TEMPORARY! only run the docker build target in CI

rwest · rwest · commit 1cf53fa2cfed · 2025-06-06T14:04:01.000-04:00
To save time while debugging.
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -52,353 +52,10 @@ env:
   JULIA_NUM_PRECOMPILE_TASKS: 1
 
 jobs:
-  build-and-test:
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ["3.9"]
-        os: [macos-13, macos-latest, ubuntu-latest]
-        include-rms: ["", "with RMS"]
-        exclude:
-          - os: macos-13  # GitHub's runners just aren't up to the task of installing Julia
-            include-rms: 'with RMS'
-    runs-on: ${{ matrix.os }}
-    name: Python ${{ matrix.python-version }} ${{ matrix.os }} Build and Test ${{ matrix.include-rms }}
-    # skip scheduled runs from forks
-    if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }}
-    defaults:
-      run:
-        shell: bash -l {0}
-    steps:
-      - name: Checkout RMG-Py
-        uses: actions/checkout@v4
-
-      - name: Setup Miniforge Python ${{ matrix.python-version }}
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          environment-file: environment.yml
-          miniforge-variant: Miniforge3
-          miniforge-version: latest
-          python-version: ${{ matrix.python-version }}
-          activate-environment: rmg_env
-          auto-update-conda: true
-          show-channel-urls: true
-          conda-remove-defaults: "true"
-
-      # list the environment for debugging purposes
-      - name: conda info
-        run: |
-          conda info
-          conda list
-
-      # Clone RMG-database
-      - name: Clone RMG-database
-        run: |
-          cd ..
-          git clone -b $RMG_DATABASE_BRANCH https://github.com/ReactionMechanismGenerator/RMG-database.git
-
-      # RMG build step
-      - run: make install
-
-      - name: Setup Juliaup
-        if: matrix.include-rms == 'with RMS'
-        uses: julia-actions/install-juliaup@v2
-        with:
-          channel: '1.10'
-
-      # RMS installation and linking to Julia
-      - name: Install and link Julia dependencies
-        if: matrix.include-rms == 'with RMS'
-        timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
-        run: . install_rms.sh
-
-      - name: Install Q2DTor
-        run: echo "" | make q2dtor
-
-      # non-regression testing
-      - name: Run Unit, Functional, and Database Tests
-        run: make test-all
-
-  regression-test:
-    runs-on: ubuntu-latest
-    name: Regression Test
-    # skip scheduled runs from forks
-    if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }}
-    env: 
-      # This is true only if this is a reference case for the regression testing:
-      REFERENCE_JOB: ${{ github.ref == 'refs/heads/main' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
-    defaults:
-      run:
-        shell: bash -l {0}
-    steps:
-      - name: Checkout RMG-Py
-        uses: actions/checkout@v4
-
-      - name: Setup Miniforge Python 3.9
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          environment-file: environment.yml
-          miniforge-variant: Miniforge3
-          miniforge-version: latest
-          python-version: 3.9
-          activate-environment: rmg_env
-          auto-update-conda: true
-          show-channel-urls: true
-          conda-remove-defaults: "true"
-
-      # list the environment for debugging purposes
-      - name: conda info
-        run: |
-          conda info
-          conda list
-
-      # Clone RMG-database
-      - name: Clone RMG-database
-        run: |
-          cd ..
