ARC/.github/workflows/ci.yml at 49931e855dc94a08c2cd70457483172f8039db6d · ReactionMechanismGenerator/ARC · GitHub

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name: CI

on:
  workflow_dispatch:
  pull_request:
    branches: [main]
    types: [opened, synchronize, reopened]
  schedule:
    - cron: '0 0 * * *'

jobs:
  build-and-test:
    name: CI and Functional Tests
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -el {0}

    steps:
      - name: Checkout ARC
        uses: actions/checkout@v4
        with:
          path: ARC

      - name: Clean Ubuntu Image
        uses: jlumbroso/free-disk-space@main
        with:
          tool-cache: true
          android: true
          dotnet: true
          haskell: true
          large-packages: true
          swap-storage: true

      - name: Set up micromamba (arc_env)
        uses: mamba-org/setup-micromamba@v2
        with:
          environment-name: arc_env
          environment-file: ARC/environment.yml
          cache-environment: true
          cache-downloads: true
          generate-run-shell: true

      - name: Install conda in micromamba base
        shell: micromamba-shell {0}
        run: |
          echo "::group::Install conda in micromamba base"
          micromamba install -n base -c conda-forge conda
          echo "::endgroup::"

      - name: Export ARC paths
        shell: micromamba-shell {0}
        working-directory: ARC
        run: |
          echo "PATH=$PATH:$PWD" >> "$GITHUB_ENV"
          echo "PYTHONPATH=$PYTHONPATH:$PWD" >> "$GITHUB_ENV"

      - name: Install Julia 1.10
        shell: micromamba-shell {0}
        run: |
          echo "::group::Install juliaup + Julia 1.10"
          # 1) Bootstrap juliaup non-interactively (-y)
          curl -fsSL https://install.julialang.org | sh -s -- -y
          # 2) Make juliaup visible *now* (CI shells won’t re-source rc files)
          export PATH="$HOME/.juliaup/bin:$PATH"
          # 3) Install & select Julia 1.10
          juliaup add 1.10
          juliaup default 1.10
          # 4) Persist for subsequent steps
          echo "PATH=$HOME/.juliaup/bin:$PATH" >> "$GITHUB_ENV"
          echo "::endgroup::"
          julia --version # Check that Julia is installed correctly

      - name: Install all extras - CI
        shell: micromamba-shell {0}
        working-directory: ARC
        env:
          MAMBA_ALWAYS_YES: "true"
          CONDA_ALWAYS_YES: "true"
        run: make install-ci

      - name: Set TS-GCN and AutoTST in PYTHONPATH
        shell: micromamba-shell {0}
        working-directory: ARC
        run: |
          echo "PYTHONPATH=$(realpath ../TS-GCN):$(realpath ../AutoTST):$PYTHONPATH" >> $GITHUB_ENV

      - name: Compile ARC molecule
        shell: micromamba-shell {0}
        working-directory: ARC
        run: |
          make compile

      - name: Run Unit Tests
        shell: micromamba-shell {0}
        working-directory: ARC
        run: |
          echo "Running Unit Tests..."
          export PYTHONPATH="${{ github.workspace }}/AutoTST:${{ github.workspace }}/KinBot:$PYTHONPATH"
          pytest arc/ --cov --cov-report=xml -ra -vv -n auto

      - name: Run Functional Tests
        shell: micromamba-shell {0}
        working-directory: ${{ github.workspace }}/ARC
        run: |
          echo "Running Functional Tests from $(pwd)..."
          export PYTHONPATH="${{ github.workspace }}/AutoTST:${{ github.workspace }}/KinBot:$PYTHONPATH"
          pytest functional/ -ra -vv -n auto

      - name: Upload coverage data
        uses: codecov/codecov-action@v3
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          file: ARC/coverage.xml
          flags: unittests,functionaltests
          name: codecov-umbrella
          verbose: true
          fail_ci_if_error: false