Update files header guard

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/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_

src/discretization/fd/stencils/include/fd_stencils.h

@@ -1,6 +1,5 @@
-#ifndef FDTD_STENCILS_H
-#define FDTD_STENCILS_H
-
+#ifndef FUNTIDES_DISCRETIZATION_FD_STENCILS_INCLUDE_FD_STENCILS_H_
+#define FUNTIDES_DISCRETIZATION_FD_STENCILS_INCLUDE_FD_STENCILS_H_
 #include <data_type.h>
 
 #include <cmath>
@@ -135,5 +134,4 @@ struct FdtdStencils
 
 }  // namespace stencils
 }  // namespace fdtd
-
-#endif  // FDTD_STENCILS_H
+#endif  // FUNTIDES_DISCRETIZATION_FD_STENCILS_INCLUDE_FD_STENCILS_H_

src/discretization/fe/Integrals.hpp

@@ -1,3 +1,6 @@
+#ifndef FUNTIDES_DISCRETIZATION_FE_INTEGRALS_H_
+#define FUNTIDES_DISCRETIZATION_FE_INTEGRALS_H_
+
 #pragma once
 
 #include "finiteElement/makutu/Qk_Hexahedron_Lagrange_GaussLobatto.hpp"
@@ -19,3 +22,5 @@ struct IntegralTypeSelector<ORDER, IntegralType::MAKUTU>
   using type =
       typename Qk_Hexahedron_Lagrange_GaussLobatto_Selector<ORDER>::type;
 };
+
+#endif  // FUNTIDES_DISCRETIZATION_FE_INTEGRALS_H_

src/main/fd/include/fd_io.h

@@ -1,6 +1,5 @@
-#ifndef FDTD_IO_H_
-#define FDTD_IO_H_
-
+#ifndef FUNTIDES_MAIN_FD_INCLUDE_FD_IO_H_
+#define FUNTIDES_MAIN_FD_INCLUDE_FD_IO_H_
 #include <cstdio>
 #include <vector>
 
@@ -107,5 +106,4 @@ struct FdtdIo
 
 }  // namespace io
 }  // namespace fdtd
-
-#endif  // FDTD_IO.H_
+#endif  // FUNTIDES_MAIN_FD_INCLUDE_FD_IO_H_

src/main/fd/include/fd_options.h

@@ -12,10 +12,8 @@
 // boundary conditions, and output settings. It provides command-line
 // argument binding and validation functionality.
 //************************************************************************
-
-#ifndef SRC_MAIN_FD_INCLUDE_FDTD_OPTIONS_HPP_
-#define SRC_MAIN_FD_INCLUDE_FDTD_OPTIONS_HPP_
-
+#ifndef FUNTIDES_MAIN_FD_INCLUDE_FD_OPTIONS_H_
+#define FUNTIDES_MAIN_FD_INCLUDE_FD_OPTIONS_H_
 #include <cxxopts.hpp>
 #include <stdexcept>
 #include <string>
@@ -334,5 +332,4 @@ class FdtdOptions
 
 }  // namespace options
 }  // namespace fdtd
-
-#endif  // SRC_MAIN_FD_INCLUDE_FDTD_OPTIONS_HPP_
+#endif  // FUNTIDES_MAIN_FD_INCLUDE_FD_OPTIONS_H_

src/main/fd/include/fd_proxy.h

@@ -12,10 +12,8 @@
 // Copyright (c) 2025
 // License: [Specify license here]
 //************************************************************************
-
-#ifndef SRC_MAIN_FD_INCLUDE_FDTD_PROXY_HPP_
-#define SRC_MAIN_FD_INCLUDE_FDTD_PROXY_HPP_
-
+#ifndef FUNTIDES_MAIN_FD_INCLUDE_FD_PROXY_H_
+#define FUNTIDES_MAIN_FD_INCLUDE_FD_PROXY_H_
 #include <chrono>
 #include <memory>
 
@@ -189,4 +187,4 @@ class FdtdProxy
 };
 
 }  // namespace fdtd
-#endif  // SRC_MAIN_FD_INCLUDE_FDTD_PROXY_HPP_
+#endif  // FUNTIDES_MAIN_FD_INCLUDE_FD_PROXY_H_

src/main/fe/include/sem_io_controller.h

@@ -1,3 +1,6 @@
+#ifndef FUNTIDES_MAIN_FE_INCLUDE_SEM_IO_CONTROLLER_H_
+#define FUNTIDES_MAIN_FE_INCLUDE_SEM_IO_CONTROLLER_H_
+
 #include <adios2.h>
 #include <data_type.h>
 
