src/cats/stats/global_stats.c

@@ -30,6 +30,7 @@
 #include "stats/grid_stats.h"
 #include "paths/output_paths.h"
 #include "bdc_memory/bdc_memory.h"
+#include "bdc_io/bdc_io.h"
 
 #ifdef USEMPI
 #include "mpi/mpi_stats.h"

src/cats/stats/lambda_stats.c

@@ -25,6 +25,7 @@
 #include "inline.h"
 #include "metadata.h"
 #include "inline_vital_rates.h"
+#include "bdc_io/bdc_io.h"
 
 
 FILE *

src/cats/stats/statistics.c

@@ -23,7 +23,7 @@
 #include <assert.h>
 #include <stdlib.h>
 #include "statistics.h"
-#include "cats_strings/cats_strings.h"
+#include "bdc_strings/bdc_strings.h"
 #include "bdc_memory/bdc_memory.h"
 #include "configuration/configuration.h"
 

src/cats/threading/threading-helpers.c

@@ -27,6 +27,8 @@
 #include "misc/cats_random.h"
 #include "stats/grid_stats.h"
 #include "bdc_memory/bdc_memory.h"
+#include "data/error.h"
+
 
 void create_custom_stats_for_thread(struct statistics *thread_stats, struct statistics *grid_stats)
 {

src/cats/vital_ages/default_vital_ages.c

@@ -20,7 +20,7 @@
 //
 
 #include "default_vital_ages.h"
-#include <logging/logging.h>
+#include <bdc_logging/logging.h>
 
 const char *get_vital_age_name(enum cats_vital_age_id idx)
 {

src/cats/vital_rates/setup_rates.c

@@ -21,7 +21,7 @@
 
 #include <math.h>
 #include <assert.h>
-#include <cats_strings/cats_strings.h>
+#include <bdc_strings/bdc_strings.h>
 #include "logging.h"
 #include "setup_rates.h"
 #include "string.h"

src/cats/vital_rates/vital_rate_ranges.c

@@ -21,7 +21,7 @@
 
 #include <math.h>
 #include "vital_rate_ranges.h"
-#include "logging/logging.h"
+#include "bdc_logging/logging.h"
 
 
 int check_vital_rate_hybrid(struct cats_vital_rate *vr)

src/cats_csv/CMakeLists.txt

@@ -13,4 +13,4 @@ target_sources(cats_csv
 
 
 set_property(TARGET cats_csv PROPERTY POSITION_INDEPENDENT_CODE ON)
-target_link_libraries(cats_logging bdc cats_strings)
\ No newline at end of file
+target_link_libraries(bdc_logging bdc bdc_strings)
\ No newline at end of file

src/cats_csv/cats_csv.c

@@ -26,8 +26,9 @@
 #include <string.h>
 
 #include "cats_csv.h"
-#include <logging/logging.h>
+#include <bdc_logging/logging.h>
 #include "bdc_memory/bdc_memory.h"
+#include "bdc_io/bdc_io.h"
 
 
 struct cats_csv *csv_new(char *header_line, int32_t expected_fields)
@@ -42,21 +43,21 @@ struct cats_csv *csv_new(char *header_line, int32_t expected_fields)
 
         struct string_array *headers = get_all_tokens(header_line, ",");
 
-        if (headers->count != expected_fields) {
-                log_message(LOG_ERROR, "%s: disparity in field count: got %d expected %d\n", __func__, headers->count,
+        if (get_string_count(headers) != expected_fields) {
+                log_message(LOG_ERROR, "%s: disparity in field count: got %d expected %d\n", __func__, get_string_count(headers),
                             expected_fields);
                 exit(EXIT_FAILURE);
         }
 
         struct cats_csv *result = malloc_or_die_trace(sizeof(struct cats_csv), __func__);
 
-        result->column_count = headers->count;
+        result->column_count = get_string_count(headers);
         result->data_row_count = 0;
         result->data = NULL;
         result->headers = malloc_or_die_trace(result->column_count * sizeof(char *), __func__);
 
-        for (int32_t i = 0; i < headers->count; i++) {
-                result->headers[i] = strdup(headers->string[i]);
+        for (int32_t i = 0; i < get_string_count(headers); i++) {
+                result->headers[i] = strdup(get_string(headers, i));
         }
 
         free_string_array(&headers);
@@ -224,8 +225,8 @@ void csv_add_row(struct cats_csv *csv, char *line)
 
         struct string_array *data = get_all_tokens(line, ",");
 
-        if (csv->column_count != data->count) {
-                log_message(LOG_ERROR, "%s: disparity in field count: got %d expected %d\n", __func__, data->count,
+        if (csv->column_count != get_string_count(data)) {
+                log_message(LOG_ERROR, "%s: disparity in field count: got %d expected %d\n", __func__, get_string_count(data),
                             csv->column_count);
                 exit(EXIT_FAILURE);
         }
@@ -233,14 +234,14 @@ void csv_add_row(struct cats_csv *csv, char *line)
 
         csv->data_row_count = csv->data_row_count + 1;
 
