Merge branch 'main' into feature/mpi-driver

Author: ABandet

.github/workflows/format-check.yaml

@@ -12,11 +12,8 @@ jobs:
         path: ['src', 'tests']
 
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-
       - name: Run clang-format style check
-        uses: jidicula/clang-format-action@v4.11.0
+        uses: jidicula/clang-format-action@v4.16.0
         with:
           clang-format-version: '18'
           check-path: ${{ matrix.path }}

README.md

@@ -115,7 +115,6 @@ The following options can be used to configure your build:
 | `COMPILE_SEM`          | Enable compilation of the SEM proxy (default: ON)                           |
 | `ENABLE_CUDA`          | Enable CUDA backend (used by Kokkos)                                        |
 | `ENABLE_PYWRAP`        | Enable Python bindings via pybind11 (experimental)                          |
-| `ENABLE_Shiva`         | Enable Shiva discretization lib (default: OFF)                              |
 | `USE_KOKKOS`           | Enable Kokkos support (serial by default, CUDA/OpenMP with flags)           |
 | `USE_VECTOR`           | Use `std::vector` for data arrays (enabled by default unless Kokkos is used)|
 

cmake/ProxyConfig.cmake

@@ -19,10 +19,6 @@ option(ENABLE_PYWRAP "Enable python binding compilation with pybind11" OFF)
 # Debugging options
 option(FD_SAVE_SNAPSHOTS "Save snapshots for FD-proxy" OFF)
 option(PRINT_ALLOC_INFO "Printout memory allocation info" OFF)
-option(ENABLE_Shiva "Enable shiva discretization" OFF)
-if (ENABLE_Shiva)
-    add_compile_definitions(ENABLE_Shiva)
-endif()
 # Build options
 option(BUILD_SHARED_LIBS "Build shared libraries" ON)
 

cmake/ProxyUtils.cmake

@@ -6,12 +6,12 @@ function(print_configuration_summary)
   message(STATUS "")
   message(STATUS "====== PROXY CONFIGURATION SUMMARY ======")
   message(STATUS "")
-  
+
   message(STATUS "Discretization Methods:")
   message(STATUS "  COMPILE_SEM:          ${COMPILE_SEM}")
   message(STATUS "  COMPILE_FD:           ${COMPILE_FD}")
   message(STATUS "")
-  
+
   message(STATUS "Programming Models:")
   message(STATUS "  USE_VECTOR:           ${USE_VECTOR}")
   message(STATUS "  USE_KOKKOS:           ${USE_KOKKOS}")
@@ -22,13 +22,12 @@ function(print_configuration_summary)
   message(STATUS "Python Wrapping:")
   message(STATUS "  ENABLE_PYWRAP:        ${ENABLE_PYWRAP}")
   message(STATUS "")
-  
+
   message(STATUS "Debugging Options:")
   message(STATUS "  FD_SAVE_SNAPSHOTS:    ${FD_SAVE_SNAPSHOTS}")
   message(STATUS "  PRINT_ALLOC_INFO:     ${PRINT_ALLOC_INFO}")
-  message(STATUS "  ENABLE_Shiva:         ${ENABLE_Shiva}")
   message(STATUS "")
-  
+
   message(STATUS "Build Options:")
   message(STATUS "  CMAKE_BUILD_TYPE:     ${CMAKE_BUILD_TYPE}")
   message(STATUS "  BUILD_SHARED_LIBS:    ${BUILD_SHARED_LIBS}")

scripts/dev/fix_include_guards.py

@@ -139,7 +139,8 @@ def fix_include_guards(filepath: Path, src_root: Path, project_name: str = "", d
 
     if not ifndef_line:
         print(f"⚠️  No include guard found in {filepath}")
-        return False
+        print(f" Add incluide guards in {filepath}")
+        return add_include_guards(filepath, src_root, project_name, dry_run)
 
     # Extract current guard name
     current_guard = re.search(r'#\s*ifndef\s+([A-Za-z0-9_]+)', ifndef_line).group(1)
@@ -193,6 +194,37 @@ def fix_include_guards(filepath: Path, src_root: Path, project_name: str = "", d
         print(f"❌ Error writing {filepath}: {e}")
         return False
 
