From 4da5e4b8bd5e3af8192040e18148905a84106008 Mon Sep 17 00:00:00 2001
From: Andreas Gattringer <andreas.gattringer@univie.ac.at>
Date: Tue, 30 Jan 2024 18:15:07 +0100
Subject: [PATCH] refactoring: added libbdc/bdc_io, bdc_strings, bdc_hashtable
and bdc_logging
---
libbdc/CMakeLists.txt | 8 +
libbdc/bdc_hashtable/CMakeLists.txt | 10 +
libbdc/bdc_hashtable/bdc_hashtable.c | 476 ++++++++++++++++++
libbdc/bdc_hashtable/bdc_hashtable.h | 88 ++++
.../bdc_hashtable/tests/test_bdc_hashtable.c | 52 ++
libbdc/bdc_io/CMakeLists.txt | 13 +
.../io_text.c => libbdc/bdc_io/bdc_io.c | 25 +-
libbdc/bdc_io/bdc_io.h | 56 +++
libbdc/bdc_io/bdc_paths.c | 136 +++++
libbdc/bdc_logging/CMakeLists.txt | 12 +
libbdc/bdc_logging/README.md | 10 +
{src/logging => libbdc/bdc_logging}/logging.c | 114 ++---
{src/logging => libbdc/bdc_logging}/logging.h | 27 +-
libbdc/bdc_strings/CMakeLists.txt | 18 +
libbdc/bdc_strings/README.md | 9 +
.../bdc_strings/bdc_strings.c | 113 ++++-
.../bdc_strings/bdc_strings.h | 127 +++--
.../bdc_strings}/pretty_print.c | 9 +-
.../bdc_strings}/string_converters.c | 16 +-
.../bdc_strings}/string_helpers.c | 28 +-
libbdc/bdc_strings/string_substitution.c | 158 ++++++
libbdc/bdc_time/bdc_time.c | 42 +-
libbdc/bdc_time/bdc_time.h | 42 +-
libbdc/bdc_time/bdc_timer.c | 21 +
src/CMakeLists.txt | 3 +-
src/cats/CMakeLists.txt | 10 +-
src/cats/actions/setup_actions.c | 2 +-
src/cats/cats.c | 2 +-
src/cats/command_line/command_line_info.c | 2 +-
src/cats/command_line/command_line_options.h | 4 +-
src/cats/configuration/load_config_spatial.c | 10 +-
src/cats/configuration/load_configuration.c | 3 +-
.../load_configuration_dispersal.c | 25 +-
.../load_configuration_environments.c | 14 +-
.../configuration/load_configuration_glm.c | 18 +-
.../configuration/load_configuration_helper.c | 10 +-
.../load_configuration_modules.c | 4 +-
.../load_configuration_overlays.c | 10 +-
.../load_configuration_species_params.c | 18 +-
src/cats/data/cats_datatypes.c | 4 +-
src/cats/data/cats_datatypes.h | 2 +-
src/cats/data/cats_global.c | 2 +-
src/cats/data/simulation_geometry.c | 2 +-
src/cats/debug/debug.c | 3 +-
src/cats/debug/debug_vital_rates.c | 1 +
src/cats/environment/environment.c | 2 +-
src/cats/environment/environment_registry.c | 8 +-
src/cats/environment/environment_registry.h | 2 +-
src/cats/environment/environment_set.c | 10 +-
src/cats/environment/load_environment.c | 2 +-
src/cats/grids/cats_grid.c | 1 +
src/cats/grids/gdal_helper.c | 4 +-
src/cats/hybrid/scalefactor.c | 2 +-
src/cats/inline_population.h | 2 +-
src/cats/lambda/eigen.c | 2 +-
src/cats/lambda/leslie_matrix.c | 2 +-
src/cats/lambda/matrix_helpers.c | 2 +-
src/cats/misc/debug.c | 1 +
src/cats/misc/filesystem.c | 2 +-
src/cats/misc/misc.h | 10 +-
src/cats/modules/load_module.c | 2 +-
src/cats/modules/modules.c | 2 +-
src/cats/mpi/mpi_debug.c | 1 +
src/cats/overlays/overlays.c | 4 +-
src/cats/paths/directory_helper.c | 8 +-
src/cats/paths/output_paths.c | 3 +-
src/cats/paths/paths.c | 4 +-
src/cats/paths/paths.h | 2 +-
src/cats/paths/paths_suitability.c | 1 +
src/cats/stats/global_stats.c | 1 +
src/cats/stats/lambda_stats.c | 1 +
src/cats/stats/statistics.c | 2 +-
src/cats/threading/threading-helpers.c | 2 +
src/cats/vital_ages/default_vital_ages.c | 2 +-
src/cats/vital_rates/setup_rates.c | 2 +-
src/cats/vital_rates/vital_rate_ranges.c | 2 +-
src/cats_csv/CMakeLists.txt | 2 +-
src/cats_csv/cats_csv.c | 21 +-
src/cats_csv/cats_csv.h | 2 +-
src/cats_ini/CMakeLists.txt | 2 +-
src/cats_ini/cats_ini.c | 4 +-
src/cats_ini/cats_ini_helpers.c | 2 +-
src/cats_ini/cats_ini_read_values.c | 6 +-
src/cats_ini/cats_ini_write_values.c | 5 +-
src/cats_strings/CMakeLists.txt | 17 -
src/cats_strings/io_text.h | 26 -
src/cats_strings/pretty_print.h | 25 -
src/cats_strings/string_converters.h | 39 --
src/cats_strings/string_helpers.h | 26 -
src/logging/CMakeLists.txt | 12 -
src/modules/butterflies/CMakeLists.txt | 2 +-
src/modules/butterflies/butterflies_main.c | 1 +
src/modules/butterflies/butterflies_paths.c | 2 +
src/modules/butterflies/butterflies_stats.c | 1 +
src/modules/cats_test_module/CMakeLists.txt | 2 +-
src/tests/CMakeLists.txt | 4 +-
src/tests/csv_test.c | 3 +-
97 files changed, 1547 insertions(+), 507 deletions(-)
create mode 100644 libbdc/bdc_hashtable/CMakeLists.txt
create mode 100644 libbdc/bdc_hashtable/bdc_hashtable.c
create mode 100644 libbdc/bdc_hashtable/bdc_hashtable.h
create mode 100644 libbdc/bdc_hashtable/tests/test_bdc_hashtable.c
create mode 100644 libbdc/bdc_io/CMakeLists.txt
rename src/cats_strings/io_text.c => libbdc/bdc_io/bdc_io.c (75%)
create mode 100644 libbdc/bdc_io/bdc_io.h
create mode 100644 libbdc/bdc_io/bdc_paths.c
create mode 100644 libbdc/bdc_logging/CMakeLists.txt
create mode 100644 libbdc/bdc_logging/README.md
rename {src/logging => libbdc/bdc_logging}/logging.c (58%)
rename {src/logging => libbdc/bdc_logging}/logging.h (66%)
create mode 100644 libbdc/bdc_strings/CMakeLists.txt
create mode 100644 libbdc/bdc_strings/README.md
rename src/cats_strings/cats_strings.c => libbdc/bdc_strings/bdc_strings.c (80%)
rename src/cats_strings/cats_strings.h => libbdc/bdc_strings/bdc_strings.h (52%)
rename {src/cats_strings => libbdc/bdc_strings}/pretty_print.c (95%)
rename {src/cats_strings => libbdc/bdc_strings}/string_converters.c (94%)
rename {src/cats_strings => libbdc/bdc_strings}/string_helpers.c (90%)
create mode 100644 libbdc/bdc_strings/string_substitution.c
delete mode 100644 src/cats_strings/CMakeLists.txt
delete mode 100644 src/cats_strings/io_text.h
delete mode 100644 src/cats_strings/pretty_print.h
delete mode 100644 src/cats_strings/string_converters.h
delete mode 100644 src/cats_strings/string_helpers.h
delete mode 100644 src/logging/CMakeLists.txt
diff --git a/libbdc/CMakeLists.txt b/libbdc/CMakeLists.txt
index 3a0a1b2..0ecb214 100644
--- a/libbdc/CMakeLists.txt
+++ b/libbdc/CMakeLists.txt
@@ -32,7 +32,11 @@ endif ()
add_subdirectory(bdc_cross_platform)
+add_subdirectory(bdc_hashtable)
+add_subdirectory(bdc_io)
+add_subdirectory(bdc_logging)
add_subdirectory(bdc_memory)
+add_subdirectory(bdc_strings)
add_subdirectory(bdc_time)
add_library(bdc STATIC "")
@@ -40,6 +44,10 @@ add_library(bdc STATIC "")
set_target_properties(bdc PROPERTIES LINKER_LANGUAGE C)
set_property(TARGET bdc PROPERTY POSITION_INDEPENDENT_CODE ON)
target_link_libraries(bdc
+ bdc_hashtable
+ bdc_io
+ bdc_logging
bdc_memory
+ bdc_strings
bdc_time)
diff --git a/libbdc/bdc_hashtable/CMakeLists.txt b/libbdc/bdc_hashtable/CMakeLists.txt
new file mode 100644
index 0000000..5e11b83
--- /dev/null
+++ b/libbdc/bdc_hashtable/CMakeLists.txt
@@ -0,0 +1,10 @@
+add_library(bdc_hashtable STATIC bdc_hashtable.c bdc_hashtable.h)
+set_property(TARGET bdc_hashtable PROPERTY POSITION_INDEPENDENT_CODE ON)
+target_link_libraries(bdc_hashtable bdc_logging)
+
+
+
+add_executable(bdc_hashtable_test tests/test_bdc_hashtable.c)
+
+
+target_link_libraries(bdc_hashtable_test bdc_strings)
\ No newline at end of file
diff --git a/libbdc/bdc_hashtable/bdc_hashtable.c b/libbdc/bdc_hashtable/bdc_hashtable.c
new file mode 100644
index 0000000..74975d3
--- /dev/null
+++ b/libbdc/bdc_hashtable/bdc_hashtable.c
@@ -0,0 +1,476 @@
+// SPDX-License-Identifier: GPL-3.0-or-later
+//
+// bdc_hashtable.c
+//
+// 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.
