includes reordered

ZocoLini · ZocoLini · commit 4ff2ea4775dd · 2025-08-19T08:57:07.000Z
diff --git a/.clang-format b/.clang-format
@@ -2,6 +2,8 @@
 ---
 Language: Cpp
 BasedOnStyle: LLVM
+SortIncludes: true
+IncludeBlocks: Regroup
 AccessModifierOffset: -4
 AlignConsecutiveAssignments: false
 AlignConsecutiveDeclarations: false
diff --git a/modules/cli/include/handlers/handlers.h b/modules/cli/include/handlers/handlers.h
@@ -10,4 +10,4 @@ typedef struct
     int (*handle)(int argc, char *argv[]);
 } Handler;
 
-#endif //HANDLERS_H
+#endif // HANDLERS_H
diff --git a/modules/cli/include/handlers/help.h b/modules/cli/include/handlers/help.h
@@ -4,4 +4,4 @@
 
 Handler create_help_handler();
 
-#endif //HELP_H
+#endif // HELP_H
diff --git a/modules/cli/include/handlers/solve.h b/modules/cli/include/handlers/solve.h
@@ -6,4 +6,4 @@
 
 Handler create_solve_handler();
 
-#endif //SOLVE_H
+#endif // SOLVE_H
diff --git a/modules/cli/include/handlers/version.h b/modules/cli/include/handlers/version.h
@@ -4,4 +4,4 @@
 
 Handler create_version_handler();
 
-#endif //VERSION_H
+#endif // VERSION_H
diff --git a/modules/cli/include/main.h b/modules/cli/include/main.h
@@ -7,4 +7,4 @@
 
 #define VERSION "0.1.0"
 
-#endif //MAIN_H
+#endif // MAIN_H
diff --git a/modules/cli/src/handlers/help.c b/modules/cli/src/handlers/help.c
@@ -1,4 +1,5 @@
 #include <stdio.h>
+
 #include "handlers/handlers.h"
 
 int handle_help(int argc, char *argv[]);
@@ -12,25 +13,30 @@ Handler create_help_handler()
 
 int handle_help(int argc, char *argv[])
 {
-    const char* help_message =
-"- [ Commands ] -\n"
-"\n"
-" Command   | Description                                                         \n"
-"==========+======================================================================\n"
-" solve     | Solves the given problem with the given configuration and data      \n"
-" version   | Displays the current version of the tool                            \n"
-" help      | Displays this help message                                          \n"
-"\n"
-"- [ Solve command options ] -\n"
-"\n"
-" Options Short    | Type | Description                                                     | Default value   |Example\n"
-" =================+======+=================================================================+=================+=====================================\n"
-" -c               | Str  | Path to the cuqdyn xml config file                              |                 |-c config/cuqdyn_conf.xml\n"
-" -s               | Str  | Path to the sacess library xml config file                      |                 |-s config/sacess_library_conf.xml\n"
-" -d               | Str  | Path to the data file (Supports text and .mat files)            |                 |-d data/lotka_volterra.txt\n"
-" -o               | Str  | Defines the output folder for the results                       | output/         |-o output\n"
-"\n"
-"Usage: %s <command> [options]...\n";
+    const char *help_message = "- [ Commands ] -\n"
+                               "\n"
+                               " Command   | Description                                                         \n"
+                               "==========+======================================================================\n"
+                               " solve     | Solves the given problem with the given configuration and data      \n"
+                               " version   | Displays the current version of the tool                            \n"
+                               " help      | Displays this help message                                          \n"
+                               "\n"
+                               "- [ Solve command options ] -\n"
+                               "\n"
+                               " Options Short    | Type | Description                                                 "
+                               "    | Default value   |Example\n"
+                               " =================+======+============================================================="
+                               "====+=================+=====================================\n"
+                               " -c               | Str  | Path to the cuqdyn xml config file                          "
+                               "    |                 |-c config/cuqdyn_conf.xml\n"
+                               " -s               | Str  | Path to the sacess library xml config file                  "
+                               "    |                 |-s config/sacess_library_conf.xml\n"
+                               " -d               | Str  | Path to the data file (Supports text and .mat files)        "
+                               "    |                 |-d data/lotka_volterra.txt\n"
+                               " -o               | Str  | Defines the output folder for the results                   "
+                               "    | output/         |-o output\n"
+                               "\n"
+                               "Usage: %s <command> [options]...\n";
 
 
     printf(help_message, argv[0]);
diff --git a/modules/cli/src/handlers/solve.c b/modules/cli/src/handlers/solve.c
@@ -1,17 +1,16 @@
-#include <nvector/nvector_serial.h>
-#include <stdio.h>
-#include <unistd.h>
-
-#include "handlers/handlers.h"
 #include "handlers/solve.h"
 
