Various improvements

.clang-format

@@ -82,7 +82,7 @@ IncludeBlocks: Regroup
 IncludeCategories:
   - Regex: '^"plssvm/'
     Priority: 1
-  - Regex: '^"(cuda|hip|CL|sycl|omp|hpx|Kokkos)'
+  - Regex: '^"(cuda|driver_types|vector_types|hip|CL|sycl|omp|hpx|Kokkos)'
     Priority: 2
   - Regex: '^"(tests|bindings)/'
     Priority: 3

.clang-tidy

@@ -1,47 +1,58 @@
-# Generated from CLion Inspection settings
 ---
-Checks: '-*,
+Checks: '
+bugprone-*,
+-bugprone-branch-clone,
+-bugprone-easily-swappable-parameters,
+-bugprone-exception-escape,
+-bugprone-macro-parentheses,
+
 cert-*,
-misc-*,
-mpi-*,
+
+clang-analyzer-*,
+-clang-analyzer-optin.core.EnumCastOutOfRange,
+
 cppcoreguidelines-*,
--cppcoreguidelines-avoid-do-while,
--cppcoreguidelines-avoid-magic-numbers,
--cppcoreguidelines-pro-bounds-pointer-arithmetic,
+-cppcoreguidelines-macro-usage,
+-cppcoreguidelines-non-private-member-variables-in-classes,
 -cppcoreguidelines-pro-bounds-constant-array-index,
-google-default-arguments,
-google-runtime-operator,
-google-explicit-constructor,
-hicpp-multiway-paths-covered,
-hicpp-exception-baseclass,
+-cppcoreguidelines-pro-bounds-pointer-arithmetic,
+
+google-*,
+-google-readability-todo,
+-google-runtime-int,
+
+hicpp-*,
+-hicpp-uppercase-literal-suffix,
+
+misc-*,
+-misc-non-private-member-variables-in-classes,
+-misc-no-recursion,
+
 modernize-*,
 -modernize-use-trailing-return-type,
--modernize-avoid-c-arrays,
--modernize-use-using,
--modernize-use-default-member-init,
--modernize-macro-to-enum,
-portability-simd-intrinsics,
+-modernize-type-traits,
+
+mpi-*,
+
+openmp-*,
+-openmp-exception-escape,
+-openmp-use-default-none,
+
+performance-*,
+-performance-avoid-endl,
+-performance-enum-size,
+
+portability-*,
+-portability-avoid-pragma-once,
+
 readability-*,
--readability-redundant-preprocessor,
--readability-named-parameter,
--readability-function-size,
--readability-simplify-boolean-expr,
+-readability-convert-member-functions-to-static,
+-readability-function-cognitive-complexity,
 -readability-identifier-length,
--readability-duplicate-include,
--readability-magic-numbers,
--readability-braces-around-statements,
--readability-redundant-member-init,
+-readability-math-missing-parentheses,
 -readability-suspicious-call-argument,
--readability-qualified-auto,
--readability-isolate-declaration,
 -readability-uppercase-literal-suffix,
--readability-container-data-pointer,
--readability-else-after-return,
--readability-redundant-access-specifiers,
--readability-function-cognitive-complexity,
--readability-implicit-bool-conversion,
--readability-container-contains,
--readability-identifier-naming,
-bugprone-*'
+'
 
-CheckOptions: { misc-non-private-member-variables-in-classes.IgnoreClassesWithAllMemberVariablesBeingPublic: true }
+UseColor: true
+HeaderFilterRegex: ".*(include\\/plssvm|bindings\\/Python|tests).*"

.github/workflows/clang_gcc_linux.yml

@@ -27,7 +27,7 @@ jobs:
       - name: "Install cmake 3.31.0"
         uses: lukka/get-cmake@v3.31.0
       - name: "Clone the PLSSVM repository into PLSSVM/"
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v6.0.1
         with:
           path: PLSSVM
       - name: "Install Python dependencies"
@@ -37,7 +37,7 @@ jobs:
       - name: "Configure PLSSVM using CMake"
         run: |
           cd PLSSVM
-          cmake --preset openmp_test -DCMAKE_CXX_COMPILER=${{ matrix.compiler }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DPLSSVM_TARGET_PLATFORMS="cpu" -DPLSSVM_ENABLE_LANGUAGE_BINDINGS=ON -DPLSSVM_ENABLE_PERFORMANCE_TRACKING=ON -DPLSSVM_ENABLE_MPI=ON -DPLSSVM_TEST_FILE_NUM_DATA_POINTS=50 -DPLSSVM_TEST_FILE_NUM_FEATURES=20 -DPLSSVM_ENABLE_LTO=OFF
+          cmake --preset openmp_test -DCMAKE_CXX_COMPILER=${{ matrix.compiler }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DPLSSVM_ENABLE_STL_DEBUG_MODE=${{ matrix.build_type == 'Debug' && 'ON' || 'OFF' }} -DPLSSVM_TARGET_PLATFORMS="cpu" -DPLSSVM_ENABLE_LANGUAGE_BINDINGS=ON -DPLSSVM_ENABLE_PERFORMANCE_TRACKING=ON -DPLSSVM_ENABLE_MPI=ON -DPLSSVM_TEST_FILE_NUM_DATA_POINTS=50 -DPLSSVM_TEST_FILE_NUM_FEATURES=20 -DPLSSVM_ENABLE_LTO=OFF
       - name: "Build PLSSVM"
         run: |
           cd PLSSVM
@@ -48,4 +48,4 @@ jobs:
           cd PLSSVM
           mkdir tmp
           export TMPDIR=$PWD/tmp
-          ctest --preset openmp_test -C ${{ matrix.build_type }} --parallel 2
+          ctest --preset openmp_test -C ${{ matrix.build_type }} --parallel 2 --output-on-failure