+//
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <assert.h>
+#include "bdc_hashtable.h"
+#include "bdc_logging/logging.h"
+#include "bdc_memory/bdc_memory.h"
+
+
+struct bdc_value {
+ union {
+ char *string;
+ int64_t int64;
+ double double_value;
+ void *pointer;
+ };
+ enum bdc_value_type type;
+};
+struct bdc_item {
+ char *key;
+ struct bdc_value *value;
+ struct bdc_item *next;
+};
+struct bdc_hash_table {
+ size_t item_count;
+ size_t bucket_count;
+ size_t *items_per_bucket;
+ //size_t max_items_pro_bucket;
+ struct bdc_item **items;
+
+};
+
+
+
+// FNV-1a hash, see https://en.wikipedia.org/wiki/Fowler%E2%80%93Noll%E2%80%93Vo_hash_function#FNV-1a_hash
+#define OFFSET 14695981039346656037UL
+#define PRIME 1099511628211UL
+
+#define DEBUG(...)
+
+// FIXME: add function to return keys
+
+uint64_t hash_function(const char *key)
+{
+ uint64_t hash = OFFSET;
+ while (*key != '\0') {
+ hash ^= (uint64_t) (unsigned char) *key;
+ hash *= PRIME;
+ key++;
+ }
+ return hash;
+}
+
+
+__attribute__((unused)) size_t hash_index(const char *key, size_t buckets)
+{
+ return (size_t) hash_function(key) & (buckets - 1);
+}
+
+
+size_t hash_idx_from_hash(uint64_t hash, size_t buckets)
+{
+ return hash & (buckets - 1);
+}
+
+
+
+struct bdc_hash_table *bdc_intern_new_hash_table(size_t buckets)
+{
+ struct bdc_hash_table *table = calloc_or_die(1, sizeof(struct bdc_hash_table));
+ table->bucket_count = buckets;
+ table->items = calloc_or_die(table->bucket_count, sizeof(struct bdc_item *));
+ table->item_count = 0;
+ //table->max_items_pro_bucket = 0;
+
+ table->items_per_bucket = calloc_or_die(table->bucket_count, sizeof(size_t));
+ DEBUG("Creating hash table with %lu buckets\n", table->bucket_count)
+
+ for (size_t i = 0; i < table->bucket_count; i++) {
+ table->items_per_bucket[i] = 0;
+ table->items[i] = NULL;
+ }
+
+ return table;
+}
+
+
+__attribute__((unused)) struct bdc_hash_table *new_hash_table(void)
+{
+ return bdc_intern_new_hash_table(MIN_SIZE);
+}
+
+
+void destroy_value(struct bdc_value **value)
+{
+ if (value == NULL || *value == NULL) return;
+ struct bdc_value *this = *value;
+ if(this->type == BDC_STRING) {
+ log_message(LOG_DEBUG, "freeing string value '%s'", this->string);
+ free(this->string);
+ this->string = NULL;
+ }
+ log_message(LOG_DEBUG, "freeing value");
+ free(this);
+ *value = NULL;
+
+}
+
+struct bdc_item *bdc_intern_get_entry(struct bdc_hash_table *table, const char *key, uint64_t hash)
+{
+ size_t hash_idx = hash_idx_from_hash(hash, table->bucket_count);
+ if (table->items[hash_idx] == NULL) return NULL;
+
+ struct bdc_item *entry = table->items[hash_idx];
+
+ if (0 == strcmp(entry->key, key)) return entry;
+
+ while (entry->next != NULL) {
+ entry = entry->next;
+ if (0 == strcmp(entry->key, key)) return entry;
+ }
+
+ return NULL;
+}
+
+
+struct bdc_item *get_entry(struct bdc_hash_table *table, const char *key)
+{
+ uint64_t hash = hash_function(key);
+
+ size_t hash_idx = hash & (table->bucket_count - 1);
+ if (table->items[hash_idx] == NULL) return NULL;
+
+ struct bdc_item *entry = table->items[hash_idx];
+ if (0 == strcmp(entry->key, key)) return entry;
+ while (entry->next != NULL) {
+ entry = entry->next;
+ if (0 == strcmp(entry->key, key)) return entry;
+ }
+
+ return NULL;
+}
+
+void destroy_item(struct bdc_item **item)
+{
+ if(item == NULL || *item == NULL) return;
+ struct bdc_item *this = *item;
+ destroy_value(&this->value);
+ free(this->key);
+ free(this);
+ *item = NULL;
+}
+
+bool remove_key(struct bdc_hash_table *table, const char *key)
+{
+ if (!bdc_key_in_hash_table(table, key)) return false;
+
+ uint64_t hash = hash_function(key);
+ size_t hash_idx = hash & (table->bucket_count - 1);
+
+ struct bdc_item *target = NULL;
+ struct bdc_item *entry = table->items[hash_idx];
+ if (0 == strcmp(entry->key, key)) {
+ target = entry;
+ table->items[hash_idx] = target->next;
+ table->items_per_bucket[hash_idx]--;
+ destroy_item(&target);
+ return true;
+ }
+ struct bdc_item *prev = NULL;
+ while (entry->next != NULL) {
+ prev = entry,
+ entry = entry->next;
+ if (0 == strcmp(entry->key, key)) {
+ target = entry;
+ prev->next = target->next;
+ table->items_per_bucket[hash_idx]--;
+ free(entry);
+ return true;
+ }
+ }
+ return false;
+}
+
+
+__attribute__((unused)) bool bdc_key_in_hash_table(struct bdc_hash_table *table, const char *key)
+{
+ return get_entry(table, key) != NULL;
+
+}
+
+
+struct bdc_value *bdc_get_value_from_key(struct bdc_hash_table *table, const char *key)
+{
+ struct bdc_item *entry = get_entry(table, key);
+ if (entry) {
+ return entry->value;
+ } else {
+ return NULL;
+ }
+}
+
+
+struct bdc_item *new_entry(const char *key, struct bdc_value *value)
+{
+ struct bdc_item *entry = calloc_or_die(1, sizeof(struct bdc_item));
+
+
+ entry->value = value;
+ log_message(LOG_DEBUG, "duplicating key '%s'", key);
+ entry->key = strdup(key);
+ entry->next = NULL;
+
+ return entry;
+}
+
+
+void print_key_val(struct bdc_item *entry)
+{
+ struct bdc_value *value = entry->value;
+ switch (value->type) {
+
+ case BDC_STRING:
+ printf("\t\t%s -> '%s'\n", entry->key, value->string);
+ break;
+ case BDC_INT64:
+ printf("\t\t%s -> %ld\n", entry->key, value->int64);
+ break;
+ case BDC_DOUBLE:
+ printf("\t\t%s -> %f\n", entry->key, value->double_value);
+ break;
+ case BDC_CUSTOM:
+ printf("\t\t%s -> %p\n", entry->key, value->pointer);
+ break;
+ }
+
+}
+
+
+__attribute__((unused)) void print_hash_table(const struct bdc_hash_table *table)
+{
+ printf("\n");
+ printf("Hash table: %lu buckets with %lu items\n", table->bucket_count,
+ table->item_count);
+ for (size_t i = 0; i < table->bucket_count; i++) {
+ if (table->items[i] == NULL) continue;
+ printf("\tentry %lu: %lu entries\n", i, table->items_per_bucket[i]);
+ size_t count = 1;
+ struct bdc_item *entry = table->items[i];
+ print_key_val(entry);
+ while (entry->next != NULL) {
+ entry = entry->next;
+ count++;
+ print_key_val(entry);
+ }
+
+ if (count != table->items_per_bucket[i]) {
+ printf("Error: mismatch between expected (%lu) and found entries (%lu)\n",
+ table->items_per_bucket[i], i);
+ }
+ }
+ printf("\n");
+}
+
+
+
+
+
+struct bdc_item *bdc_intern_add_entry(struct bdc_hash_table *table, struct bdc_item *entry, uint64_t hash)
+{
+ size_t hash_idx = hash_idx_from_hash(hash, table->bucket_count);
+ entry->next = table->items[hash_idx];
+ table->items[hash_idx] = entry;
+ table->items_per_bucket[hash_idx] += 1;
+ table->item_count += 1;
+
+ return entry;
+}
+
+
+void rehash_table(struct bdc_hash_table *table)
+{
+ log_message(LOG_INFO, "%s: rehashing!", __func__);
+ struct bdc_hash_table *tmp = bdc_intern_new_hash_table(table->bucket_count * 2);
+
+ for (size_t i = 0; i < table->bucket_count; i++) {
+ if (table->items[i] == NULL) continue;
+ struct bdc_item *entry = table->items[i];
+ struct bdc_item *next = entry->next;
+ uint64_t hash = hash_function(entry->key);
+ bdc_intern_add_entry(tmp, entry, hash);
+
+ while (next) {
+ entry = next;
+ next = entry->next;
+ hash = hash_function(entry->key);
+ bdc_intern_add_entry(tmp, entry, hash);
+ }
+
+ }
+
+ free(table->items);
+ free(table->items_per_bucket);
+ table->items = tmp->items;
+ table->items_per_bucket = tmp->items_per_bucket;