 #include <config.h>
+#include <nvector/nvector_serial.h>
+#include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 #include <sunmatrix/sunmatrix_dense.h>
+#include <unistd.h>
 
-#include "functions.h"
 #include "cuqdyn.h"
+#include "functions.h"
+#include "handlers/handlers.h"
 
 #if defined(MPI) || defined(MPI2)
 #include <mpi.h>
diff --git a/modules/cli/src/handlers/version.c b/modules/cli/src/handlers/version.c
@@ -15,10 +15,11 @@ Handler create_version_handler()
 
 int handle_version(int argc, char *argv[])
 {
-    const char *help_message = "- [Version] -\n"
-                               "cli        %s  —  Command line interface for the CUQDYN algorithm (by Borja Castellano)\n"
-                               "cuqdyn-c   %s  —  C implementation of the CUQDYN algorithm (by Borja Castellano)\n"
-                               "sacess     %s  —  C implementation of the Scatter Search algorithm\n";
+    const char *help_message =
+            "- [Version] -\n"
+            "cli        %s  —  Command line interface for the CUQDYN algorithm (by Borja Castellano)\n"
+            "cuqdyn-c   %s  —  C implementation of the CUQDYN algorithm (by Borja Castellano)\n"
+            "sacess     %s  —  C implementation of the Scatter Search algorithm\n";
 
     return printf(help_message, CLI_VERSION, CUQDYN_C_VERSION, SACESS_C_VERSION);
 }
diff --git a/modules/cuqdyn-c/include/config.h b/modules/cuqdyn-c/include/config.h
@@ -13,19 +13,19 @@ typedef struct
 {
     int y_count;
     int p_count;
-    char** exprs;
+    char **exprs;
 } OdeExpr;
 
 typedef struct
 {
     int len;
-    double* array;
+    double *array;
 } Y0;
 
 typedef struct
 {
     int count;
-    char** exprs;
+    char **exprs;
 } StatesTransformer;
 
 typedef struct
@@ -36,12 +36,12 @@ typedef struct
     StatesTransformer states_transformer;
 } CuqdynConf;
 
-typedef void* CuqDynContext;
+typedef void *CuqDynContext;
 
 CuqDynContext init_cuqdyn_context_from_file(const char *filename);
 CuqDynContext get_cuqdyn_context();
 
 extern CuqdynConf *get_cuqdyn_conf(CuqDynContext context);
 extern void destroy_cuqdyn_context(CuqDynContext context);
 
-#endif //CONFIG_H
+#endif // CONFIG_H
diff --git a/modules/cuqdyn-c/include/cuqdyn.h b/modules/cuqdyn-c/include/cuqdyn.h
@@ -1,18 +1,18 @@
 #ifndef CUQDYN_H
 #define CUQDYN_H
 
-#include <sundials/sundials_nvector.h>
 #include <sundials/sundials_matrix.h>
+#include <sundials/sundials_nvector.h>
 
 #define NewDenseMatrix(m, n) SUNDenseMatrix(m, n, get_sundials_ctx())
 #define New_Serial(n) N_VNew_Serial(n, get_sundials_ctx())
 
 typedef SUNMatrix States;
 /*
-*   TransposedStates where:
-*   - Each col corresponds to a time point
-*   - Rows 0-n: Solution components (y1, y2, ..., yn)
-*/
+ *   TransposedStates where:
+ *   - Each col corresponds to a time point
+ *   - Rows 0-n: Solution components (y1, y2, ..., yn)
+ */
 typedef SUNMatrix TransposedStates;
 typedef SUNMatrix ObservablesStates;
 typedef SUNMatrix ObservablesTransposedStates;
@@ -31,9 +31,9 @@ typedef struct
     N_Vector times;
 } CuqdynResult;
 
-CuqdynResult* create_cuqdyn_result(SUNMatrix predicted_data_median, N_Vector predicted_params_median,
-    SUNMatrix q_low, SUNMatrix q_up, N_Vector times);
-void destroy_cuqdyn_result(CuqdynResult* result);
+CuqdynResult *create_cuqdyn_result(SUNMatrix predicted_data_median, N_Vector predicted_params_median, SUNMatrix q_low,
+                                   SUNMatrix q_up, N_Vector times);
+void destroy_cuqdyn_result(CuqdynResult *result);
 CuqdynResult *cuqdyn_algo(const char *data_file, const char *sacess_conf_file, const char *output_file);
 
 typedef struct
@@ -42,7 +42,7 @@ typedef struct
     long len;
 } LongArray;
 