+def add_include_guards(filepath: Path, src_root: Path, project_name: str = "", dry_run: bool = False) -> bool:
+    """
+    Add include guards to a file that doesn't have them.
+    
+    Returns:
+        True if the file was modified, False otherwise
+    """
+    try:
+        with open(filepath, 'r', encoding='utf-8') as f:
+            content = f.read()
+    except Exception as e:
+        print(f"❌ Error reading {filepath}: {e}")
+        return False
+
+    guard_name = generate_guard_name(filepath, src_root, project_name)
+
+    print(f" {filepath.relative_to(src_root.parent)}:")
+    print(f"   Adding guard: {guard_name}")
+
+    if dry_run:
+        return True
+
+    new_content = f"#ifndef {guard_name}\n#define {guard_name}\n\n{content.rstrip()}\n\n#endif  // {guard_name}\n"
+
+    try:
+        with open(filepath, 'w', encoding='utf-8') as f:
+            f.write(new_content)
+        return True
+    except Exception as e:
+        print(f"❌ Error writing {filepath}: {e}")
+        return False
 
 def main():
     import argparse
@@ -228,6 +260,8 @@ def main():
 
     extensions = [f".{ext.strip()}" for ext in args.extensions.split(',')]
     exclude_dirs = args.exclude
+
+    exclude_dirs = [d.strip("/") for d in args.exclude]
 
     print(f"🔍 Searching for header files in {src_root}")
     print(f"   Extensions: {', '.join(extensions)}")

src/CMakeLists.txt

@@ -23,8 +23,7 @@ endforeach()
 
 file(GLOB_RECURSE ALL_SOURCE_FILES ${GLOBS})
 
-# Example: filter out files whose path contains "Shiva" or "SEMKernels"
-list(FILTER ALL_SOURCE_FILES EXCLUDE REGEX "Shiva")
+# Example: filter out files whose path contains "SEMKernels"
 list(FILTER ALL_SOURCE_FILES EXCLUDE REGEX "SEMKernels")
 
 # Make the format target

src/discretization/CMakeLists.txt

@@ -3,18 +3,13 @@ add_library(discretization INTERFACE)
 target_include_directories( discretization INTERFACE
                             $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/fe/SEMKernels/src/>
                             $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/fe/SEMKernels/src/finiteElement/>
-                            $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/fe/SEMKernels/src/Shiva/src/>
                             $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/>
                             ${CMAKE_BINARY_DIR}/include
-                          ) 
+                          )
 message(STATUS "Binary include dir: ${CMAKE_BINARY_DIR}/include")
 
 add_subdirectory( fe/SEMKernels )
 
 target_link_libraries( discretization INTERFACE proxy_utils )
 
-if (ENABLE_Shiva)
-    target_link_libraries( discretization INTERFACE Shiva::shiva )
-endif()
-
 add_subdirectory(fd)

src/discretization/fd/abckernels/include/fd_abckernels.h

@@ -1,6 +1,5 @@
-#ifndef FDTD_PML_HPP
-#define FDTD_PML_HPP
-
+#ifndef FUNTIDES_DISCRETIZATION_FD_ABCKERNELS_INCLUDE_FD_ABCKERNELS_H_
+#define FUNTIDES_DISCRETIZATION_FD_ABCKERNELS_INCLUDE_FD_ABCKERNELS_H_
 #include "data_type.h"
 #include "fd_macros.h"
 
@@ -233,4 +232,4 @@ struct FdtdAbcKernels
 
 }  // namespace abckernel
 }  // namespace fdtd
-#endif  // FDTD_PML_HPP
+#endif  // FUNTIDES_DISCRETIZATION_FD_ABCKERNELS_INCLUDE_FD_ABCKERNELS_H_

src/discretization/fd/kernels/include/fd_kernels.h

@@ -1,6 +1,5 @@
-#ifndef FDTD_KERNEL_H
-#define FDTD_KERNEL_H
-
+#ifndef FUNTIDES_DISCRETIZATION_FD_KERNELS_INCLUDE_FD_KERNELS_H_
+#define FUNTIDES_DISCRETIZATION_FD_KERNELS_INCLUDE_FD_KERNELS_H_
 #include "data_type.h"
 #include "fd_abckernels.h"
 #include "fd_macros.h"
@@ -163,4 +162,4 @@ struct FdtdKernels
 
 }  // namespace kernel
 }  // namespace fdtd
-#endif  // FDTD_KERNEL_H
+#endif  // FUNTIDES_DISCRETIZATION_FD_KERNELS_INCLUDE_FD_KERNELS_H_

src/discretization/fd/kernels/include/fd_macros.h

@@ -1,6 +1,5 @@
-#ifndef FDTD_MACROS_H
-#define FDTD_MACROS_H
-
+#ifndef FUNTIDES_DISCRETIZATION_FD_KERNELS_INCLUDE_FD_MACROS_H_
+#define FUNTIDES_DISCRETIZATION_FD_KERNELS_INCLUDE_FD_MACROS_H_
 #define POW2(x) ((x) * (x))
 #define IDX3(i, j, k) (nz * ny * (i) + nz * (j) + (k))
 #define IDX3_l(i, j, k)                                                      \
@@ -53,5 +52,4 @@
 #else
 #define FDFENCE
 #endif
-
-#endif  // FDTD_MACROS_H
+#endif  // FUNTIDES_DISCRETIZATION_FD_KERNELS_INCLUDE_FD_MACROS_H_