+ table->bucket_count = tmp->bucket_count;
+
+ free(tmp);
+ tmp = NULL;
+
+}
+
+
+struct bdc_item *bdc_ht_add_string(struct bdc_hash_table *table, const char *key, const char *value)
+{
+ struct bdc_value *val = calloc(1, sizeof(struct bdc_value));
+ log_message(LOG_DEBUG, "duplicating value '%s", value);
+ val->string = strdup(value);
+ val->type = BDC_STRING;
+ return intern_bdc_add_entry(table, key, val);
+}
+
+
+struct bdc_item *bdc_ht_add_custom(struct bdc_hash_table *table, const char *key, void *value)
+{
+ struct bdc_value *val = calloc(1, sizeof(struct bdc_value));
+ val->pointer = value;
+ val->type = BDC_CUSTOM;
+ return intern_bdc_add_entry(table, key, val);
+}
+
+
+struct bdc_item *bdc_ht_add_int64(struct bdc_hash_table *table, const char *key, int64_t value)
+{
+ struct bdc_value *val = calloc(1, sizeof(struct bdc_value));
+ val->int64 = value;
+ val->type = BDC_INT64;
+ return intern_bdc_add_entry(table, key, val);
+}
+
+
+struct bdc_item *bdc_ht_add_double(struct bdc_hash_table *table, const char *key, double value)
+{
+ struct bdc_value *val = calloc(1, sizeof(struct bdc_value));
+ val->double_value = value;
+ val->type = BDC_DOUBLE;
+ return intern_bdc_add_entry(table, key, val);
+}
+
+
+struct bdc_item *intern_bdc_add_entry(struct bdc_hash_table *table, const char *key, struct bdc_value *value)
+{
+ uint64_t hash = hash_function(key);
+ size_t hash_idx = hash_idx_from_hash(hash, table->bucket_count);
+ switch (value->type) {
+ case BDC_STRING:
+ log_message(LOG_DEBUG, "adding entry %s %s with hash %lu to bucket %lu", key, value->string,
+ hash_function(key), hash_idx);
+ break;
+ case BDC_INT64:
+ log_message(LOG_DEBUG, "adding entry %s %ld with hash %lu to bucket %lu", key, value->int64,
+ hash_function(key), hash_idx);
+ break;
+ case BDC_DOUBLE:
+ log_message(LOG_DEBUG, "adding entry %s %f with hash %lu to bucket %lu", key,
+ value->double_value,
+ hash_function(key), hash_idx);
+ break;
+ case BDC_CUSTOM:
+ log_message(LOG_DEBUG, "adding entry %s %p with hash %lu to bucket %lu", key, value->pointer,
+ hash_function(key), hash_idx);
+ break;
+ }
+
+
+ struct bdc_item *entry = bdc_intern_get_entry(table, key, hash);
+
+ if (entry != NULL) {
+ log_message(LOG_DEBUG, "replacing key '%s'", entry->key);
+ destroy_value(&entry->value);
+ entry->value = value;
+
+ if (entry->value->type == BDC_STRING) {
+ log_message(LOG_DEBUG, "setting value of '%s' to '%s'", key, entry->value->string);
+ }
+ return entry;
+ }
+ assert(entry == NULL);
+ entry = new_entry(key, value);
+ bdc_intern_add_entry(table, entry, hash);
+
+ if (table->items_per_bucket[hash_idx] > 2) {
+ rehash_table(table);
+ }
+
+ log_message(LOG_DEBUG, "added key '%s'\n", key);
+ return entry;
+}
+
+
+bool bdc_ht_get_int64_from_key(struct bdc_hash_table *table, const char *key, int64_t *result)
+{
+ struct bdc_value *value = bdc_get_value_from_key(table, key);
+ if (!value) return false;
+ if (value->type != BDC_INT64) return false;
+ *result = value->int64;
+ return true;
+}
+
+
+__attribute__((unused)) bool bdc_ht_get_double_from_key(struct bdc_hash_table *table, const char *key, double *result)
+{
+ struct bdc_value *value = bdc_get_value_from_key(table, key);
+ if (!value) return false;
+ if (value->type != BDC_DOUBLE) return false;
+ *result = value->double_value;
+ return true;
+}
+
+
+bool bdc_ht_get_string_from_key(struct bdc_hash_table *table, const char *key, char **result)
+{
+ struct bdc_value *value = bdc_get_value_from_key(table, key);
+ if (!value) return false;
+ if (value->type != BDC_STRING) return false;
+ *result = strdup(value->string);
+ return true;
+}
+
+void destroy_hash_table(struct bdc_hash_table **ht)
+{
+ if (ht == NULL || *ht == NULL) return;
+ struct bdc_hash_table *t = *ht;
+ size_t count = t->bucket_count;
+ for (size_t i = 0; i < count; i++){
+ struct bdc_item *item = t->items[i];
+ while(item){
+ struct bdc_item *this = item;
+ item = item->next;
+ if (this->value->type == BDC_STRING) {
+ log_message(LOG_DEBUG, "freeing item '%s' -> '%s'", this->key, this->value->string);
+ free(this->value->string);
+ }
+ free(this->value);
+ free(this->key);
+ free(this);
+ this = NULL;
+ }
+ free(item);
+ }
+ free(t->items_per_bucket);
+ free(t->items);
+ free(t);
+ *ht = NULL;
+}
\ No newline at end of file
diff --git a/libbdc/bdc_hashtable/bdc_hashtable.h b/libbdc/bdc_hashtable/bdc_hashtable.h
new file mode 100644
index 0000000..9b7f9ec
--- /dev/null
+++ b/libbdc/bdc_hashtable/bdc_hashtable.h
@@ -0,0 +1,88 @@
+// SPDX-License-Identifier: GPL-3.0-or-later
+//
+// bdc_hashtable.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 BDC_HASHTABLE_H
+#define BDC_HASHTABLE_H
+
+#include <stdint.h>
+#include <stddef.h>
+#include <stdbool.h>
+
+#define MIN_SIZE 1024
+
+
+enum bdc_value_type {
+ BDC_STRING = 0,
+ BDC_INT64 = 1,
+ BDC_DOUBLE = 2,
+ BDC_CUSTOM
+};
+
+
+
+
+struct bdc_hash_table;
+struct bdc_value;
+
+bool remove_key(struct bdc_hash_table *table, const char *key);
+struct bdc_item *intern_bdc_add_entry(struct bdc_hash_table *table, const char *key, struct bdc_value *value);
+
+struct bdc_item *bdc_ht_add_string(struct bdc_hash_table *table, const char *key, const char *value);
+
+struct bdc_item *bdc_ht_add_custom(struct bdc_hash_table *table, const char *key, void *custom);
+
+struct bdc_item *bdc_ht_add_int64(struct bdc_hash_table *table, const char *key, int64_t value);
+
+struct bdc_item *bdc_ht_add_double(struct bdc_hash_table *table, const char *key, double value);
+
+__attribute__((unused)) struct bdc_hash_table *new_hash_table(void);
+
+__attribute__((unused)) void print_hash_table(const struct bdc_hash_table *table);
+
+struct bdc_value *bdc_get_value_from_key(struct bdc_hash_table *table, const char *key);
+
+__attribute__((unused)) bool bdc_key_in_hash_table(struct bdc_hash_table *table, const char *key);
+
+bool bdc_ht_get_int64_from_key(struct bdc_hash_table *table, const char *key, int64_t *result);
+
+bool bdc_ht_get_string_from_key(struct bdc_hash_table *table, const char *key, char **result);
+
+__attribute__((unused)) bool bdc_ht_get_double_from_key(struct bdc_hash_table *table, const char *key, double *result);
+void destroy_hash_table(struct bdc_hash_table **ht);
+
+#define bdc_ht_get_data_from_key(TABLE, KEY, RESULT) _GENERIC((RESULT), \
+ int64_t *: bdc_ht_get_int64_from_key, \
+ char **: bdc_ht_get_string_from_key, \
+ double *: bdc_ht_get_value_from_key, \
+)(TABLE, KEY, (RESULT))
+
+#define bdc_ht_add_entry(table, key, value) \
+ _Generic((value),\
+ int64_t: bdc_ht_add_int64, \
+ int: bdc_ht_add_int64, \
+ double: bdc_ht_add_double, \
+ void *: bdc_ht_add_custom, \
+ char *: bdc_ht_add_string)(table, key, value)
+
+
+// move to private later // FIXME
+void rehash_table(struct bdc_hash_table *table);
+#endif //BDC_HASHTABLE_H
diff --git a/libbdc/bdc_hashtable/tests/test_bdc_hashtable.c b/libbdc/bdc_hashtable/tests/test_bdc_hashtable.c
new file mode 100644
index 0000000..9ebc916
--- /dev/null
+++ b/libbdc/bdc_hashtable/tests/test_bdc_hashtable.c
@@ -0,0 +1,52 @@
+
+// SPDX-License-Identifier: GPL-3.0-or-later
+//
+// test_bdc_hashtable.c
+//
+// 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.