-        csv->data = realloc(csv->data, csv->data_row_count * sizeof(char **));
+        csv->data = realloc_or_die(csv->data, csv->data_row_count * sizeof(char **));
 
         int32_t row = csv->data_row_count - 1;
 
         csv->data[row] = malloc_or_die_trace(fields * sizeof(char *), __func__);
 
         for (int32_t i = 0; i < csv->column_count; i++) {
-                csv->data[row][i] = strdup(data->string[i]);
+                csv->data[row][i] = strdup(get_string(data,i));
 
         }
 

src/cats_csv/cats_csv.h

@@ -24,7 +24,7 @@
 
 #include <stdint.h>
 #include <stdio.h>
-#include <cats_strings/cats_strings.h>
+#include <bdc_strings/bdc_strings.h>
 
 ///@brief Data structure for simple csv files
 struct cats_csv {

src/cats_ini/CMakeLists.txt

@@ -18,4 +18,4 @@ target_sources(cats_ini
 
 
 set_property(TARGET cats_ini PROPERTY POSITION_INDEPENDENT_CODE ON)
-target_link_libraries(cats_logging cats_strings bdc)
+target_link_libraries(bdc_strings bdc_logging bdc)

src/cats_ini/cats_ini.c

@@ -28,8 +28,8 @@
 #include <string.h>
 #include <stddef.h>
 
-#include <cats_strings/cats_strings.h>
-#include <logging/logging.h>
+#include <bdc_strings/bdc_strings.h>
+#include <bdc_logging/logging.h>
 #include "cats_ini.h"
 
 

src/cats_ini/cats_ini_helpers.c

@@ -25,7 +25,7 @@
 #include "cats_ini_helpers.h"
 #include "cats_ini_write_values.h"
 #include "misc/misc.h"
-#include <logging/logging.h>
+#include <bdc_logging/logging.h>
 
 void add_complement_value_read(struct cats_ini *ini, char *section, char *key)
 {

src/cats_ini/cats_ini_read_values.c

@@ -22,12 +22,10 @@
 #include <assert.h>
 #include <stdlib.h>
 #include <string.h>
-#include "../logging/logging.h"
+#include "bdc_logging/logging.h"
 #include "cats_ini.h"
-#include "../cats_strings/cats_strings.h"
+#include "bdc_strings/bdc_strings.h"
 #include "cats_ini_read_values.h"
-
-#include "../cats_strings/string_helpers.h"
 #include "cats_ini_helpers.h"
 #include <stdio.h>
 

src/cats_ini/cats_ini_write_values.c

@@ -20,10 +20,9 @@
 //
 
 #include "cats_ini_helpers.h"
-#include "../cats_strings/string_helpers.h"
 #include "cats_ini.h"
-#include "../logging/logging.h"
-#include "../cats_strings/cats_strings.h"
+#include "bdc_logging/logging.h"
+#include "bdc_strings/bdc_strings.h"
 #include <stddef.h>
 #include <string.h>
 #include <stdlib.h>

src/cats_strings/CMakeLists.txt

-add_library(cats_strings STATIC "" ../cats_defs.h ../cats_windows.h string_converters.c string_converters.h)
-
-target_sources(cats_strings
-               PRIVATE
-               cats_strings.c
-               io_text.c
-               string_helpers.c
-               pretty_print.c
-               PUBLIC
-               cats_strings.h
-               io_text.h
-               pretty_print.h
-               string_helpers.h
-               )
-
-set_property(TARGET cats_strings PROPERTY POSITION_INDEPENDENT_CODE ON)
-target_link_libraries(cats_logging cats_time)
\ No newline at end of file

src/cats_strings/pretty_print.h

-// SPDX-License-Identifier: GPL-3.0-or-later
-//
-// pretty_print.h
-//
-// Copyright (C) 2011-2024, University of Vienna and Vienna Institute for Nature Conservation & Analyses, Andreas Gattringer.
-//
-// This program is free software; you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation; either version 3 of the License, or (at
-// your option) any later version.
-//
-// This program is distributed in the hope that it will be useful, but
-// WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-// General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with this program; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-//
-
-#ifndef CATS_PRETTY_PRINT_H
-#define CATS_PRETTY_PRINT_H
-
-#endif //CATS_PRETTY_PRINT_H

src/cats_time/CMakeLists.txt

-add_library(cats_time STATIC "" ../cats_defs.h ../cats_windows.h)
-
-target_sources(cats_time
-               PRIVATE
-               cats_time.c cats_time.h
-               )
-
-set_property(TARGET cats_time PROPERTY POSITION_INDEPENDENT_CODE ON)
-target_link_libraries(cats_time)
\ No newline at end of file

src/modules/butterflies/CMakeLists.txt

@@ -24,4 +24,4 @@ target_sources(cats-butterflies
 
 
 set_property(TARGET cats-butterflies PROPERTY POSITION_INDEPENDENT_CODE ON)
-target_link_libraries(cats-butterflies cats_logging libcats)
+target_link_libraries(cats-butterflies bdc_logging libcats)

src/modules/butterflies/butterflies_main.c

@@ -39,6 +39,7 @@ struct cats_debug_options cats_debug;
 #include "lambda/leslie_matrix.h"
 #include "actions/setup_actions.h"
 #include "butterflies_scale.h"
+#include "bdc_io/bdc_io.h"
 
 
 cats_dt_rates bf_expected_local_eggs_per_female(struct cats_configuration *conf, struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col)