
| id: format_scoring_output | |
| run: | | |
| python ./tools/code/format_evaluation_file.py --hub_path "./repo" | |
| # Commit the changes | |
| # ------------------------- | |
| - name: Commit changes | |
| uses: EndBug/add-and-commit@v7 | |
| with: | |
| cwd: './repo' | |
| add: ${{ steps.format_scoring_output.outputs.scoring_file_latest }} ${{ steps.format_scoring_output.outputs.scoring_file_snapshot }} # put here file changes | |
| message: "Update forecast scoring" | |
| default_author: github_actions | |
| push: true | |
| # Save data to json db | |
| call-persisting-wf: | |
| needs: scoring_job | |
| uses: european-modelling-hubs/flu-forecast-hub/.github/workflows/persist_changes.yml@main | |
| with: | |
| changes-list: ${{ needs.scoring_job.outputs.changed_files }} | |
| secrets: | |
| envPAT: ${{ secrets.GITHUB_TOKEN }} | |