-          git clone -b $RMG_DATABASE_BRANCH https://github.com/ReactionMechanismGenerator/RMG-database.git
-
-      # RMG build step
-      - run: make install
-      
-      - name: Make separate No-RMS conda env
-        run: |
-          conda create --name rmg_env_without_rms --clone rmg_env
-
-      - name: Setup Juliaup
-        uses: julia-actions/install-juliaup@v2
-        with:
-          channel: '1.10'
-
-      # RMS installation and linking to Julia
-      - name: Install and link Julia dependencies
-        timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
-        run: |
-          . install_rms.sh
-
-      - name: Install Q2DTor
-        run: echo "" | make q2dtor
-
-      # Regression Testing - Test Execution
-      - name: Regression Tests - Execution
-        id: regression-execution
-        run: |
-          for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation RMS_liquidSurface_ch4o2cat fragment RMS_constantVIdealGasReactor_fragment minimal_surface;
-          do
-            if python rmg.py test/regression/"$regr_test"/input.py; then
-              echo "$regr_test" "Executed Successfully"
-            else
-              echo "$regr_test" "Failed to Execute" | tee -a $GITHUB_STEP_SUMMARY
-              export FAILED=Yes
-            fi
-          done
-          if [[ ${FAILED} ]]; then
-            echo "One or more regression tests could not be executed." | tee -a $GITHUB_STEP_SUMMARY
-            echo "Please download the failed results or check the above log to see why." | tee -a $GITHUB_STEP_SUMMARY
-            exit 1
-          fi
-
-      # Upload Regression Results as Failed if above step failed
-      - name: Upload Failed Results
-        if: ${{ failure() && steps.regression-execution.conclusion == 'failure' }}
-        uses: actions/upload-artifact@v4
-        with:
-          name: failed_regression_results
-          path: |
-            test/regression
-
-      # Upload Regression Results as Stable if Scheduled or Push to Main
-      - name: Upload Results as Reference
-        # upload the results for scheduled CI (on main) and pushes to main
-        if: ${{ env.REFERENCE_JOB == 'true' }}
-        uses: actions/upload-artifact@v4
-        with:
-          name: stable_regression_results
-          path: |
-            test/regression
-
-      # Upload Regression Results as Dynamic if Push to non-main Branch
-      - name: Upload Results as Dynamic
-        if: ${{ env.REFERENCE_JOB == 'false' }}
-        uses: actions/upload-artifact@v4
-        with:
-          name: dynamic_regression_results
-          path: |
-            test/regression
-
-      - name: mkdir stable_regression_results
-        if: ${{ env.REFERENCE_JOB == 'false' }}
-        run: mkdir stable_regression_results
-
-      # Retrieve Stable Results for reference
-      - name: Find ID of Reference Results
-        env:
-          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        # this will search for the last successful execution of CI on main
-        run: |
-          run_id=$(gh run list -R ReactionMechanismGenerator/RMG-Py --workflow="Continuous Integration" --branch main --limit 15 --json databaseId,conclusion --jq 'map(select(.conclusion == "success")) | .[0].databaseId')
-          if [ -z "$run_id" ] || [ "$run_id" = "null" ]; then
-            echo "::error::No successful reference run found"
-            exit 1
-          fi
-          echo "CI_RUN_ID=$run_id" >> $GITHUB_ENV
-
-      - name: Retrieve Stable Regression Results
-        if: ${{ env.REFERENCE_JOB == 'false' }}
-        uses: actions/download-artifact@v4
-        with:
-        # download stable regression results
-          run-id: ${{ env.CI_RUN_ID }}
-          repository: ReactionMechanismGenerator/RMG-Py
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          name: stable_regression_results
-          path: stable_regression_results
-
-      # Regression Testing - Actual Comparisons
-      - name: Regression Tests - Compare to Baseline
-        id: regression-comparison
-        if: ${{ env.REFERENCE_JOB == 'false' }}
-        env:
-          REFERENCE: stable_regression_results
-        run: |
-          conda activate rmg_env_without_rms
-          
-          exec 2> >(tee -a regression.stderr >&2) 1> >(tee -a regression.stdout)
-          mkdir -p "test/regression-diff"
-          for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation fragment RMS_constantVIdealGasReactor_fragment minimal_surface;
-          do
-            echo ""
-            echo "### Regression test $regr_test:"
-            # Memory Usage and Execution Time
-            echo -n 'Reference: '
-            grep "Execution time" $REFERENCE/"$regr_test"/RMG.log | tail -1
-            echo -n 'Current:   '
-            grep "Execution time" test/regression/"$regr_test"/RMG.log | tail -1
-            echo -n 'Reference: '
-            grep "Memory used:" $REFERENCE/"$regr_test"/RMG.log | tail -1
-            echo -n 'Current:   '
-            grep "Memory used:" test/regression/"$regr_test"/RMG.log | tail -1
-
-            echo "<details>"
-            # Compare the edge and core
-            if python scripts/checkModels.py \
-                "$regr_test-core" \
-                $REFERENCE/"$regr_test"/chemkin/chem_annotated.inp \
-                $REFERENCE/"$regr_test"/chemkin/species_dictionary.txt \
-                test/regression/"$regr_test"/chemkin/chem_annotated.inp \