.github/workflows/clang_macos.yml

@@ -7,51 +7,41 @@ on:
   workflow_dispatch:
 jobs:
   macOS-Test:
-    runs-on: macos-13
+    runs-on: macos-15-intel
     strategy:
       matrix:
         build_type: [Debug, Release]
     steps:
       - name: "Install cmake 3.31.0"
         uses: lukka/get-cmake@v3.31.0
-      - name: "Install LLVM and Clang"
-        uses: KyleMayes/install-llvm-action@v2
-        with:
-          version: "15.0"
       - name: "Install dependencies via brew"
         run: |
-          brew install python3
-          brew install numpy
           brew install libomp
+      - name: "Set up Python"
+        uses: actions/setup-python@v6.1.0
+        with:
+          python-version: "3.12"
       - name: "Install Python dependencies"
         run: |
-          python3 -m pip install -U pip
-          pip install argparse scikit-learn humanize --break-system-packages
-      - name: "Set PYTHONPATH"
-        run: |
-          export PYTHONPATH=$(python3 -c "import site; print(site.getsitepackages()[0])")
-          echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
+          pip install --upgrade pip setuptools wheel
+          pip install numpy scikit-learn humanize
       - name: "Clone the PLSSVM repository into PLSSVM/"
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v6.0.1
         with:
           path: PLSSVM
       - name: "Configure PLSSVM using CMake"
         run: |
           cd PLSSVM
-          export LDFLAGS="-L/opt/homebrew/opt/libomp/lib"
-          export CPPFLAGS="-I/opt/homebrew/opt/libomp/include"
-          cmake --preset openmp_test -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DPLSSVM_TARGET_PLATFORMS="cpu" -DPLSSVM_ENABLE_LANGUAGE_BINDINGS=ON -DPLSSVM_ENABLE_PERFORMANCE_TRACKING=ON -DPLSSVM_ENABLE_MPI=OFF -DPLSSVM_TEST_FILE_NUM_DATA_POINTS=50 -DPLSSVM_TEST_FILE_NUM_FEATURES=20 -DPLSSVM_ENABLE_LTO=OFF
+          cmake --preset openmp_test -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DPLSSVM_TARGET_PLATFORMS="cpu" -DPLSSVM_ENABLE_LANGUAGE_BINDINGS=ON -DPLSSVM_ENABLE_PERFORMANCE_TRACKING=ON -DPLSSVM_ENABLE_MPI=OFF -DPLSSVM_TEST_FILE_NUM_DATA_POINTS=50 -DPLSSVM_TEST_FILE_NUM_FEATURES=20 -DPLSSVM_ENABLE_LTO=OFF -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp" -DOpenMP_CXX_LIB_NAMES="omp" -DOpenMP_omp_LIBRARY="/usr/local/opt/libomp/lib/libomp.dylib" -DOpenMP_CXX_INCLUDE_DIRS="/usr/local/opt/libomp/include"
       - name: "Build PLSSVM"
         shell: bash
         run: |
           cd PLSSVM
-          export LDFLAGS="-L/opt/homebrew/opt/libomp/lib"
-          export CPPFLAGS="-I/opt/homebrew/opt/libomp/include"
+          export CPLUS_INCLUDE_PATH="/usr/local/opt/libomp/include":$CPLUS_INCLUDE_PATH
           cmake --build --preset openmp_test --config ${{ matrix.build_type }}
           echo "${GITHUB_WORKSPACE}/PLSSVM/build" >> $GITHUB_PATH
       - name: "Run tests"
         run: |
           cd PLSSVM
-          export LDFLAGS="-L/opt/homebrew/opt/libomp/lib"
-          export CPPFLAGS="-I/opt/homebrew/opt/libomp/include"
-          ctest --preset openmp_test -C ${{ matrix.build_type }} -E ".*executable.*" --parallel 2
+          export LD_LIBRARY_PATH="/usr/local/opt/libomp/lib":$LD_LIBRARY_PATH
+          ctest --preset openmp_test -C ${{ matrix.build_type }} -E ".*Executable.*" --parallel 2 --output-on-failure

