Merge branch 'csrc-sdsu:main' into cylinder_branch

Author: yiyuef

.github/workflows/ci.yml

@@ -34,6 +34,47 @@ jobs:
           DEFAULT_BRANCH: main
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
+      - name: Install system deps
+        run: |
+          wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key | sudo apt-key add -
+          sudo add-apt-repository "deb http://apt.llvm.org/noble/ llvm-toolchain-noble-20 main"
+          sudo apt-get update
+          sudo apt-get install -y build-essential cmake clang clang-tidy-20 clang-format perl libarmadillo-dev libopenblas-dev libsuperlu-dev libeigen3-dev
+
+      - name: Gather source files
+        id: files
+        run: |
+          # list C/C++ source files tracked by git
+          echo "::set-output name=sources::$(git ls-files '*.c' '*.cc' '*.cpp' '*.cxx' '*.h' '*.hpp' '*.hh' | tr '\n' ' ')"
+          
+      - name: Configure with CMake (generate compile_commands.json)
+        run: |
+          mkdir -p build
+          ls -al /usr/share/eigen3/cmake
+          cmake -S . -B build -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DEigen3_DIR=/usr/share/eigen3/cmake
+          ls -la build/compile_commands.json
+    
+      - name: clang-tidy (fail on warnings/errors)
+        run: |
+          if [ -z "${{ steps.files.outputs.sources }}" ]; then
+            echo "No C/C++ sources found — skipping clang-tidy."
+          else
+            # Run clang-tidy using compile_commands.json. Collect output and fail if diagnostics are present.
+            # Note: clang-tidy often prints diagnostics to stdout/stderr; we capture and grep for "warning:" or "error:".
+            printf '%s\n' ${{ steps.files.outputs.sources }} > /tmp/clang_tidy_files.txt
+            set -o pipefail
+            perl -pi -e 's/-I(.*?)third_party_install/-isystem \1third_party_install/g' build/compile_commands.json
+            clang-tidy-20 --format-style='llvm' -p build $(cat /tmp/clang_tidy_files.txt) 2>&1 | tee clang-tidy.out || true
+            if grep -E "warning:|error:" clang-tidy.out >/dev/null; then
+              echo "clang-tidy reported warnings/errors — failing the job."
+              echo ""
+              tail -n +1 clang-tidy.out
+              exit 1
+            else
+              echo "clang-tidy: no warnings/errors detected."
+            fi
+          fi
+
   build-MOLE-ubuntu:
     runs-on: ubuntu-latest
     needs: lint-new-code
@@ -167,11 +208,11 @@ jobs:
           fi
 
           if [ -n "$CHANGED" ]; then
-            echo "changed=true" >> $GITHUB_OUTPUT
+            echo "changed=true" >> "$GITHUB_OUTPUT"
             echo "Documentation sources have changed:"
             echo "$CHANGED"
           else
-            echo "changed=false" >> $GITHUB_OUTPUT
+            echo "changed=false" >> "$GITHUB_OUTPUT"
             echo "No documentation sources changed"
           fi
 

README.md

@@ -221,15 +221,3 @@ The archival copy of the MOLE User Manual is maintained on [Zenodo](https://zeno
 }
 ```
 
-## Gallery
-
-Now, some cool pictures obtained with MOLE:
-
-![Obtained with curvilinear operators](doc/assets/img/4thOrder.png)
-![Obtained with curvilinear operators](doc/assets/img/4thOrder2.png)
-![Obtained with curvilinear operators](doc/assets/img/4thOrder3.png)
-![Obtained with curvilinear operators](doc/assets/img/grid2.png)
-![Obtained with curvilinear operators](doc/assets/img/grid.png)
-![Obtained with curvilinear operators](doc/assets/img/WavyGrid.png)
-![Obtained with curvilinear operators](doc/assets/img/wave2D.png)
-![Obtained with curvilinear operators](doc/assets/img/burgers.png)