-                test/regression/"$regr_test"/chemkin/species_dictionary.txt &> checkModels.err
-            then
-              echo "<summary>$regr_test Passed Core Comparison ✅</summary>"
-            else
-              echo "<summary>$regr_test Failed Core Comparison ❌</summary>"
-              cp "$regr_test-core.log" test/regression-diff/
-              export FAILED=Yes
-            fi
-            echo "" # blank line so next block is interpreted as markdown
-            cat "$regr_test-core.log" || (echo "Dumping the whole log failed, please download it from GitHub actions. Here are the first 100 lines:" && head -n100 "$regr_test-core.log")
-            echo "</details>"
-            if [ -s checkModels.err ]; then
-              echo "<details>"
-              echo "<summary>Errors occurred during core comparison ⚠️</summary>"
-              cat checkModels.err
-              echo "</details>"
-            fi
-            echo "<details>"
-            if python scripts/checkModels.py \
-                "$regr_test-edge" \
-                $REFERENCE/"$regr_test"/chemkin/chem_edge_annotated.inp \
-                $REFERENCE/"$regr_test"/chemkin/species_edge_dictionary.txt \
-                test/regression/"$regr_test"/chemkin/chem_edge_annotated.inp \
-                test/regression/"$regr_test"/chemkin/species_edge_dictionary.txt &> checkModels.err
-            then
-              echo "<summary>$regr_test Passed Edge Comparison ✅</summary>"
-            else
-              echo "<summary>$regr_test Failed Edge Comparison ❌</summary>"
-              cp "$regr_test-edge.log" test/regression-diff/
-              export FAILED=Yes
-            fi
-            echo "" # blank line so next block is interpreted as markdown
-            cat "$regr_test-edge.log" || (echo "Dumping the whole log failed, please download it from GitHub actions. Here are the first 100 lines:" && head -n100 "$regr_test-edge.log")
-            echo "</details>"
-            if [ -s checkModels.err ]; then
-              echo "<details>"
-              echo "<summary>Errors occurred during edge comparison ⚠️</summary>"
-              cat checkModels.err
-              echo "</details>"
-            fi
-
-            # Check for Regression between Reference and Dynamic (skip superminimal)
-            if [ -f test/regression/"$regr_test"/regression_input.py ];
-            then
-              echo "<details>"
-              if python rmgpy/tools/regression.py \
-                test/regression/"$regr_test"/regression_input.py \
-                $REFERENCE/"$regr_test"/chemkin \
-                test/regression/"$regr_test"/chemkin 2> regression.py.err
-              then
-                echo "<summary>$regr_test Passed Observable Testing ✅</summary>"
-              else
-                echo "<summary>$regr_test Failed Observable Testing ❌</summary>"
-                export FAILED=Yes
-              fi
-              echo "</details>"
-              if [ -s regression.py.err ]; then
-                echo "<details>"
-                echo "<summary>Errors occurred during observable testing ⚠️</summary>"
-                cat regression.py.err
-                echo "</details>"
-              fi
-            fi
-            echo ""
-          done
-          if [[ ${FAILED} ]]; then
-            echo "⚠️ One or more regression tests failed." | tee -a $GITHUB_STEP_SUMMARY >&2
-            echo "Please download the failed results and run the tests locally or check the log to see why." | tee -a $GITHUB_STEP_SUMMARY >&2
-          fi
-
-      - name: Prepare Results for PR Comment
-        if: ${{ env.REFERENCE_JOB == 'false' }}
-        env:
-          PR_NUMBER: ${{ github.event.number || github.event.after || github.event_name }}
-        run: |
-          echo $PR_NUMBER > summary.txt
-          echo "## Regression Testing Results" >> summary.txt
-          cat regression.stderr >> summary.txt
-          echo "<details>" >> summary.txt
-          echo "<summary>Detailed regression test results.</summary>" >> summary.txt
-          cat regression.stdout >> summary.txt
-          echo "</details>" >> summary.txt
-          echo "" >> summary.txt
-          echo "_beep boop this comment was written by a bot_ :robot:" >> summary.txt
-          cat summary.txt > $GITHUB_STEP_SUMMARY
-
-      - name: Upload regression summary artifact
-        # the annotate workflow uses this artifact to add a comment to the PR
-        uses: actions/upload-artifact@v4
-        if: ${{ github.event_name == 'pull_request' }}
-        with:
-          name: regression_summary
-          path: summary.txt
-
-      - name: Upload Comparison Results
-        uses: actions/upload-artifact@v4
-        with:
-          name: regression_test_comparison_results
-          path: |
-            test/regression-diff
-
-      # Install and Call codecov only if the tests were successful (permitting failures in the regression comparison tests)
-      - name: Code coverage install and run
-        if: success() || ( failure() && steps.regression-execution.conclusion == 'success' )
-        run: |
-          conda install -y -c conda-forge codecov
-          codecov
-
   build-and-push-docker:
     # after testing and on pushes to main, build and push docker image
     #
     # taken from https://github.com/docker/build-push-action
-    needs: [build-and-test, regression-test]
     runs-on: ubuntu-latest
     # Run on push to main or on pull requests
     if: |