-LongArray create_array(long * values, long len);
+LongArray create_array(long *values, long len);
 LongArray create_empty_array();
 long array_get_index(LongArray array, long index);
 
diff --git a/modules/cuqdyn-c/include/data_reader.h b/modules/cuqdyn-c/include/data_reader.h
@@ -3,6 +3,7 @@
 
 #include <sundials/sundials_nvector.h>
 #include <sunmatrix/sunmatrix_dense.h>
+
 #include "cuqdyn.h"
 
 /* This function wich type of data file is being read (.txt or .mat) and
@@ -33,4 +34,4 @@ int read_data_file(const char *data_file, N_Vector *t, ObservedData *y);
  */
 int read_txt_data_file(const char *data_file, N_Vector *t, ObservedData *y);
 
-#endif //FILE_READER_H
+#endif // FILE_READER_H
diff --git a/modules/cuqdyn-c/include/ess_solver.h b/modules/cuqdyn-c/include/ess_solver.h
@@ -6,7 +6,7 @@
 /// texp, yexp and initial_condition are arguments needed to execute the objective functions, like
 /// the one defined in functions.c.
 /// rank and nproc are used to define the rank of the process and the number of processes in an MPI environment.
-N_Vector execute_ess_solver(const char *config_file, const char *output,
-  N_Vector texp, SUNMatrix yexp, N_Vector initial_condition, N_Vector initial_params);
+N_Vector execute_ess_solver(const char *config_file, const char *output, N_Vector texp, SUNMatrix yexp,
+                            N_Vector initial_condition, N_Vector initial_params);
 
-#endif //ESS_SOLVER_H
+#endif // ESS_SOLVER_H
diff --git a/modules/cuqdyn-c/include/functions.h b/modules/cuqdyn-c/include/functions.h
@@ -6,6 +6,6 @@
 /// Function used to solve the ODE using cvodes
 int ode_model_fun(sunrealtype t, N_Vector y, N_Vector ydot, void *data);
 /// Objetive function for the lotka_volterra problem used by the sacess library
-void* obj_func(double *x, void *data);
+void *obj_func(double *x, void *data);
 
-#endif //LOTKA_VOLTERRA_H
+#endif // LOTKA_VOLTERRA_H
diff --git a/modules/cuqdyn-c/include/matlab.h b/modules/cuqdyn-c/include/matlab.h
@@ -54,4 +54,4 @@ SUNMatrix subtract_two_matrices(SUNMatrix a, SUNMatrix b);
  * quantile assigns the minimum or maximum values of the elements in A.
  */
 sunrealtype quantile(N_Vector, sunrealtype);
-#endif //MATLAB_H
+#endif // MATLAB_H
diff --git a/modules/cuqdyn-c/include/ode_solver.h b/modules/cuqdyn-c/include/ode_solver.h
@@ -2,10 +2,11 @@
 #define EDO_SOLVER_H
 
 #include <nvector/nvector_serial.h>
-#include <sundials/sundials_types.h>
 #include <sundials/sundials_matrix.h>
+#include <sundials/sundials_types.h>
+
 #include "cuqdyn.h"
 
 TransposedStates solve_ode(N_Vector parameters, N_Vector initial_values, sunrealtype t0, N_Vector times);
 
-#endif //EDO_SOLVER_H
+#endif // EDO_SOLVER_H
diff --git a/modules/cuqdyn-c/include/states_transformer.h b/modules/cuqdyn-c/include/states_transformer.h
@@ -5,10 +5,11 @@
 #ifndef STATES_TRANSFORMER_H
 #define STATES_TRANSFORMER_H
 #include <sunmatrix/sunmatrix_dense.h>
+
 #include "cuqdyn.h"
 
 /// This function destroys the transposed state matrix and returns a new transposed matrix with the observables
 /// states if a transformation expr is defined in the config XML.
 ObservablesTransposedStates transform_states(TransposedStates states);
 
