src/cats/grids/gdal_helper.c

@@ -26,7 +26,7 @@
 #include <cpl_string.h>
 #include <assert.h>
 
-#include <logging/logging.h>
+#include <bdc_logging/logging.h>
 #include "gdal_load.h"
 #include "configuration/configuration.h"
 #include "misc/misc.h"
@@ -167,7 +167,7 @@ void verify_raster_geometry(GDALDatasetH dataset, struct simulation_geometry *ge
                 log_message(LOG_INFO, "GEOM: global projection string not set, ignoring projection '%s'", projection);
         } else {
                 if (strcmp(projection, geometry->projection_string) != 0) {
-                        enum cats_log_level ll;
+                        enum bdc_log_level ll;
                         if (geometry->ignore_raster_projection) {
                                 ll = LOG_INFO;
                         } else {

src/cats/hybrid/scalefactor.c

@@ -29,7 +29,7 @@
 #endif
 
 #include <cats_ini/cats_ini.h>
-#include <logging/logging.h>
+#include <bdc_logging/logging.h>
 
 #include "cats/command_line/command_line_options.h"
 #include "configuration/load_vital_rates.h"

src/cats/inline_population.h

@@ -26,7 +26,7 @@
 #include "cats_global.h"
 #include <math.h>
 #include "data/cats_datatypes.h"
-#include "logging/logging.h"
+#include "bdc_logging/logging.h"
 #include "assert.h"
 #include "configuration/configuration.h"
 #include "inline_overlays.h"

src/cats/lambda/eigen.c

@@ -25,7 +25,7 @@
 #include <stdbool.h>
 #include <math.h>
 
-#include <logging/logging.h>
+#include <bdc_logging/logging.h>
 #include "eigen.h"
 #include "matrix_helpers.h"
 #include "inline.h"

src/cats/lambda/leslie_matrix.c

@@ -24,7 +24,7 @@
 #include "dispersal/dispersal.h"
 #include "leslie_matrix.h"
 #include "bdc_memory/bdc_memory.h"
-#include "logging/logging.h"
+#include "bdc_logging/logging.h"
 #include "configuration/configuration.h"
 #include "inline.h"
 #include "matrix_helpers.h"

src/cats/lambda/matrix_helpers.c

@@ -21,7 +21,7 @@
 //
 
 #include <assert.h>
-#include <logging/logging.h>
+#include <bdc_logging/logging.h>
 #include "bdc_memory/bdc_memory.h"
 #include "cats_global.h"
 

src/cats/misc/debug.c

@@ -24,6 +24,7 @@
 #include "misc.h"
 #include "inline.h"
 #include "bdc_memory/bdc_memory.h"
+#include "bdc_io/bdc_io.h"
 
 
 void

src/cats/misc/filesystem.c

@@ -25,7 +25,7 @@
 #include <errno.h>
 #include <string.h>
 
-#include <logging/logging.h>
+#include <bdc_logging/logging.h>
 #include "filesystem.h"
 #include "data/error.h"
 #ifndef CATS_ON_WINDOWS

src/cats/misc/misc.h

@@ -24,20 +24,12 @@
 
 #include <string.h>
 #include "data/error.h"
+
 #define TEXT_DIVIDER "=================================================================================================="
 
 const char *cats_version(void);
 
 
-// this is kept as a macro, so we can print calling function
-#define ENSURE_FILE_OPENED(FILE_HANDLE, FILENAME)\
-if (! (FILE_HANDLE))\
-{\
-        fprintf(stderr, "ERROR: Couldn't open file %s in %s: %d (%s)\n", FILENAME, __FILE__, __LINE__, __func__);\
-        exit(E_UNREADABLE_FILE);\
-}
-
-
 void set_program_name(const char *name);
 