@@ -122,3 +125,5 @@ class SemIOController
     snaps_writer_.EndStep();
   }
 };
+
+#endif  // FUNTIDES_MAIN_FE_INCLUDE_SEM_IO_CONTROLLER_H_

src/main/fe/include/sem_proxy.h

@@ -1,5 +1,5 @@
-#ifndef MAIN_FE_INCLUDE_SEM_PROXY_H_
-#define MAIN_FE_INCLUDE_SEM_PROXY_H_
+#ifndef FUNTIDES_MAIN_FE_INCLUDE_SEM_PROXY_H_
+#define FUNTIDES_MAIN_FE_INCLUDE_SEM_PROXY_H_
 #include <data_type.h>
 #include <utils.h>
 
@@ -168,4 +168,4 @@ class SEMproxy
   meshType getMesh(string meshArg);
   model::AnisotropyType getAnisotropy(std::string anisotropyArg);
 };
-#endif  // MAIN_FE_INCLUDE_SEM_PROXY_H_
+#endif  // FUNTIDES_MAIN_FE_INCLUDE_SEM_PROXY_H_

src/main/fe/include/sem_proxy_options.h

@@ -1,3 +1,6 @@
+#ifndef FUNTIDES_MAIN_FE_INCLUDE_SEM_PROXY_OPTIONS_H_
+#define FUNTIDES_MAIN_FE_INCLUDE_SEM_PROXY_OPTIONS_H_
+
 #pragma once
 
 #include <cxxopts.hpp>
@@ -88,3 +91,5 @@ class SemProxyOptions
         cxxopts::value<std::string>(o.anisotropy));
   }
 };
+
+#endif  // FUNTIDES_MAIN_FE_INCLUDE_SEM_PROXY_OPTIONS_H_

src/model/grid/include/fd_boundary.h

@@ -2,9 +2,8 @@
  * @file fd_boundary.h
  * @brief Absorbing boundary layer management
  */
-#ifndef SRC_MODEL_GRID_INCLUDE_FDTD_BOUNDARY_H_
-#define SRC_MODEL_GRID_INCLUDE_FDTD_BOUNDARY_H_
-
+#ifndef FUNTIDES_MODEL_GRID_INCLUDE_FD_BOUNDARY_H_
+#define FUNTIDES_MODEL_GRID_INCLUDE_FD_BOUNDARY_H_
 namespace model
 {
 namespace fdgrid
@@ -121,5 +120,4 @@ class BoundaryLayers
 
 }  // namespace fdgrid
 }  // namespace model
-
-#endif  // SRC_MODEL_GRID_INCLUDE_FDTD_BOUNDARY_H_
+#endif  // FUNTIDES_MODEL_GRID_INCLUDE_FD_BOUNDARY_H_

src/model/grid/include/fd_grid_geometry.h

@@ -2,9 +2,8 @@
  * @file fdtd_grid_geometry.h
  * @brief Grid geometry and indexing utilities
  */
-#ifndef SRC_MODEL_GRID_INCLUDE_FDTD_GRID_GEOMETRY_H_
-#define SRC_MODEL_GRID_INCLUDE_FDTD_GRID_GEOMETRY_H_
-
+#ifndef FUNTIDES_MODEL_GRID_INCLUDE_FD_GRID_GEOMETRY_H_
+#define FUNTIDES_MODEL_GRID_INCLUDE_FD_GRID_GEOMETRY_H_
 #include <fd_options.h>
 
 #include <cstddef>
@@ -117,5 +116,4 @@ class GridGeometry
 
 }  // namespace fdgrid
 }  // namespace model
-
-#endif  // SRC_MODEL_GRID_INCLUDE_FDTD_GRID_GEOMETRY_H_
+#endif  // FUNTIDES_MODEL_GRID_INCLUDE_FD_GRID_GEOMETRY_H_

src/model/grid/include/fd_grids.h

@@ -2,9 +2,8 @@
  * @file fdtd_grids.h
  * @brief FDTD grid facade (backward compatibility wrapper)
  */
-#ifndef SRC_MODEL_GRID_INCLUDE_FDTD_GRIDS_H_
-#define SRC_MODEL_GRID_INCLUDE_FDTD_GRIDS_H_
-
+#ifndef FUNTIDES_MODEL_GRID_INCLUDE_FD_GRIDS_H_
+#define FUNTIDES_MODEL_GRID_INCLUDE_FD_GRIDS_H_
 #include <fd_options.h>
 
 #include "fd_boundary.h"
@@ -162,5 +161,4 @@ class FdtdGrids
 
 }  // namespace fdgrid
 }  // namespace model
-
-#endif  // SRC_MODEL_GRID_INCLUDE_FDTD_GRIDS_H_
+#endif  // FUNTIDES_MODEL_GRID_INCLUDE_FD_GRIDS_H_

src/model/grid/include/fd_model_io.h

@@ -2,9 +2,8 @@
  * @file fdtd_model_io.h
  * @brief Model file I/O operations
  */
-#ifndef SRC_MODEL_GRID_INCLUDE_FDTD_MODEL_IO_H_
-#define SRC_MODEL_GRID_INCLUDE_FDTD_MODEL_IO_H_
-
+#ifndef FUNTIDES_MODEL_GRID_INCLUDE_FD_MODEL_IO_H_
+#define FUNTIDES_MODEL_GRID_INCLUDE_FD_MODEL_IO_H_
 #include <fstream>
 #include <stdexcept>
 #include <string>
@@ -253,5 +252,4 @@ class ModelIO
 