+//
+
+#include <stdlib.h>
+#include "bdc_hashtable/bdc_hashtable.h"
+#include "bdc_strings/bdc_strings.h"
+
+
+int main(int argc, char **argv)
+{
+ //logging_initialize(LOG_DEBUG, NULL, NULL, false);
+ struct bdc_hash_table *t = new_hash_table();
+ bdc_ht_add_string(t, "a", "b12345");
+ bdc_ht_add_string(t, "a", "c123123");
+ bdc_ht_add_string(t, "b", "d21542");
+ bdc_ht_add_string(t, "c", "d316315");
+ bdc_ht_add_string(t, "d", "d1326536");
+ bdc_ht_add_string(t, "a", "d316136");
+ remove_key(t, "a");
+ bdc_ht_add_string(t, "a", "e13616136136");
+ destroy_hash_table(&t);
+
+ struct string_substitution *s = new_substituter();
+ add_substitution(s, "%a", "<was a>");
+ add_substitution(s, "%b", "<was b>");
+ add_substitution(s, "%c", "<was c>");
+ const char *orig = "%c-%a-%b-%c-aa-%d";
+ char *x = substitute_string(orig, s);
+ printf("%s -> %s\n", orig, x);
+ destroy_substituter(&s);
+ free(x);
+ return 0;
+}
\ No newline at end of file
diff --git a/libbdc/bdc_io/CMakeLists.txt b/libbdc/bdc_io/CMakeLists.txt
new file mode 100644
index 0000000..8436cfb
--- /dev/null
+++ b/libbdc/bdc_io/CMakeLists.txt
@@ -0,0 +1,13 @@
+add_library(bdc_io STATIC "" ../bdc_cross_platform/bdc_cross_platform.h )
+
+target_sources(bdc_io
+ PRIVATE
+ bdc_io.c
+ bdc_paths.c
+ PUBLIC
+ bdc_io.h
+)
+
+
+set_property(TARGET bdc_io PROPERTY POSITION_INDEPENDENT_CODE ON)
+target_link_libraries(bdc_io bdc_strings)
diff --git a/src/cats_strings/io_text.c b/libbdc/bdc_io/bdc_io.c
similarity index 75%
rename from src/cats_strings/io_text.c
rename to libbdc/bdc_io/bdc_io.c
index 19cac9b..1a0c931 100644
--- a/src/cats_strings/io_text.c
+++ b/libbdc/bdc_io/bdc_io.c
@@ -1,6 +1,6 @@
// SPDX-License-Identifier: GPL-3.0-or-later
//
-// io_text.c
+// bdc_io.c
//
// Copyright (C) 2011-2024, University of Vienna and Vienna Institute for Nature Conservation & Analyses, Andreas Gattringer.
//
@@ -19,13 +19,12 @@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
//
-#include "cats_global.h"
+#include <stdio.h>
#include <assert.h>
#include <string.h>
-#include <stdlib.h>
-#include <logging/logging.h>
-#include "cats_strings.h"
+#include "bdc_memory/bdc_memory.h"
+#include "bdc_io.h"
char *read_single_line(FILE *file)
{
@@ -33,9 +32,9 @@ char *read_single_line(FILE *file)
char buffer[MAX_STRING_BUFF_LENGTH] = {0};
fgets(buffer, MAX_STRING_BUFF_LENGTH, file);
fflush(stdout);
- char *result = right_trim(buffer);
- if (strlen(result)) return strdup(result);
+
+ if (strlen(buffer)) return strdup(buffer);
return NULL;
}
@@ -47,7 +46,7 @@ char *slurp_file(const char *filename)
FILE *file = fopen(filename, "r");
if (!file) {
- log_message(LOG_ERROR, "%s: File '%s' does not exist or could not be opened.", __func__, filename);
+ fprintf(stderr, "%s: File '%s' does not exist or could not be opened.\n", __func__, filename);
return NULL;
}
@@ -56,15 +55,9 @@ char *slurp_file(const char *filename)
long size = ftell(file);
fseek(file, 0L, SEEK_SET);
- char *buffer = malloc(size + 1);
-
- if (!buffer) {
- log_message(LOG_ERROR, "%s: failed to allocate memory", __func__);
- exit(EXIT_FAILURE);
- }
-
+ char *buffer = malloc_or_die(size + 1);
fread(buffer, sizeof(char), size, file);
fclose(file);
buffer[size] = '\0';
return buffer;
-}
+}
\ No newline at end of file
diff --git a/libbdc/bdc_io/bdc_io.h b/libbdc/bdc_io/bdc_io.h
new file mode 100644
index 0000000..54ade85
--- /dev/null
+++ b/libbdc/bdc_io/bdc_io.h
@@ -0,0 +1,56 @@
+// SPDX-License-Identifier: GPL-3.0-or-later
+//
+// bdc_io.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 BDC_IO_H
+#define BDC_IO_H
+
+#define MAX_STRING_BUFF_LENGTH 4096
+#if defined(WIN32) || defined (_WIN32)
+#define DIRECTORY_SEPARATOR "\\"
+#else
+#define DIRECTORY_SEPARATOR "/"
+#endif
+
+
+#include "bdc_strings/bdc_strings.h"
+
+char *slurp_file(const char *filename);
+char *read_single_line(FILE *file);
+
+#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(EXIT_FAILURE);\
+}
+
+char *assemble_path(const struct string_array *path);
+
+char *assemble_filename(struct string_array *path, struct string_array *filename, char *field_separator, char *extension);
+
+bool check_and_create_directory_if_needed(const struct string_array *directory_path);
+
+bool directory_exists(const char *path);
+
+bool directory_writable(const char *path);
+
+void make_directory(const char *path);
+#endif //BDC_IO_H
diff --git a/libbdc/bdc_io/bdc_paths.c b/libbdc/bdc_io/bdc_paths.c
new file mode 100644
index 0000000..586572d
--- /dev/null
+++ b/libbdc/bdc_io/bdc_paths.c
@@ -0,0 +1,136 @@
+// SPDX-License-Identifier: GPL-3.0-or-later
+//
+// bdc_paths.c
+//
+// 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.
+//
+
+#include <string.h>
+#include <sys/stat.h>
+#include <stdio.h>
+#include <errno.h>
+
+#include "bdc_io.h"
+#include "bdc_cross_platform/bdc_cross_platform.h"
+
+#ifdef BDC_ON_WINDOWS
+#include <direct.h>
+#else
+#include <unistd.h>
+#endif
+
+
+
+bool directory_exists(const char *path)
+{
+ struct stat info;
+ int rc = stat(path, &info);
+ if (rc == 0 && info.st_mode & S_IFDIR) return true;
+
+ if (rc == 0) {
+ fprintf(stderr, "Path '%s' is not a directory. Exiting.\n", path);
+ exit(EXIT_FAILURE);
+ }
+
+ fprintf(stderr, "Directory '%s' does not exist\n", path);
+ return false;
+}
+
+
+bool directory_writable(const char *path)
+{
+ int rc = access(path, F_OK);
+
+ if (rc == 0) {
+ return true;
+ }
+
+ fprintf(stderr, "directory %s exists but cannot be accessed or written to.\n", path);
+ return false;
+}
+
+
+void make_directory(const char *path)
+{
+#ifndef BDC_ON_WINDOWS
+ int rc = mkdir(path, S_IRWXU);
+#else
+ int rc = _mkdir(path);
+#endif
+ if (rc == 0) return;
+
+ int error = errno;
+ fprintf(stderr, "unable to create directory %s: %s\n", path, strerror(error));
+ exit(EXIT_FAILURE);
+}
+
+
+char *assemble_path(const struct string_array *path)
+{
+ return string_array_paste(path, DIRECTORY_SEPARATOR);
+}
+
+
+char *
+assemble_filename(struct string_array *path, struct string_array *filename, char *field_separator, char *extension)
+{
+ char *name_string = string_array_paste(filename, field_separator);
+ char *result = NULL;
+
+ if (path && get_string_count(path) > 0) {
+ char *path_string = string_array_paste(path, DIRECTORY_SEPARATOR);
+ if (extension && strlen(extension)) {
+ char *fn = compound_string(name_string, extension, ".");
+ result = compound_string(path_string, fn, DIRECTORY_SEPARATOR);
+ free(fn);
+ } else {
+ result = compound_string(path_string, name_string, DIRECTORY_SEPARATOR);
+ }
+ free(path_string);
+ } else {
+
+ if (extension && strlen(extension)) {
+ result = compound_string(name_string, extension, ".");
+ } else {
+ result = strdup(name_string);
+ }
+ }
+
+ free(name_string);
+ return result;
+}
+
+
+bool check_and_create_directory_if_needed(const struct string_array *directory_path)
+{
+ if (directory_path == NULL || get_string_count(directory_path) == 0) {
+ fprintf(stderr, "Unable to check directory - no path specified\n");
+ exit(EXIT_FAILURE);
+ }
+
+ char *dir = assemble_path(directory_path);
+
+
+ if (!directory_exists(dir)) {
+ fprintf(stderr, "directory '%s' does not exist. Trying to create.\n", dir);
+ make_directory(dir);
+ }
+
+ bool writeable = directory_writable(dir);
+ free(dir);
+ return writeable;
+}
\ No newline at end of file
diff --git a/libbdc/bdc_logging/CMakeLists.txt b/libbdc/bdc_logging/CMakeLists.txt
new file mode 100644
index 0000000..3391d98
--- /dev/null
+++ b/libbdc/bdc_logging/CMakeLists.txt
@@ -0,0 +1,12 @@
+add_library(bdc_logging STATIC "")
+
+target_sources(bdc_logging
+ PRIVATE
+ logging.c
+ PUBLIC
+ logging.h
+ )
+
+target_include_directories(bdc_logging PUBLIC ".")
