Add clangd tidy checks

.cmake/benchmarking.cmake

@@ -13,7 +13,7 @@ FetchContent_Declare(
 
 # Keep project warning policy from being applied to third-party sources.
 set(_CMAKE_CXX_FLAGS_BACKUP "${CMAKE_CXX_FLAGS}")
-foreach(flag IN ITEMS "-Wswitch-enum" "-Werror=switch-enum")
+foreach(flag IN ITEMS "-Wswitch-enum" "-Werror=switch-enum" "-Werror" "-Wundef")
     string(REPLACE "${flag}" "" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
 endforeach()
 

.github/workflows/lint.yml

@@ -0,0 +1,80 @@
+name: LINT
+
+on:
+  pull_request:
+    branches:
+      - '*'
+    paths:
+      - '.github/workflows/ci_build.yml'
+      - '.cmake/**'
+      - 'apps/**'
+      - 'include/**'
+      - 'src/**'
+      - 'integration_tests/**'
+      - 'tests/**'
+      - 'benchmarks/CMakeLists.txt'
+      - 'benchmarks/src/**'
+      - 'CMakeLists.txt'
+      - '.clang-tidy'
+      - 'scripts/clang_tidy.sh'
+      - '.github/workflows/lint.yml'
+  push:
+    branches:
+      - dev
+      - main
+    paths:
+      - '.github/workflows/ci_build.yml'
+      - '.cmake/**'
+      - 'apps/**'
+      - 'include/**'
+      - 'src/**'
+      - 'integration_tests/**'
+      - 'CMakeLists.txt'
+      - '.clang-tidy'
+      - 'scripts/clang_tidy.sh'
+      - '.github/workflows/lint.yml'
+      - 'benchmarks/src/**'
+      - 'CMakeLists.txt'
+  workflow_dispatch:
+
+jobs:
+  lint:
+    runs-on: ubuntu-24.04
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install build tools
+        run: |
+          sudo apt update
+          sudo apt install -y gcc-13 g++-13 mold ninja-build clangd-20
+          sudo update-alternatives --install /usr/bin/clangd clangd /usr/bin/clangd-20 100
+        shell: bash
+
+      - name: Setup python
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.12'
+
+      - name: install python dependencies
+        run: |
+          python -m pip install numpy
+        shell: bash
+
+      - name: Install clangd-tidy
+        run: python -m pip install clangd-tidy
+        shell: bash
+
+      - name: Configure (generate compile_commands.json)
+        run: |
+          cmake -S . -B build -G Ninja \
+            -DCMAKE_BUILD_TYPE=Debug \
+            -DCMAKE_EXPORT_COMPILE_COMMANDS=ON \
+            -DBUILD_WITH_NATIVE=Off
+        env:
+          CC: gcc-13
+          CXX: g++-13
+
+      - name: Run clangd-tidy
+        run: |
+          clangd-tidy $(find src/ apps/ include/ -name "*.cpp" -o -name "*.hpp" -o -name "*.tpp" 2>/dev/null) -p=build

.gitignore

@@ -64,7 +64,6 @@ examples/**/tm.out
 examples/**/traj2box
 examples/**/*.cao
 
-
 *.gcov
 
 googletest
@@ -77,3 +76,11 @@ venv
 .venv
 env
 .env
+
+# local clangd output for checks for ci -- not to be committed
+clangd-tidy-report.log
+
+# sometimes useful to make a syslink into the main dir from the build dir, but not to be committed
+compile_commands.json
+
+CMakePresets.json

.vscode/settings.json

@@ -143,11 +143,15 @@
         "coulombic",
         "Coulombics",
         "Coupl",
+        "Cueq",
+        "cuequivariance",
         "datapoints",
+        "Derivs",
         "DFTD",
         "dxyz",
         "ekin",
         "equil",
+        "Fennol",
         "filterwarnings",
         "forcexyz",
         "freset",
@@ -214,6 +218,7 @@
         "RSTFILEEXCEPTION",
         "RSTFILEOUTPUT",
         "SHAKEEXCEPTION",
+        "Slakos",
         "sonarlint",
         "STDOUTOUTPUT",
         "STREQ",
@@ -241,4 +246,4 @@
     "esbonio.sphinx.confDir": "",
     "workbench.colorTheme": "Visual Studio Dark - C++",
     "sonarlint.pathToCompileCommands": "${workspaceFolder}/.build/compile_commands.json"
-}
+}