-#endif //STATES_TRANSFORMER_H
+#endif // STATES_TRANSFORMER_H
diff --git a/modules/cuqdyn-c/src/config.c b/modules/cuqdyn-c/src/config.c
@@ -1,4 +1,5 @@
 #include "config.h"
+
 #include <unistd.h>
 
 static CuqDynContext context = NULL;
diff --git a/modules/cuqdyn-c/src/cuqdyn.c b/modules/cuqdyn-c/src/cuqdyn.c
@@ -100,15 +100,16 @@ CuqdynResult *cuqdyn_algo(const char *data_file, const char *sacess_conf_file, c
         resid_loo = NewDenseMatrix(m, n);
         predicted_params_matrix = NewDenseMatrix(m, config->ode_expr.p_count);
 
-        N_Vector texp = copy_vector_remove_indices(times, create_array((long[]) {}, 0));
-        SUNMatrix yexp = copy_matrix_remove_rows(observed_data, create_array((long[]) {}, 0));
+        N_Vector texp = copy_vector_remove_indices(times, create_array((long[]){}, 0));
+        SUNMatrix yexp = copy_matrix_remove_rows(observed_data, create_array((long[]){}, 0));
 
-        N_Vector tmp_initial_condition = copy_vector_remove_indices(initial_condition, create_array((long[]) {}, 0));
+        N_Vector tmp_initial_condition = copy_vector_remove_indices(initial_condition, create_array((long[]){}, 0));
 
         N_Vector predicted_params =
-            execute_ess_solver(sacess_conf_file, output_file, texp, yexp, tmp_initial_condition, NULL);
+                execute_ess_solver(sacess_conf_file, output_file, texp, yexp, tmp_initial_condition, NULL);
 
-        memcpy(NV_DATA_S(initial_params), NV_DATA_S(predicted_params), NV_LENGTH_S(predicted_params) * sizeof(sunrealtype));
+        memcpy(NV_DATA_S(initial_params), NV_DATA_S(predicted_params),
+               NV_LENGTH_S(predicted_params) * sizeof(sunrealtype));
         N_VDestroy(predicted_params);
     }
 
@@ -154,12 +155,12 @@ CuqdynResult *cuqdyn_algo(const char *data_file, const char *sacess_conf_file, c
 
     for (long i = start_index; i < end_index; ++i)
     {
-        LongArray indices_to_remove = create_array((long[]) {i + 1}, 1);
+        LongArray indices_to_remove = create_array((long[]){i + 1}, 1);
 
         N_Vector texp = copy_vector_remove_indices(times, indices_to_remove);
         SUNMatrix yexp = copy_matrix_remove_columns(observed_data, indices_to_remove);
 
-        N_Vector tmp_initial_condition = copy_vector_remove_indices(initial_condition, create_array((long[]) {}, 0));
+        N_Vector tmp_initial_condition = copy_vector_remove_indices(initial_condition, create_array((long[]){}, 0));
 
         N_Vector predicted_params =
                 execute_ess_solver(sacess_conf_file, output_file, texp, yexp, tmp_initial_condition, initial_params);
@@ -205,16 +206,20 @@ CuqdynResult *cuqdyn_algo(const char *data_file, const char *sacess_conf_file, c
                 MPI_Recv(&slaved_index, 1, MPI_LONG, slave, 0, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
 
                 // Receriving the residuals of other processes
-                MPI_Recv(NV_DATA_S(residuals), NV_LENGTH_S(residuals), MPI_DOUBLE, slave, 1, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
+                MPI_Recv(NV_DATA_S(residuals), NV_LENGTH_S(residuals), MPI_DOUBLE, slave, 1, MPI_COMM_WORLD,
+                         MPI_STATUS_IGNORE);
                 set_matrix_row(resid_loo, residuals, slaved_index, 0, NV_LENGTH_S(residuals));
 
                 // Receiving the predicted data matrix
-                MPI_Recv(SM_DATA_D(predicted_data), predicted_data_len, MPI_DOUBLE, slave, 2, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
+                MPI_Recv(SM_DATA_D(predicted_data), predicted_data_len, MPI_DOUBLE, slave, 2, MPI_COMM_WORLD,
+                         MPI_STATUS_IGNORE);
                 matrix_array_set_index(media_matrix, slaved_index - 1, predicted_data);
 
                 // Receiving the predicted params
-                MPI_Recv(NV_DATA_S(predicted_params), NV_LENGTH_S(predicted_params), MPI_DOUBLE, slave, 3, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
-                set_matrix_row(predicted_params_matrix, predicted_params, slaved_index, 0, NV_LENGTH_S(predicted_params));
+                MPI_Recv(NV_DATA_S(predicted_params), NV_LENGTH_S(predicted_params), MPI_DOUBLE, slave, 3,
+                         MPI_COMM_WORLD, MPI_STATUS_IGNORE);
+                set_matrix_row(predicted_params_matrix, predicted_params, slaved_index, 0,
+                               NV_LENGTH_S(predicted_params));
             }
         }
 #endif
@@ -227,7 +232,7 @@ CuqdynResult *cuqdyn_algo(const char *data_file, const char *sacess_conf_file, c
         SUNMatDestroy(predicted_obs_states);
     }
 