+target_link_libraries(bdc_logging bdc_memory bdc_time bdc_cross_platform)
+set_property(TARGET bdc_logging PROPERTY POSITION_INDEPENDENT_CODE ON)
\ No newline at end of file
diff --git a/libbdc/bdc_logging/README.md b/libbdc/bdc_logging/README.md
new file mode 100644
index 0000000..32e219e
--- /dev/null
+++ b/libbdc/bdc_logging/README.md
@@ -0,0 +1,10 @@
+# bdc_logging
+
+This is a library to handle logging.
+
+## Dependencies
+* bdc_memory
+* bdc_time
+* bdc_cross_platform (header only)
+
+
diff --git a/src/logging/logging.c b/libbdc/bdc_logging/logging.c
similarity index 58%
rename from src/logging/logging.c
rename to libbdc/bdc_logging/logging.c
index a7c0ed5..73e5f82 100644
--- a/src/logging/logging.c
+++ b/libbdc/bdc_logging/logging.c
@@ -21,27 +21,26 @@
#include <stdbool.h>
#include <stdio.h>
-#include <stdint.h>
#include <string.h>
#include <stdarg.h>
#include <stdlib.h>
-#include "logging.h"
+
#include "bdc_memory/bdc_memory.h"
#include "bdc_time/bdc_time.h"
-#include "misc/misc.h"
-
+#include "bdc_io/bdc_io.h"
+#include "bdc_logging/logging.h"
-enum cats_log_level internal_current_log_level = LOG_INFO;
+enum bdc_log_level internal_current_log_level = LOG_INFO;
int32_t logging_mpi_rank = -1;
-struct bdc_time cats_logging_start_time;
-FILE *cats_log_file = NULL;
-char *cats_log_file_name = NULL;
+struct bdc_time bdc_logging_start_time;
+FILE *bdc_log_file = NULL;
+char *bdc_log_file_name = NULL;
const char *logging_module_name = NULL;
bool time_initialized = false;
bool logging_quiet = false;
-const char *get_log_level_name(enum cats_log_level level)
+const char *get_log_level_name(enum bdc_log_level level)
{
switch (level) {
case LOG_DEBUG:
@@ -50,7 +49,6 @@ const char *get_log_level_name(enum cats_log_level level)
return "INFO";
case LOG_RAW:
case LOG_EMPTY:
- return "";
case LOG_MARK:
return "";
case LOG_IMPORTANT:
@@ -70,58 +68,52 @@ const char *get_log_level_name(enum cats_log_level level)
}
-const char *get_log_level_color(enum cats_log_level level)
+const char *get_log_level_color(enum bdc_log_level level)
{
switch (level) {
case LOG_RAW:
case LOG_DEBUG:
- return C_RESET;
case LOG_INFO:
- return C_RESET;
case LOG_EMPTY:
- return C_RESET;
case LOG_MARK:
return C_RESET;
case LOG_IMPORTANT:
- return C_YELLOW;
case LOG_WARNING:
return C_YELLOW;
case LOG_ERROR:
- return C_RED;
case LOG_MPI:
- return C_RED;
case LOG_UNIMPLEMENTED:
- return C_RED;
case LOG_UNKNOWN:
return C_RED;
+
}
return C_RESET;
}
-void set_log_level(enum cats_log_level new_level)
+void set_log_level(enum bdc_log_level new_level)
{
internal_current_log_level = new_level;
}
-
// - mpi world rank can be added later
// FIXME: if start_time is NULL, generate
-void logging_initialize(enum cats_log_level level, const struct bdc_time *start_time, const char *log_file_name, bool quiet)
+void
+logging_initialize(enum bdc_log_level level, const struct bdc_time *start_time, const char *log_file_name, bool quiet)
{
set_log_level(level);
logging_quiet = quiet;
if (start_time != NULL) {
- cats_logging_start_time = *start_time;
+ bdc_logging_start_time = *start_time;
time_initialized = true;
}
if (log_file_name != NULL) {
- cats_log_file_name = strdup(log_file_name);
- cats_log_file = fopen(log_file_name, "w");
- ENSURE_FILE_OPENED(cats_log_file, cats_log_file_name)
+ bdc_log_file_name = strdup(log_file_name);
+ bdc_log_file = fopen(log_file_name, "w");
+ ENSURE_FILE_OPENED(bdc_log_file, bdc_log_file_name)
}
}
@@ -138,13 +130,16 @@ void logging_set_mpi_rank(int mpi_world_rank)
logging_mpi_rank = mpi_world_rank;
}
+
// actual logging function(s), only to be called from log_message
-void log_msg(const char *msg, enum cats_log_level loglevel);
-void log_msg_simple(const char *msg, enum cats_log_level loglevel);
+void log_msg(const char *msg, enum bdc_log_level loglevel);
+
+void log_msg_simple(const char *msg, enum bdc_log_level loglevel);
+
// logging wrapper function
__attribute__ ((__format__ (__printf__, 2, 3)))
-void log_message(enum cats_log_level level, const char *fmt, ...)
+void log_message(enum bdc_log_level level, const char *fmt, ...)
{
if (level < internal_current_log_level) return;
@@ -165,13 +160,13 @@ void log_message(enum cats_log_level level, const char *fmt, ...)
}
-enum cats_log_level get_log_level(void)
+enum bdc_log_level get_log_level(void)
{
return internal_current_log_level;
}
-void log_message_simple(enum cats_log_level level, const char *fmt, ...)
+__attribute__((unused)) void log_message_simple(enum bdc_log_level level, const char *fmt, ...)
{
if (level < internal_current_log_level) return;
char *message = NULL;
@@ -190,26 +185,26 @@ void log_message_simple(enum cats_log_level level, const char *fmt, ...)
}
-void log_msg(const char *msg, enum cats_log_level loglevel)
+void log_msg(const char *msg, enum bdc_log_level loglevel)
{
if (loglevel < internal_current_log_level) return;
if (loglevel == LOG_RAW) {
- if (! logging_quiet) fprintf(stdout, "%s", msg);
- if (cats_log_file != NULL) fprintf(cats_log_file, "%s", msg);
+ if (!logging_quiet) fprintf(stdout, "%s", msg);
+ if (bdc_log_file != NULL) fprintf(bdc_log_file, "%s", msg);
return;
}
if (loglevel == LOG_EMPTY) {
- if (! logging_quiet) fprintf(stdout, "\n");
- if (cats_log_file != NULL) fprintf(cats_log_file, "\n");
+ if (!logging_quiet) fprintf(stdout, "\n");
+ if (bdc_log_file != NULL) fprintf(bdc_log_file, "\n");
return;
}
const char *color = get_log_level_color(loglevel);
if (loglevel == LOG_MARK) {
- if (! logging_quiet) fprintf(stdout, "%s%s%s\n", color, msg, C_RESET);
- if (cats_log_file != NULL) fprintf(cats_log_file, "%s%s%s\n", color, msg, C_RESET);
+ if (!logging_quiet) fprintf(stdout, "%s%s%s\n", color, msg, C_RESET);
+ if (bdc_log_file != NULL) fprintf(bdc_log_file, "%s%s%s\n", color, msg, C_RESET);
return;
}
const char *log_default = "unknown";
@@ -222,55 +217,60 @@ void log_msg(const char *msg, enum cats_log_level loglevel)
if (logging_mpi_rank >= 0) {
- if (! logging_quiet) fprintf(stdout, "(%02d)::", logging_mpi_rank);
- if (cats_log_file != NULL) fprintf(cats_log_file, "(%02d)::", logging_mpi_rank);
+ if (!logging_quiet) fprintf(stdout, "(%02d)::", logging_mpi_rank);
+ if (bdc_log_file != NULL) fprintf(bdc_log_file, "(%02d)::", logging_mpi_rank);
}
if (time_initialized) {
- double secs = seconds_monotonic_since(&cats_logging_start_time);
- if (cats_log_file != NULL) {
