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Scoring

Scoring #11

Workflow file for this run

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
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")
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 changes to artifact for later persisting
- name: Save changes to artifact
env:
changed_files: ${{ steps.format_scoring_output.outputs.scoring_file_latest }} ${{ steps.format_scoring_output.outputs.scoring_file_snapshot }}
run: |
echo "{ \"pr-changes\" : \"$changed_files\" }" > pr_changes.json
- name: Upload changes
uses: actions/upload-artifact@v2
with:
name: pr_changes
path: ./pr_changes.json