.vscode/tasks.json

@@ -0,0 +1,74 @@
+{
+    "version": "2.0.0",
+    "tasks": [
+        {
+            "label": "clangd-tidy (changed)",
+            "type": "shell",
+            "command": "bash",
+            "args": [
+                "-c",
+                "scripts/clang_tidy.sh"
+            ],
+            "options": {
+                "cwd": "${workspaceFolder}"
+            },
+            "problemMatcher": [
+                {
+                    "owner": "clangd-tidy",
+                    "fileLocation": [
+                        "absolute"
+                    ],
+                    "pattern": {
+                        "regexp": "^(.*?):(\\d+):(\\d+):\\s*(warning|error|note):\\s*(.*)$",
+                        "file": 1,
+                        "line": 2,
+                        "column": 3,
+                        "severity": 4,
+                        "message": 5
+                    }
+                }
+            ],
+            "group": "build"
+        },
+        {
+            "label": "clangd-tidy (all)",
+            "type": "shell",
+            "command": "bash",
+            "args": [
+                "-c",
+                "scripts/clang_tidy.sh --all"
+            ],
+            "options": {
+                "cwd": "${workspaceFolder}"
+            },
+            "problemMatcher": [
+                {
+                    "owner": "clangd-tidy",
+                    "fileLocation": [
+                        "absolute"
+                    ],
+                    "pattern": {
+                        "regexp": "^(.*?):(\\d+):(\\d+):\\s*(warning|error|note):\\s*(.*)$",
+                        "file": 1,
+                        "line": 2,
+                        "column": 3,
+                        "severity": 4,
+                        "message": 5
+                    }
+                }
+            ],
+            "group": "build"
+        },
+        {
+            "type": "cmake",
+            "label": "CMake: build",
+            "command": "build",
+            "targets": [
+                "all"
+            ],
+            "group": "build",
+            "problemMatcher": [],
+            "detail": "CMake template build task"
+        }
+    ]
+}

apps/PQ.cpp

@@ -20,13 +20,12 @@
 <GPL_HEADER>
 ******************************************************************************/
 
-#include <cstdlib>      // for EXIT_SUCCESS
-#include <exception>    // for exception
-#include <filesystem>   // for remove_all
-#include <iostream>     // for operator<<
-#include <memory>       // for unique_ptr
-#include <string>       // for string, char_traits
-#include <vector>       // for vector
+#include <cstdlib>     // for EXIT_SUCCESS
+#include <exception>   // for exception
+#include <iostream>    // for operator<<
+#include <memory>      // for unique_ptr
+#include <string>      // for string, char_traits
+#include <vector>      // for vector
 
 #include "commandLineArgs.hpp"   // for CommandLineArgs
 #include "engine.hpp"            // for Engine

benchmarks/perf/perfBenchSetup.hpp

@@ -37,7 +37,6 @@
 #include "matrix.hpp"
 #include "molecule.hpp"
 #include "simulationBox.hpp"
-#include "vector3d.hpp"
 
 namespace potential
 {
@@ -72,7 +71,9 @@ namespace benchSetup
                 0.25 * d
             };
             atom->setPosition(pos);
-            atom->setPositionOld(pos);   // at-rest start (stable for constraints)
+            atom->setPositionOld(
+                pos
+            );   // at-rest start (stable for constraints)
             atom->setVelocity({0.01 * (d + 1.0), -0.015, 0.02});
             atom->setForce({0.1, -0.2, 0.05});
             atom->setShiftForce({0.0, 0.0, 0.0});
@@ -94,11 +95,19 @@ namespace benchSetup
     {
         auto nonCoulomb = potential::ForceFieldNonCoulomb();
         nonCoulomb.setNonCoulombPairsMatrix(
-            linearAlgebra::Matrix<std::shared_ptr<potential::NonCoulombPair>>(2, 2)
+            linearAlgebra::Matrix<std::shared_ptr<potential::NonCoulombPair>>(
+                2,
+                2
+            )
         );
 
-        auto pair =
-            potential::LennardJonesPair(std::size_t(0), std::size_t(1), 12.0, 2.0, 3.0);
+        auto pair = potential::LennardJonesPair(
+            std::size_t(0),
+            std::size_t(1),
+            12.0,
+            2.0,
+            3.0
+        );
         nonCoulomb.setNonCoulombPairsMatrix(0, 1, pair);
         nonCoulomb.setNonCoulombPairsMatrix(1, 0, pair);
 
@@ -118,10 +127,12 @@ namespace benchSetup
 
         for (std::size_t m = 0; m < nMolecules; ++m)
         {
-            auto molecule = makeMolecule(nAtomsPerMol, 3.0 * static_cast<double>(m));
+            auto molecule =
+                makeMolecule(nAtomsPerMol, 3.0 * static_cast<double>(m));
 
             for (std::size_t i = 0; i < nAtomsPerMol; ++i)
-                box.addAtom(molecule.getAtoms()[i]);   // share the atom pointers
+                box.addAtom(molecule.getAtoms()[i]
+                );   // share the atom pointers
 
             box.addMolecule(molecule);
         }

benchmarks/perf/perfBoxTransforms.cpp

@@ -33,7 +33,6 @@
 
 #include "orthorhombicBox.hpp"
 #include "triclinicBox.hpp"
-#include "vector3d.hpp"
 
 static constexpr long ITERATIONS = 20000;
 

benchmarks/perf/perfConstraints.cpp

@@ -33,13 +33,11 @@
 #define CALLGRIND_ZERO_STATS
 #endif
 
-#include "perfBenchSetup.hpp"
 #include "bondConstraint.hpp"
 #include "constraints.hpp"
-#include "molecule.hpp"
+#include "perfBenchSetup.hpp"
 #include "simulationBox.hpp"
 #include "timingsSettings.hpp"
-#include "vector3d.hpp"
 
 static constexpr long ITERATIONS = 1000;
 
@@ -59,7 +57,13 @@ int main()
 
     for (std::size_t m = 0; m < molecules.size(); ++m)
         constr.addBondConstraint(
-            constraints::BondConstraint(&molecules[m], &molecules[m], 0, 1, 0.85)
+            constraints::BondConstraint(
+                &molecules[m],
+                &molecules[m],
+                0,
+                1,
+                0.85
+            )
         );
 
     constr.calculateConstraintBondRefs(box);