- fprintf(cats_log_file, "% 16.4f::", secs);
+ double secs = seconds_monotonic_since(&bdc_logging_start_time);
+ if (bdc_log_file != NULL) {
+ fprintf(bdc_log_file, "% 16.4f::", secs);
}
- if (! logging_quiet) fprintf(stdout, "% 16.4f::", secs);
+ if (!logging_quiet) fprintf(stdout, "% 16.4f::", secs);
} else {
- if (cats_log_file != NULL) {
- fprintf(cats_log_file, " ::");
+ if (bdc_log_file != NULL) {
+ fprintf(bdc_log_file, " ::");
}
- if (! logging_quiet) fprintf(stdout, " ::");
+ if (!logging_quiet) fprintf(stdout, " ::");
}
if (logging_module_name != NULL) {
- if (! logging_quiet) fprintf(stdout, "%s%s::[%s] %s%s\n", color, loglevel_name, logging_module_name, msg, C_RESET);
- if (cats_log_file) fprintf(cats_log_file, "%s%s::[%s] %s%s\n", color, loglevel_name, logging_module_name, msg, C_RESET);
+ if (!logging_quiet)
+ fprintf(stdout, "%s%s::[%s] %s%s\n", color, loglevel_name, logging_module_name, msg, C_RESET);
+ if (bdc_log_file)
+ fprintf(bdc_log_file, "%s%s::[%s] %s%s\n", color, loglevel_name, logging_module_name, msg,
+ C_RESET);
} else {
- if (! logging_quiet) fprintf(stdout, "%s%s::%s%s\n", color, loglevel_name, msg, C_RESET);
- if (cats_log_file) fprintf(cats_log_file, "%s%s::%s%s\n", color, loglevel_name, msg, C_RESET);
+ if (!logging_quiet) fprintf(stdout, "%s%s::%s%s\n", color, loglevel_name, msg, C_RESET);
+ if (bdc_log_file) fprintf(bdc_log_file, "%s%s::%s%s\n", color, loglevel_name, msg, C_RESET);
}
}
-void log_msg_simple(const char *msg, enum cats_log_level loglevel)
+void log_msg_simple(const char *msg, enum bdc_log_level loglevel)
{
if (loglevel < internal_current_log_level) return;
const char *log_default = "unknown";
const char *loglevel_name = log_default;
- if (loglevel <= LOG_UNKNOWN && loglevel >= LOG_DEBUG) {
+ if (loglevel <= LOG_UNKNOWN) {
loglevel_name = get_log_level_name(loglevel);
}
const char *color = get_log_level_color(loglevel);
if (logging_mpi_rank >= 0) {
- if (! logging_quiet) fprintf(stdout, "(%02d)%s%s: %s%s", logging_mpi_rank, color, loglevel_name, msg, C_RESET);
- if (cats_log_file != NULL) fprintf(cats_log_file, "(%02d)%s%s: %s%s", logging_mpi_rank, color, loglevel_name, msg, C_RESET);
+ if (!logging_quiet)
+ fprintf(stdout, "(%02d)%s%s: %s%s", logging_mpi_rank, color, loglevel_name, msg, C_RESET);
+ if (bdc_log_file != NULL)
+ fprintf(bdc_log_file, "(%02d)%s%s: %s%s", logging_mpi_rank, color, loglevel_name, msg,
+ C_RESET);
} else {
- if (! logging_quiet) fprintf(stdout, "%s%s::%s%s\n", color, loglevel_name, msg, C_RESET);
- if (cats_log_file != NULL) fprintf(cats_log_file, "%s%s::%s%s\n", color, loglevel_name, msg, C_RESET);
+ if (!logging_quiet) fprintf(stdout, "%s%s::%s%s\n", color, loglevel_name, msg, C_RESET);
+ if (bdc_log_file != NULL) fprintf(bdc_log_file, "%s%s::%s%s\n", color, loglevel_name, msg, C_RESET);
}
-
}
diff --git a/src/logging/logging.h b/libbdc/bdc_logging/logging.h
similarity index 66%
rename from src/logging/logging.h
rename to libbdc/bdc_logging/logging.h
index 52eefe7..2a5ac64 100644
--- a/src/logging/logging.h
+++ b/libbdc/bdc_logging/logging.h
@@ -19,14 +19,15 @@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
//
-#ifndef CATS_LOGGING_H_
-#define CATS_LOGGING_H_
+#ifndef BDC_LOGGING_H_
+#define BDC_LOGGING_H_
+
#include <stdbool.h>
-#include "cats_defs.h"
#include <time.h>
+
#include "bdc_time/bdc_time.h"
-#if defined(__MINGW32__) || defined(CATS_ON_WINDOWS)
+#if defined(__MINGW32__) || defined(WIN32)
// no color codes
#define C_RED ""
#define C_GREEN ""
@@ -41,7 +42,7 @@
#define C_WHITE "\x1B[37m"
#endif
-enum cats_log_level {
+enum bdc_log_level {
LOG_DEBUG,
LOG_INFO,
LOG_EMPTY,
@@ -55,19 +56,25 @@ enum cats_log_level {
LOG_UNKNOWN
};
-void logging_initialize(enum cats_log_level level, const struct bdc_time *start_time, const char *log_file_name, bool quiet);
+void
+logging_initialize(enum bdc_log_level level, const struct bdc_time *start_time, const char *log_file_name, bool quiet);
void logging_set_mpi_rank(int mpi_world_rank);
void logging_set_module_name(const char *name);
__attribute__ ((__format__ (__printf__, 2, 3)))
-void log_message(enum cats_log_level level, const char *fmt, ...);
+void log_message(enum bdc_log_level level, const char *fmt, ...);
+
+enum bdc_log_level get_log_level(void);
+
+__attribute__((unused)) void log_message_simple(enum bdc_log_level level, const char *fmt, ...);
-enum cats_log_level get_log_level(void);
+void set_log_level(enum bdc_log_level new_level);
-void log_message_simple(enum cats_log_level level, const char *fmt, ...);
+#define INCOMPLETE_IMPLEMENTATION() log_message(LOG_ERROR, "%s: not yet implemented", __func__)
+#define MISSING_IMPLEMENTATION(X) log_message(LOG_ERROR, "%s: missing functionality %s", __func__, (X))
+#define ABORT_IMPLEMENTATION() log_message(LOG_ERROR, "%s:%s:%d: not yet implemented", __FILE__, __func__, __LINE__); exit(EXIT_FAILURE)
-void set_log_level(enum cats_log_level new_level);
#endif
\ No newline at end of file
diff --git a/libbdc/bdc_strings/CMakeLists.txt b/libbdc/bdc_strings/CMakeLists.txt
new file mode 100644
index 0000000..78d25f7
--- /dev/null
+++ b/libbdc/bdc_strings/CMakeLists.txt
@@ -0,0 +1,18 @@
+add_library(bdc_strings STATIC "" ../bdc_cross_platform/bdc_cross_platform.h
+
+)
+
+target_sources(bdc_strings
+ PRIVATE
+ bdc_strings.c
+ pretty_print.c
+ string_helpers.c
+ string_substitution.c
+ string_converters.c
+ PUBLIC
+ bdc_strings.h
+
+ )
+
+set_property(TARGET bdc_strings PROPERTY POSITION_INDEPENDENT_CODE ON)
+target_link_libraries(bdc_strings bdc_logging bdc_hashtable)
\ No newline at end of file
diff --git a/libbdc/bdc_strings/README.md b/libbdc/bdc_strings/README.md
new file mode 100644
index 0000000..2a86721
--- /dev/null
+++ b/libbdc/bdc_strings/README.md
@@ -0,0 +1,9 @@
+# bdc_strings
+
+
+This is a library to handle strings.
+
+## Dependencies
+* bdc_logging
+* bdc_hashtable
+
diff --git a/src/cats_strings/cats_strings.c b/libbdc/bdc_strings/bdc_strings.c
similarity index 80%
rename from src/cats_strings/cats_strings.c
rename to libbdc/bdc_strings/bdc_strings.c
index 4843f1b..64a6733 100644
--- a/src/cats_strings/cats_strings.c
+++ b/libbdc/bdc_strings/bdc_strings.c
@@ -1,6 +1,6 @@
// SPDX-License-Identifier: GPL-3.0-or-later
//
-// cats_strings.c
+// bdc_strings.c
//
// Copyright (C) 2011-2024, University of Vienna and Vienna Institute for Nature Conservation & Analyses, Andreas Gattringer.