 }  // namespace fdgrid
 }  // namespace model
-
-#endif  // SRC_MODEL_GRID_INCLUDE_FDTD_MODEL_IO_H_
+#endif  // FUNTIDES_MODEL_GRID_INCLUDE_FD_MODEL_IO_H_

src/model/grid/include/fd_velocity_model.h

@@ -2,9 +2,8 @@
  * @file fdtd_velocity_model.h
  * @brief Velocity model storage and initialization
  */
-#ifndef SRC_MODEL_GRID_INCLUDE_FDTD_VELOCITY_MODEL_H_
-#define SRC_MODEL_GRID_INCLUDE_FDTD_VELOCITY_MODEL_H_
-
+#ifndef FUNTIDES_MODEL_GRID_INCLUDE_FD_VELOCITY_MODEL_H_
+#define FUNTIDES_MODEL_GRID_INCLUDE_FD_VELOCITY_MODEL_H_
 #include <data_type.h>
 #include <fd_options.h>
 
@@ -127,5 +126,4 @@ class VelocityModel
 
 }  // namespace fdgrid
 }  // namespace model
-
-#endif  // SRC_MODEL_GRID_INCLUDE_FDTD_VELOCITY_MODEL_H_
+#endif  // FUNTIDES_MODEL_GRID_INCLUDE_FD_VELOCITY_MODEL_H_

src/model/mesh/api/include/builder.h

@@ -1,3 +1,6 @@
+#ifndef FUNTIDES_MODEL_MESH_API_INCLUDE_BUILDER_H_
+#define FUNTIDES_MODEL_MESH_API_INCLUDE_BUILDER_H_
+
 #pragma once
 
 #include <model.h>
@@ -19,3 +22,5 @@ class ModelBuilderBase
       const = 0;
 };
 }  // namespace model
+
+#endif  // FUNTIDES_MODEL_MESH_API_INCLUDE_BUILDER_H_

src/model/mesh/api/include/face_connectivity.h

@@ -1,6 +1,5 @@
-#ifndef SRC_MODEL_MESH_API_FACE_CONNECTIVITY_H_
-#define SRC_MODEL_MESH_API_FACE_CONNECTIVITY_H_
-
+#ifndef FUNTIDES_MODEL_MESH_API_INCLUDE_FACE_CONNECTIVITY_H_
+#define FUNTIDES_MODEL_MESH_API_INCLUDE_FACE_CONNECTIVITY_H_
 #include "model.h"
 
 namespace model
@@ -83,5 +82,4 @@ class FaceConnectivityApi
 };
 
 }  // namespace model
-
-#endif  // SRC_MODEL_MESH_API_FACE_CONNECTIVITY_H_
+#endif  // FUNTIDES_MODEL_MESH_API_INCLUDE_FACE_CONNECTIVITY_H_

src/model/mesh/api/include/model.h

@@ -1,6 +1,5 @@
-#ifndef SRC_MODEL_MODELAPI_INCLUDE_MODEL_API_H_
-#define SRC_MODEL_MODELAPI_INCLUDE_MODEL_API_H_
-
+#ifndef FUNTIDES_MODEL_MESH_API_INCLUDE_MODEL_H_
+#define FUNTIDES_MODEL_MESH_API_INCLUDE_MODEL_H_
 #include "data_type.h"
 #include "parallel_topology.h"
 #include "sem_macros.h"
@@ -394,4 +393,4 @@ class ModelApi
 };
 
 }  // namespace model
-#endif  // SRC_MODEL_MODELAPI_INCLUDE_MODEL_API_H_
+#endif  // FUNTIDES_MODEL_MESH_API_INCLUDE_MODEL_H_

src/model/mesh/api/include/partitioning.h

@@ -1,6 +1,5 @@
-#ifndef SRC_MODEL_MESH_API_INCLUDE_PARTITIONING_H_
-#define SRC_MODEL_MESH_API_INCLUDE_PARTITIONING_H_
-
+#ifndef FUNTIDES_MODEL_MESH_API_INCLUDE_PARTITIONING_H_
+#define FUNTIDES_MODEL_MESH_API_INCLUDE_PARTITIONING_H_
 #include "cartesian_params.h"
 
 namespace model
@@ -45,5 +44,4 @@ class PartitioningStrategy
 };
 
 }  // namespace model
-
-#endif  // SRC_MODEL_MESH_API_INCLUDE_PARTITIONING_H_
+#endif  // FUNTIDES_MODEL_MESH_API_INCLUDE_PARTITIONING_H_