 #endif
\ No newline at end of file

src/cats/modules/load_module.c

@@ -20,7 +20,7 @@
 //
 
 #include <dlfcn.h>
-#include <logging/logging.h>
+#include <bdc_logging/logging.h>
 #include <string.h>
 #include "configuration/configuration.h"
 #include "load_module.h"

src/cats/modules/modules.c

@@ -24,7 +24,7 @@
 #include <string.h>
 #include <stdlib.h>
 #include "modules.h"
-#include "cats_strings/cats_strings.h"
+#include "bdc_strings/bdc_strings.h"
 
 void init_cats_module(struct cats_module *module, int32_t id)
 {

src/cats/mpi/mpi_debug.c

@@ -26,6 +26,7 @@
 #include "mpi_debug.h"
 #include "mpi_grid_helpers.h"
 #include "paths/output_paths.h"
+#include "bdc_io/bdc_io.h"
 
 
 char *get_node_name(const struct cats_configuration *conf)

src/cats/overlays/overlays.c

@@ -93,8 +93,8 @@ enum overlay_type get_overlay_type_from_name(const char *name, const struct stri
         if (!strcmp(name, "resources")) return OL_RESOURCE;
 
         if (registered_names != NULL) {
-                for (int32_t i = 0; i < registered_names->count; i++) {
-                        if (!strcmp(name, registered_names->string[i])) {
+                for (int32_t i = 0; i < get_string_count(registered_names); i++) {
+                        if (!strcmp(name, get_string(registered_names,i))) {
                                 return OL_CUSTOM;
                         }
                 }

src/cats/paths/directory_helper.c

@@ -22,7 +22,7 @@
 #include "cats_global.h"
 
 #include <string.h>
-#include <logging/logging.h>
+#include <bdc_logging/logging.h>
 #include "misc/filesystem.h"
 #include "paths/paths.h"
 #include "paths/output_paths.h"
@@ -32,7 +32,7 @@
 
 bool check_and_create_directory_if_needed(const struct string_array *path)
 {
-        if (path == NULL || path->count == 0) {
+        if (path == NULL || get_string_count(path) == 0) {
                 fprintf(stderr, "Unable to check directory - no path specified\n");
                 log_message(LOG_ERROR, "\tunable to check directory - no path specified");
                 exit_cats(E_SYSTEM_ERROR);
@@ -94,8 +94,8 @@ void ensure_needed_directories_exist(const struct cats_configuration *conf, cons
         struct string_array *output = new_string_array_init(conf->output.output_directory);
         check_and_create_directory_if_needed(output);
         free_string_array(&output);
-        for (int32_t i = 0; i < output_dirs->count; i++) {
-                struct string_array *path = get_output_directory(conf, output_dirs->string[i]);
+        for (int32_t i = 0; i < get_string_count(output_dirs); i++) {
+                struct string_array *path = get_output_directory(conf, get_string(output_dirs,i));
                 check_and_create_directory_if_needed(path);
                 free_string_array(&path);
 

src/cats/paths/output_paths.c

@@ -22,7 +22,7 @@
 #include <string.h>
 #include <assert.h>
 
-#include <logging/logging.h>
+#include <bdc_logging/logging.h>
 
 #include "data/cats_grid.h"
 #include "temporal/phase_names.h"
@@ -30,6 +30,7 @@
 
 #include "output_paths.h"
 #include "paths.h"
+#include "bdc_io/bdc_io.h"
 
 
 const char *get_base_output_directory(const struct cats_configuration *conf)

src/cats/paths/paths.c

@@ -28,7 +28,7 @@
 #include "cats_global.h"
 #include "data/cats_grid.h"
 #include "configuration/configuration.h"
-#include "cats_strings/cats_strings.h"
+#include "bdc_strings/bdc_strings.h"
 
 
 #include "temporal/phase_names.h"
@@ -60,7 +60,7 @@ char *assemble_filename(struct string_array *path, struct string_array *filename
         char *name_string = string_array_paste(filename, filesep);
         char *result = NULL;
 