//
@@ -19,24 +19,57 @@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
//
-#include "cats_global.h"
+#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#include "cats_strings.h"
-#include <logging/logging.h>
+#include "bdc_strings.h"
+#include "bdc_logging/logging.h"
#include "bdc_memory/bdc_memory.h"
-#include <assert.h>
+
+struct string_array {
+ int count;
+ char **string;
+ enum JSON_HINT *typehint;
+};
void asprintf_check(int rc)
{
if (rc >= 0) return;
- log_message(LOG_ERROR, "error in asprintf_ could not allocate memory or other error. rc: %d", rc);
+ log_message(LOG_ERROR, "error in asprintf - could not allocate memory or other error. rc: %d", rc);
exit(EXIT_FAILURE);
}
+void snprintf_check(int rc, size_t expected)
+{
+ if (rc >= 0 && (rc == expected || rc + 1 == expected)) return;
+ if (rc < 0) {
+ log_message(LOG_ERROR, "error in snprintf - error : %d", rc);
+ exit(EXIT_FAILURE);
+ }
+ if (rc < expected - 1) {
+ log_message(LOG_DEBUG, "error in snprintf - output truncated: %d of %ld bytes written", rc, expected);
+ }
+}
+
+int get_string_count(const struct string_array *array)
+{
+ assert(array != NULL);
+ return array->count;
+}
+
+
+const char *get_string(const struct string_array *array, int count)
+{
+ assert(array != NULL);
+ assert(count >= 0);
+ assert(count < array->count);
+ return array->string[count];
+
+}
+
void string_array_add(struct string_array *array, const char *string)
{
if (!array) {
@@ -51,6 +84,8 @@ void string_array_add(struct string_array *array, const char *string)
DBG_STRING(log_message(LOG_RAW, "%s: address: %p\n", __func__, array);)
DBG_STRING(log_message(LOG_RAW, "%s: count: %d\n", __func__, array->count);)
DBG_STRING(log_message(LOG_RAW, "%s: trying to add: %s\n", __func__, string);)
+ DBG_STRING(log_message(LOG_RAW, "%p: string address: %p\n", __func__, array->string);)
+ DBG_STRING(log_message(LOG_RAW, "%s: new size: %zu\n", __func__, new_size);)
array->string = realloc_or_die(array->string, new_size);
array->typehint = realloc_or_die(array->typehint, sizeof(enum JSON_HINT) * (array->count + 1));
@@ -66,7 +101,7 @@ void string_array_add(struct string_array *array, const char *string)
}
-void string_array_add_conditional(struct string_array *array, char *string, bool condition)
+__attribute__((unused)) void string_array_add_conditional(struct string_array *array, char *string, bool condition)
{
if (!condition) return;
string_array_add(array, string);
@@ -79,8 +114,10 @@ void string_array_add_int(struct string_array *array, int32_t number, const char
if (!format_string || !strlen(format_string)) f = "%d";
int count = snprintf(NULL, 0, f, number) + 1;
+ snprintf_check(count, -1);
char *tmp = malloc_or_die(count);
- snprintf(tmp, count, f, number);
+ int rc = snprintf(tmp, count, f, number);
+ snprintf_check(rc, count);
string_array_add(array, tmp);
array->typehint[array->count - 1] = JSON_NUMERIC;
@@ -94,6 +131,7 @@ void string_array_add_int64(struct string_array *array, int64_t number, char *fo
if (!format_string || !strlen(format_string)) f = "%ld";
int count = snprintf(NULL, 0, f, number) + 1;
+ snprintf_check(count, -1);
char *tmp = malloc_or_die(count);
snprintf(tmp, count, f, number);
@@ -103,20 +141,22 @@ void string_array_add_int64(struct string_array *array, int64_t number, char *fo
}
-void string_array_add_double(struct string_array *array, double number, const char *format_string)
+__attribute__((unused)) void string_array_add_double(struct string_array *array, double number, const char *format_string)
{
const char *f = format_string;
if (!format_string || !strlen(format_string)) f = "%f";
int count = snprintf(NULL, 0, f, number) + 1;
+ snprintf_check(count, -1);
char *tmp = malloc_or_die(count);
- snprintf(tmp, count, f, number);
+ int rc = snprintf(tmp, count, f, number);
+ snprintf_check(rc, count);
string_array_add(array, tmp);
array->typehint[array->count - 1] = JSON_NUMERIC;
free(tmp);
}
-void
+__attribute__((unused)) void
string_array_add_int_conditional(struct string_array *array, int32_t number, const char *format_string, bool condition)
{
if (!condition) return;
@@ -134,11 +174,18 @@ struct string_array *new_string_array()
return result;
}
-const char *get_nth_string_from_array(const struct string_array *array, int n)
+
+__attribute__((unused)) const char *string_array_get_string(const struct string_array *array, int n)
{
+
+ if (array == NULL || array->string == NULL) {
+ log_message(LOG_ERROR, "%s: string array or contents are NULL", __func__);
+ exit(EXIT_FAILURE);
+ }
assert(array != NULL);
+
if (n < 0 && n >= array->count) {
- log_message(LOG_ERROR, "%s: requested string index %d out of range [0, %d]", __func__ , n, array->count);
+ log_message(LOG_ERROR, "%s: requested string index %d out of range [0, %d]", __func__, n, array->count);
exit(EXIT_FAILURE);
}
@@ -146,6 +193,7 @@ const char *get_nth_string_from_array(const struct string_array *array, int n)
}
+
struct string_array *new_string_array_init(const char *entry)
{
struct string_array *result = new_string_array();
@@ -207,16 +255,16 @@ int32_t count_fields(const char *line, const char *sep)
// untested trivial
-void abort_on_null_token(const char *token, char *orig, int count)
+void abort_on_null_token(const char *token, const char *orig, int count)
{
if (token != NULL) return;
log_message(LOG_WARNING, "%s: string '%s' has not enough (%d) tokens", __func__, orig, count);
abort();
- exit(EXIT_FAILURE);
+ //exit(EXIT_FAILURE);
}
-struct string_array *get_all_tokens(char *line, const char *sep)
+struct string_array *get_all_tokens(const char *line, const char *sep)
{
const int32_t max_count = count_fields(line, sep);
@@ -229,6 +277,7 @@ struct string_array *get_all_tokens(char *line, const char *sep)
char *token = strtok_r(copy, sep, &saveptr);
abort_on_null_token(token, line, max_count);
+
char *to_add = strdup(token);
to_add = left_trim(right_trim(to_add));
string_array_add(result, to_add);
@@ -253,7 +302,7 @@ struct string_array *get_all_tokens(char *line, const char *sep)
}
-char *get_nth_token(char *line, const char *sep, int32_t n)
+__attribute__((unused)) char *get_nth_token(char *line, const char *sep, int32_t n)
{
char *result = NULL;
struct string_array *tokens = get_all_tokens(line, sep);
@@ -265,7 +314,7 @@ char *get_nth_token(char *line, const char *sep, int32_t n)
}
-char *remove_0th_token(char *line, const char *sep)
+char *remove_0th_token(const char *line, const char *sep)
{
char *result = NULL;
struct string_array *tokens = get_all_tokens(line, sep);
@@ -302,7 +351,7 @@ char *json_dict(const struct string_array *header, const struct string_array *da
char *result = calloc_or_die(1, len);
- size_t written = 0;
+ size_t written; // = 0;
result[0] = '{'; // written: 1
written = 1;
@@ -361,7 +410,7 @@ char *string_array_paste(const struct string_array *array, const char *sep)
if (length == 0) {
log_message(LOG_ERROR, "%s: empty string, exiting", __func__);
abort();
- exit(EXIT_FAILURE);
+ // exit(EXIT_FAILURE);
}
length += (array->count - 1) * strlen(sep); // space for separator
@@ -382,7 +431,7 @@ char *string_array_paste(const struct string_array *array, const char *sep)
}
-void print_string_array(const struct string_array *array)
+__attribute__((unused)) void print_string_array(const struct string_array *array)
{
log_message(LOG_RAW, "string array with %d entries:\n", array->count);
for (int32_t i = 0; i < array->count; i++) {
@@ -392,7 +441,7 @@ void print_string_array(const struct string_array *array)
}
-int32_t string_array_index(const struct string_array *array, const char *needle)
+__attribute__((unused)) int32_t string_array_string_index(const struct string_array *array, const char *needle)
{
if (array == NULL) {
log_message(LOG_ERROR, "%s: called with empty parameter array", __func__);
@@ -407,7 +456,7 @@ int32_t string_array_index(const struct string_array *array, const char *needle)
}
-bool in_string_array(const struct string_array *array, const char *needle)
+__attribute__((unused)) bool string_array_contains_string(const struct string_array *array, const char *needle)
{
for (int32_t i = 0; i < array->count; i++) {
if (strcmp(needle, array->string[i]) == 0) return true;
@@ -442,6 +491,20 @@ char *compound_string(const char *s1, const char *s2, const char *sep)
size_t len = strlen(s1) + strlen(s2) + strlen(sep) + 1;
result = malloc_or_die(len);
- snprintf(result, len, "%s%s%s", s1, sep, s2);
+ //printf("s1: %s (%ld)\n", s1, strlen(s1));
+ //printf("sep: %s (%ld)\n", sep, strlen(sep));
+ //printf("s2: %s (%ld)\n", s2, strlen(s2));
+ //printf("len: %ld\n", len);
+ int rc = snprintf(result, len, "%s%s%s", s1, sep, s2);
+ //printf("res: %s (%ld)\n", result, strlen(result));
+ snprintf_check(rc, len);
return result;
-}
\ No newline at end of file
+}
+
+
+bool string_is_empty_or_null(const char *name)
+{
+ if (name == NULL) return true;
+ if (strlen(name) == 0) return true; // FIXME CHECK ONLY FIRST X BYTES
+ return false;
+}
diff --git a/src/cats_strings/cats_strings.h b/libbdc/bdc_strings/bdc_strings.h
similarity index 52%
rename from src/cats_strings/cats_strings.h
rename to libbdc/bdc_strings/bdc_strings.h
index d0031c2..7e64d17 100644
--- a/src/cats_strings/cats_strings.h
+++ b/libbdc/bdc_strings/bdc_strings.h
@@ -1,6 +1,6 @@
// SPDX-License-Identifier: GPL-3.0-or-later
//
-// cats_strings.h
+// bdc_strings.h
//
// Copyright (C) 2011-2024, University of Vienna and Vienna Institute for Nature Conservation & Analyses, Andreas Gattringer.