-N_VDestroy(residuals);
+    N_VDestroy(residuals);
 
 #ifdef MPI
     printf("%ld iterations of rank %d finalized\n", iterations, rank);
diff --git a/modules/cuqdyn-c/src/data_reader.c b/modules/cuqdyn-c/src/data_reader.c
@@ -1,12 +1,11 @@
 #include "data_reader.h"
 
-
 #include <nvector/nvector_serial.h>
 #include <stddef.h>
 #include <stdio.h>
 #include <string.h>
 
-#include "../include/cuqdyn.h"
+#include "cuqdyn.h"
 #include "sundials/sundials_types.h"
 #include "sunmatrix/sunmatrix_dense.h"
 
@@ -56,7 +55,7 @@ int read_txt_data_file(const char *data_file, N_Vector *t, TransposedObservedDat
     {
         fscanf(f, "%lf", &tmp);
         data_t[i] = tmp;
-        sunrealtype *data_yi = ((SUNMatrixContent_Dense)(*y)->content)->cols[i];
+        sunrealtype *data_yi = ((SUNMatrixContent_Dense) (*y)->content)->cols[i];
         for (int j = 0; j < cols - 1; ++j)
         {
             fscanf(f, "%lf", &tmp);
diff --git a/modules/cuqdyn-c/src/ess_solver.c b/modules/cuqdyn-c/src/ess_solver.c
diff --git a/modules/cuqdyn-c/src/functions.c b/modules/cuqdyn-c/src/functions.c
diff --git a/modules/cuqdyn-c/src/matlab.c b/modules/cuqdyn-c/src/matlab.c
diff --git a/modules/cuqdyn-c/src/ode_solver.c b/modules/cuqdyn-c/src/ode_solver.c

Original file line number	Diff line number	Diff line change
`@@ -4,4 +4,4 @@`
`4`	`4`
`5`	`5`	`Handler create_help_handler();`
`6`	`6`
`7`		`-#endif //HELP_H`
	`7`	`+#endif // HELP_H`
Original file line number	Diff line number	Diff line change
`@@ -6,4 +6,4 @@`
`6`	`6`
`7`	`7`	`Handler create_solve_handler();`
`8`	`8`
`9`		`-#endif //SOLVE_H`
	`9`	`+#endif // SOLVE_H`
Original file line number	Diff line number	Diff line change
`@@ -4,4 +4,4 @@`
`4`	`4`
`5`	`5`	`Handler create_version_handler();`
`6`	`6`
`7`		`-#endif //VERSION_H`
	`7`	`+#endif // VERSION_H`
Original file line number	Diff line number	Diff line change
`@@ -7,4 +7,4 @@`
`7`	`7`
`8`	`8`	`#define VERSION "0.1.0"`
`9`	`9`
`10`		`-#endif //MAIN_H`
	`10`	`+#endif // MAIN_H`
Original file line number	Diff line number	Diff line change
`@@ -15,10 +15,11 @@ Handler create_version_handler()`
`15`	`15`
`16`	`16`	`int handle_version(int argc, char *argv[])`
`17`	`17`	`{`
`18`		`- const char *help_message = "- [Version] -\n"`
`19`		`- "cli %s — Command line interface for the CUQDYN algorithm (by Borja Castellano)\n"`
`20`		`- "cuqdyn-c %s — C implementation of the CUQDYN algorithm (by Borja Castellano)\n"`
`21`		`- "sacess %s — C implementation of the Scatter Search algorithm\n";`
	`18`	`+ const char *help_message =`
	`19`	`+ "- [Version] -\n"`
	`20`	`+ "cli %s — Command line interface for the CUQDYN algorithm (by Borja Castellano)\n"`
	`21`	`+ "cuqdyn-c %s — C implementation of the CUQDYN algorithm (by Borja Castellano)\n"`
	`22`	`+ "sacess %s — C implementation of the Scatter Search algorithm\n";`
`22`	`23`
`23`	`24`	`return printf(help_message, CLI_VERSION, CUQDYN_C_VERSION, SACESS_C_VERSION);`
`24`	`25`	`}`