-        if (path && path->count > 0) {
+        if (path && get_string_count(path) > 0) {
                 char *path_string = string_array_paste(path, "/");
                 if (extension && strlen(extension)) {
                         char *fn = compound_string(name_string, extension, ".");

src/cats/paths/paths.h

@@ -22,7 +22,7 @@
 #pragma once
 
 #include <stdint.h>
-#include <cats_strings/cats_strings.h>
+#include <bdc_strings/bdc_strings.h>
 
 struct cats_configuration;
 struct cats_environment_variable;

src/cats/paths/paths_suitability.c

@@ -26,6 +26,7 @@
 #include "temporal/timeformat.h"
 #include "data/species_parameters.h"
 #include "path_patterns.h"
+#include "bdc_io/bdc_io.h"
 
 
 char *

src/cats/performance/timer.c

@@ -54,9 +54,9 @@ struct timeval *time_difference(struct timeval *start, struct timeval *end)
 }
 
 
-struct cats_timer start_new_timer(void)
+struct bdc_timer start_new_timer(void)
 {
-        struct cats_timer t = {0};
+        struct bdc_timer t = {0};
         t.start_clock = clock();
         //gettimeofday(&t.start_timeval, NULL);
         get_time(&t.start_timeval);
@@ -64,7 +64,7 @@ struct cats_timer start_new_timer(void)
 }
 
 
-void start_timer(struct cats_timer *t)
+void start_timer(struct bdc_timer *t)
 {
         assert(t != NULL);
         t->start_clock = clock();
@@ -73,7 +73,7 @@ void start_timer(struct cats_timer *t)
 }
 
 
-void stop_timer(struct cats_timer *t)
+void stop_timer(struct bdc_timer *t)
 {
         assert(t != NULL);
         clock_t now = clock();
@@ -97,7 +97,7 @@ void stop_timer(struct cats_timer *t)
 }
 
 
-void log_timer(const struct cats_timer *t, const char *string, int loglevel, const struct simulation_time *time,
+void log_timer(const struct bdc_timer *t, const char *string, int loglevel, const struct simulation_time *time,
                const struct cats_configuration *conf)
 {
         const char *phase_default = "?";
@@ -117,7 +117,7 @@ void log_timer(const struct cats_timer *t, const char *string, int loglevel, con
 }
 
 
-void stop_and_log_timer(struct cats_timer *t, const char *string, int loglevel, const struct simulation_time *time,
+void stop_and_log_timer(struct bdc_timer *t, const char *string, int loglevel, const struct simulation_time *time,
                         const struct cats_configuration *conf)
 {
         stop_timer(t);
@@ -127,7 +127,7 @@ void stop_and_log_timer(struct cats_timer *t, const char *string, int loglevel,
 
 
 void
-stop_log_and_restart_timer(struct cats_timer *t, const char *string, int loglevel, const struct simulation_time *time,
+stop_log_and_restart_timer(struct bdc_timer *t, const char *string, int loglevel, const struct simulation_time *time,
                            const struct cats_configuration *conf)
 {
         stop_timer(t);

src/cats/performance/timer.h

@@ -22,28 +22,23 @@
 #pragma once
 
 #include "configuration/configuration.h"
+#include "bdc_time/bdc_time.h"
 
-struct cats_timer {
-        clock_t start_clock;
-        struct timeval start_timeval;
-        double time_normal;
-        double time_real;
-};
 
 struct simulation_time;
 
-struct cats_timer start_new_timer(void);
+struct bdc_timer start_new_timer(void);
 
-void log_timer(const struct cats_timer *t, const char *string, int loglevel, const struct simulation_time *time,
+void log_timer(const struct bdc_timer *t, const char *string, int loglevel, const struct simulation_time *time,
                const struct cats_configuration *conf);
 
-void start_timer(struct cats_timer *t);
+void start_timer(struct bdc_timer *t);
 
-void stop_timer(struct cats_timer *t);
+void stop_timer(struct bdc_timer *t);
 
-void stop_and_log_timer(struct cats_timer *t, const char *string, int loglevel, const struct simulation_time *time,
+void stop_and_log_timer(struct bdc_timer *t, const char *string, int loglevel, const struct simulation_time *time,
                         const struct cats_configuration *conf);
 
 void
-stop_log_and_restart_timer(struct cats_timer *t, const char *string, int loglevel, const struct simulation_time *time,
+stop_log_and_restart_timer(struct bdc_timer *t, const char *string, int loglevel, const struct simulation_time *time,
                            const struct cats_configuration *conf);
\ No newline at end of file