ci.yml

name: TOPAS-nBio CI

on:
  push:
    branches:
      - main
      - develop
    paths-ignore:
      - '*.md'
  workflow_dispatch:
  pull_request:
    branches:
      - main
      - develop
    paths-ignore:
      - '*.md'

jobs:
  docker-tests:
    name: Docker Tests
    runs-on: ubuntu-latest
    env:
      TOPAS_DOCKER_IMAGE: opentopas/opentopas:latest
      G4DATA_DIR: ${{ github.workspace }}/.cache/GEANT4/G4DATA
      TEST_SUITE_DIR: ${{ github.workspace }}/qi-topas-nbio
      NRTEST_ENV: ${{ github.workspace }}/.cache/nrtest-env

    steps:
      - name: Checkout sources
        uses: actions/checkout@v4

      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.11'

      - name: Cache Geant4 data
        id: cache-g4data
        uses: actions/cache@v4
        with:
          path: ${{ env.G4DATA_DIR }}
          key: g4data-G4EMLOW-8.6.1-G4ENSDFSTATE-3.0

      - name: Download Geant4 EMLOW & ENSDFSTATE datasets
        if: steps.cache-g4data.outputs.cache-hit != 'true'
        run: |
          set -euo pipefail
          mkdir -p "$G4DATA_DIR"
          cd "$G4DATA_DIR"
          curl -sSLO https://cern.ch/geant4-data/datasets/G4EMLOW.8.6.1.tar.gz
          tar -xzf G4EMLOW.8.6.1.tar.gz
          rm G4EMLOW.8.6.1.tar.gz
          curl -sSLO https://cern.ch/geant4-data/datasets/G4ENSDFSTATE.3.0.tar.gz
          tar -xzf G4ENSDFSTATE.3.0.tar.gz
          rm G4ENSDFSTATE.3.0.tar.gz

      - name: Pull OpenTOPAS Docker image
        run: docker pull $TOPAS_DOCKER_IMAGE

      - name: Download TOPAS docker launcher
        run: |
          curl -sSfL https://raw.githubusercontent.com/OpenTOPAS/OpenTOPAS/main/docker/topas-docker -o docker-run
          chmod +x docker-run

      - name: Install nrtest tooling
        run: |
          python -m venv "$NRTEST_ENV"
          source "$NRTEST_ENV/bin/activate"
          python -m pip install --upgrade pip
          python -m pip install nrtest git+https://github.com/davidchall/nrtest-topas.git

      - name: Fetch qi-topas-nbio tests (latest tag)
        run: |
          set -euo pipefail
          if ! command -v jq >/dev/null 2>&1; then
            sudo apt-get update
            sudo apt-get install -y jq
          fi
          LATEST_TAG=$(curl -sS https://api.github.com/repos/topas-nbio/qi-topas-nbio/releases/latest | jq -r '.tag_name // empty')
          if [ -z "$LATEST_TAG" ]; then
            echo "Unable to determine latest release tag; falling back to main"
            LATEST_TAG=main
          fi
          git clone --depth 1 --branch "$LATEST_TAG" https://github.com/topas-nbio/qi-topas-nbio.git "$TEST_SUITE_DIR"

      - name: Configure nrtest app manifest
        run: |
          cat <<EOF > "$TEST_SUITE_DIR/apps/topas-docker.json"
          {
            "name": "topas",
            "version": "$GITHUB_SHA",
            "exe": "$GITHUB_WORKSPACE/.github/scripts/run-topas-docker.sh"
          }
          EOF

      - name: Run qi-topas-nbio test suite
        id: nrtest
        env:
          TOPAS_NBIO_ROOT: ${{ github.workspace }}
          TOPAS_DOCKER_LAUNCHER: ${{ github.workspace }}/docker-run
          G4DATA_DIR: ${{ env.G4DATA_DIR }}
        run: |
          set -euo pipefail
          source "$NRTEST_ENV/bin/activate"
          cd "$TEST_SUITE_DIR"
          if [ -d benchmarks ]; then
            find benchmarks -mindepth 1 -maxdepth 1 -type d -regex '.*/[0-9].*' -exec rm -rf {} +
          fi
          BENCHMARK_DIR="benchmarks/${GITHUB_RUN_ID}-${GITHUB_RUN_ATTEMPT}-$(date +%Y-%m-%d-%H%M%S)"
          rm -rf "$BENCHMARK_DIR"
          mkdir -p "$(dirname "$BENCHMARK_DIR")"
          echo "benchmark_dir=$TEST_SUITE_DIR/$BENCHMARK_DIR" >> "$GITHUB_OUTPUT"
          if ! nrtest execute apps/topas-docker.json tests/ -o "$BENCHMARK_DIR"; then
            echo "::group::nrtest failing stdout/stderr"
            while IFS= read -r -d '' log; do
              rel_path=${log#"$TEST_SUITE_DIR"/}
              echo "----- $rel_path -----"
              tail -n 200 "$log" || true
            done < <(find "$BENCHMARK_DIR" -type f \( -name stdout.txt -o -name stderr.txt -o -name '*.log' \) -print0)
            echo "::endgroup::"
            exit 1
          fi

#      - name: Compare output file sizes against baseline
#        if: steps.nrtest.outputs.benchmark_dir != ''
#        env:
#          TEST_SUITE_DIR: ${{ env.TEST_SUITE_DIR }}
#        run: |
#          set -euo pipefail
#          BASELINE_DIR="$TEST_SUITE_DIR/benchmarks/TOPAS-nBio-v4.0_2025Nov09"
#          NEW_DIR="${{ steps.nrtest.outputs.benchmark_dir }}"
#          if [ ! -d "$BASELINE_DIR" ]; then
#            echo "::warning file=benchmarks::Baseline directory $BASELINE_DIR not found; skipping comparison step."
#            exit 0
#          fi
#          status=0
#          while IFS= read -r relpath; do
#            base_file="$BASELINE_DIR/$relpath"
#            new_file="$NEW_DIR/$relpath"
#            if [ ! -f "$new_file" ]; then
#              echo "::error file=$relpath::Missing new file for baseline artifact"
#              status=1
#              continue
#            fi
#            base_size=$(wc -c < "$base_file" | tr -d '[:space:]')
#            new_size=$(wc -c < "$new_file" | tr -d '[:space:]')
#            if [ "$base_size" != "$new_size" ]; then
#              echo "::error file=$relpath::File size mismatch for $relpath (baseline=${base_size}B, new=${new_size}B)"
#              status=1
#            fi
#          done < <(cd "$BASELINE_DIR" && find . -type f \( -name '*.phsp' -o -name '*.csv' -o -name '*.txt' -o -name '*.xyz' -o -name '*.out' \) -print | sed 's|^\./||')
#          exit $status

      - name: Upload nrtest benchmark
        if: always() && steps.nrtest.outputs.benchmark_dir != ''
        uses: actions/upload-artifact@v4
        with:
          name: nrtest-results-${{ github.run_id }}
          path: ${{ steps.nrtest.outputs.benchmark_dir }}