.github/workflows/documentation.yml

@@ -16,7 +16,7 @@ jobs:
     steps:
       # checkout repository
       - name: "Checkout PLSSVM"
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v6.0.1
         with:
           path: PLSSVM
       # install dependencies
@@ -25,8 +25,8 @@ jobs:
           sudo apt update
           sudo apt-get install -y doxygen graphviz
       # install new CMake version
-      - name: "Install cmake 3.31.0"
-        uses: lukka/get-cmake@v3.31.0
+      - name: "Install cmake 4.2.1"
+        uses: lukka/get-cmake@v4.2.1
       # configure project via CMake
       - name: "Configure"
         run: |

.github/workflows/format.yml

@@ -13,7 +13,7 @@ jobs:
     steps:
       # checkout repository
       - name: "Checkout PLSSVM"
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v6.0.1
         with:
           path: PLSSVM
       # install dependencies
@@ -22,8 +22,8 @@ jobs:
           sudo apt install libomp-dev clang-format
           pip install "git+https://github.com/vancraar/cmake_format@master"
       # install new CMake version
-      - name: "Install cmake 3.31.0"
-        uses: lukka/get-cmake@v3.31.0
+      - name: "Install cmake 4.2.1"
+        uses: lukka/get-cmake@v4.2.1
       # configure project via CMake
       - name: "Configure"
         run: |
@@ -47,7 +47,7 @@ jobs:
       # upload the clang-format git patch, if available
       - name: "Upload clang-format patch"
         if: always()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6.0.0
         with:
           name: clang-format-patch
           path: PLSSVM/clang-format-patch.txt
@@ -70,7 +70,7 @@ jobs:
       # upload the cmake-format git patch, if available
       - name: "Upload cmake-format patch"
         if: always()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6.0.0
         with:
           name: cmake-format-patch
           path: PLSSVM/cmake-format-patch.txt

.github/workflows/msvc_windows.yml

@@ -17,7 +17,7 @@ jobs:
       - name: "Install cmake 3.31.0"
         uses: lukka/get-cmake@v3.31.0
       - name: "Clone the PLSSVM repository into PLSSVM/"
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v6.0.1
         with:
           path: PLSSVM
       - name: "Install Python dependencies"
@@ -27,7 +27,7 @@ jobs:
       - name: "Configure PLSSVM using CMake"
         run: |
           cd PLSSVM
-          cmake --preset openmp_test -DCMAKE_CONFIGURATION_TYPES=${{ matrix.build_type }} -DPLSSVM_TARGET_PLATFORMS="cpu" -DPLSSVM_ENABLE_LANGUAGE_BINDINGS=ON -DPLSSVM_ENABLE_PERFORMANCE_TRACKING=ON -DPLSSVM_ENABLE_MPI=OFF -DPLSSVM_TEST_FILE_NUM_DATA_POINTS=50 -DPLSSVM_TEST_FILE_NUM_FEATURES=20
+          cmake --preset openmp_test -DCMAKE_CONFIGURATION_TYPES=${{ matrix.build_type }} -DPLSSVM_ENABLE_STL_DEBUG_MODE=${{ matrix.build_type == 'Debug' && 'ON' || 'OFF' }} -DPLSSVM_TARGET_PLATFORMS="cpu" -DPLSSVM_ENABLE_LANGUAGE_BINDINGS=ON -DPLSSVM_ENABLE_PERFORMANCE_TRACKING=ON -DPLSSVM_ENABLE_MPI=OFF -DPLSSVM_TEST_FILE_NUM_DATA_POINTS=50 -DPLSSVM_TEST_FILE_NUM_FEATURES=20
       - name: "Build PLSSVM"
         shell: bash
         run: |
@@ -37,4 +37,4 @@ jobs:
       - name: "Run tests"
         run: |
           cd PLSSVM
-          ctest --preset openmp_test -C ${{ matrix.build_type }} -E ".*executable.*" --parallel 2
+          ctest --preset openmp_test -C ${{ matrix.build_type }} -E ".*Executable.*" --parallel 2 --output-on-failure

.github/workflows/pip.yml

@@ -21,11 +21,11 @@ jobs:
         run: |
           sudo apt install libopenmpi-dev
       - name: "Clone the PLSSVM repository into PLSSVM/"
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v6.0.1
         with:
           path: PLSSVM
       - name: "Set up Python"
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6.1.0
         with:
           python-version: "3.11"
       - name: "Create and activate virtual environment"

.gitignore

@@ -75,9 +75,10 @@ docs/*
 !docs/plssvm-scale.1.in
 
 # data in test folder
-!tests/data/
 tests/data/*
-!tests/data/model/
-!tests/data/libsvm/
-!tests/data/arff/
-!tests/data/predict/
+
+# model files
+*.model
+
+# auto-generated AdaptiveCpp directory for JIT related information
+.acpp-*