//
@@ -21,51 +21,44 @@
#ifndef CATS_STRING_H_
#define CATS_STRING_H_
+
#include <stdlib.h>
#include <stdbool.h>
#include <stdint.h>
-#include "data/error.h"
+#include <stdio.h>
+
+struct string_array;
+struct string_substitution;
enum JSON_HINT {
JSON_STRING = 0,
JSON_QUOTED = 0,
JSON_UNQUOTED = 1,
JSON_NUMERIC = 1
};
+// constants
+#define TEXT_DIVIDER "=================================================================================================="
+#define PAD_NAME 55
+#define PAD_VALUE 35
-struct string_array {
- int count;
- char **string;
- enum JSON_HINT *typehint;
-};
-
-
-
-
-#include <stdio.h>
-
-#define MAX_STRING_BUFF_LENGTH 2048
-
-char *read_single_line(FILE *file);
-
-char *slurp_file(const char *filename);
+//#define DEBUG_STRING
+#ifdef DEBUG_STRING
+#define DBG_STRING(X) {X;}while(0);
+#else
+#define DBG_STRING(X)
+#endif
-#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);\
-}
+// string array functions
+struct string_array *new_string_array(void);
-void asprintf_check(int rc);
+const char *get_string(const struct string_array *array, int count);
-struct string_array *new_string_array(void);
+int get_string_count(const struct string_array *array);
void free_string_array(struct string_array **array);
-int32_t count_fields(const char *line, const char *sep);
+struct string_array *get_all_tokens(const char *line, const char *sep);
-struct string_array *get_all_tokens(char *line, const char *seperator);
void string_array_add(struct string_array *array, const char *string);
@@ -73,33 +66,42 @@ void string_array_add_int64(struct string_array *array, int64_t number, char *fo
char *string_array_paste(const struct string_array *array, const char *sep);
-char *assemble_filename(struct string_array *path, struct string_array *filename, char *filesep, char *extension);
void string_array_add_int(struct string_array *array, int32_t number, const char *format_string);
struct string_array *new_string_array_init(const char *entry);
-void string_array_add_conditional(struct string_array *array, char *string, bool conditon);
+__attribute__((unused)) void string_array_add_conditional(struct string_array *array, char *string, bool conditon);
-void string_array_add_double(struct string_array *array, double number, const char *format_string);
+__attribute__((unused)) void string_array_add_double(struct string_array *array, double number, const char *format_string);
-void
+__attribute__((unused)) void
string_array_add_int_conditional(struct string_array *array, int32_t number, const char *format_string, bool condition);
-const char *get_nth_string_from_array(const struct string_array *array, int n);
-void print_string_array(const struct string_array *array);
-char *remove_0th_token(char *line, const char *sep);
+__attribute__((unused)) const char *string_array_get_string(const struct string_array *array, int n);
+
+__attribute__((unused)) void print_string_array(const struct string_array *array);
-char *get_nth_token(char *line, const char *sep, int32_t n);
struct string_array *copy_string_array(const struct string_array *src);
char *json_dict(const struct string_array *header, const struct string_array *data);
-int32_t string_array_index(const struct string_array *array, const char *needle);
+int32_t string_array_string_index(const struct string_array *array, const char *needle);
+
+__attribute__((unused)) bool string_array_contains_string(const struct string_array *array, const char *needle);
+
+
+// string functions
+char *trim_both(char *line);
+
+int32_t count_fields(const char *line, const char *sep);
+
-bool in_string_array(const struct string_array *array, const char *needle);
+char *remove_0th_token(const char *line, const char *sep);
+
+__attribute__((unused)) char *get_nth_token(char *line, const char *sep, int32_t n);
size_t substring_count(const char *haystack, const char *needle);
@@ -115,14 +117,20 @@ char *right_trim(char *line);
char *left_trim(char *line);
-void abort_on_null_token(const char *token, char *orig, int count);
+bool string_is_empty_or_null(const char *name);
-#define PAD_NAME 55
-#define PAD_VALUE 35
+void abort_on_null_token(const char *token, const char *orig, int count);
+// helper functions
+
+void asprintf_check(int rc);
+void snprintf_check(int rc, size_t expected);
+
+
+// pretty print functions
void print_string(int indent, const char *name, const char *value);
-void print_subcategory(int indent, const char *category_name, int64_t category_number, char *name);
+void print_subcategory(int indent, const char *category_name, int64_t category_number, const char *name);
void print_category(int indent, const char *category, const char *name);
@@ -130,15 +138,38 @@ void print_integer(int indent, const char *name, int64_t value);
void print_rate(int indent, const char *name, long double value);
+
+
+// string substitution
+
+void add_substitution(struct string_substitution *substituter, const char *key, const char *initial_value);
+
+void update_substitution(struct string_substitution *substituter, const char *key, const char *initial_value);
+
+struct string_substitution *new_substituter(void);
+
+char *substitute_string(const char *string, const struct string_substitution *substituter);
+
+void destroy_substituter(struct string_substitution **substituter);
+
+struct string_substitution *copy_substituter(const struct string_substitution *from);
+
+void add_substitution_integer(struct string_substitution *substituter, const char *key, int32_t initial_value);
+
+void set_integer_pattern(struct string_substitution *substituter, const char *key, const char *pattern);
+
+
+// conversion function
const char *bool_to_string(bool b);
-#ifdef DEBUG_STRING
-#define DBG_STRING(X) {X;}while(0);
-#else
-#define DBG_STRING(X)
-#endif
+bool string_to_float(char *string, float *value);
+
+bool string_to_bool(char *string, bool *value);
+
+bool string_to_double(const char *string, double *value);
-// implemented in string_helpers.h
+bool string_to_integer(const char *string, int32_t *value);
+bool string_to_long_double(const char *string, long double *value);
#endif
diff --git a/src/cats_strings/pretty_print.c b/libbdc/bdc_strings/pretty_print.c
similarity index 95%
rename from src/cats_strings/pretty_print.c
rename to libbdc/bdc_strings/pretty_print.c
index fb94e70..a3797c3 100644
--- a/src/cats_strings/pretty_print.c
+++ b/libbdc/bdc_strings/pretty_print.c
@@ -19,10 +19,11 @@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
//
-#include "cats_global.h"
+
#include <inttypes.h>
-#include "cats_strings.h"
-#include "logging/logging.h"
+#include "bdc_strings.h"
+#include "bdc_logging/logging.h"
+
void print_string(int indent, const char *name, const char *value)
{
@@ -32,7 +33,7 @@ void print_string(int indent, const char *name, const char *value)
}
-void print_subcategory(int indent, const char *category_name, int64_t category_number, char *name)
+void print_subcategory(int indent, const char *category_name, int64_t category_number, const char *name)
{
indent *= 2;
if (indent > 0) log_message(LOG_RAW, "%*s", indent, "");
diff --git a/src/cats_strings/string_converters.c b/libbdc/bdc_strings/string_converters.c
similarity index 94%
rename from src/cats_strings/string_converters.c
rename to libbdc/bdc_strings/string_converters.c
index 5578c1e..c7b8b74 100644
--- a/src/cats_strings/string_converters.c
+++ b/libbdc/bdc_strings/string_converters.c
@@ -25,8 +25,10 @@
#include <string.h>
#include <errno.h>
#include <stdlib.h>
-#include "string_converters.h"
-#include "logging/logging.h"
+
+
+#include "bdc_logging/logging.h"
+
const char *true_values[] = {"1", "y", "t"};
const char *false_values[] = {"0", "n", "f"};
@@ -34,7 +36,7 @@ const int true_counts = (int) (sizeof(true_values) / sizeof(char *));
const int false_counts = (int) (sizeof(false_values) / sizeof(char *));
-bool string_to_double(char *string, double *value)
+bool string_to_double(const char *string, double *value)
{
if (string == NULL || strlen(string) == 0) return false;
@@ -82,7 +84,7 @@ bool string_to_float(char *string, float *value)
}
-bool string_to_long_double(char *string, long double *value)
+bool string_to_long_double(const char *string, long double *value)
{
if (string == NULL || strlen(string) == 0) return false;
@@ -127,7 +129,7 @@ bool string_to_bool(char *string, bool *value)
}
-bool string_to_integer(char *string, int32_t *value)
+bool string_to_integer(const char *string, int32_t *value)
{
if (string == NULL || strlen(string) == 0) return false;
@@ -148,3 +150,7 @@ bool string_to_integer(char *string, int32_t *value)
return false;
}
+
+
+
+
diff --git a/src/cats_strings/string_helpers.c b/libbdc/bdc_strings/string_helpers.c
similarity index 90%
rename from src/cats_strings/string_helpers.c
rename to libbdc/bdc_strings/string_helpers.c
index eb6553f..9c46586 100644
--- a/src/cats_strings/string_helpers.c
+++ b/libbdc/bdc_strings/string_helpers.c
@@ -19,12 +19,11 @@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
//
-#include "cats_global.h"
#include <stdlib.h>
#include <stdbool.h>
#include <string.h>
#include <ctype.h>
-#include <logging/logging.h>
+#include "bdc_logging/logging.h"
#include "bdc_memory/bdc_memory.h"
@@ -78,6 +77,13 @@ char *left_trim(char *line)
}
+char *trim_both(char *line)
+{
+ return left_trim(right_trim(line));
+
+}
+
+
size_t substring_count(const char *haystack, const char *needle)
{
size_t count = 0;
@@ -134,8 +140,8 @@ char *replace_substring(const char *original, const char *search, const char *re
exit(EXIT_FAILURE);
}
- size_t occurrences = substring_count(original, search);
- size_t result_len = strlen(original) + strlen(replacement) * occurrences - strlen(search) * occurrences + 1;
+ size_t n_occurrences = substring_count(original, search);
+ size_t result_len = strlen(original) + strlen(replacement) * n_occurrences - strlen(search) * n_occurrences + 1;
char *result = calloc_or_die(1, result_len);
@@ -144,20 +150,24 @@ char *replace_substring(const char *original, const char *search, const char *re
size_t bytes_copied = 0;
- for (size_t i = 0; i < occurrences; i++) {
+ for (size_t i = 0; i < n_occurrences; i++) {
char *next_occurrence = strstr(orig_loc, search);
- if (next_occurrence == NULL) { break; }
+ if (next_occurrence == NULL || strlen(next_occurrence) == 0) { break; }
+
+ // how many bytes are before our first hit?
size_t bytes_to_copy = strlen(orig_loc) - strlen(next_occurrence);
+
+
if (bytes_to_copy) {
bytes_copied += bytes_to_copy;
strncpy(result_loc, orig_loc, bytes_to_copy);
result_loc += bytes_to_copy;
- orig_loc += bytes_to_copy + search_len;
+ orig_loc += bytes_to_copy;
}
-
-
strncpy(result_loc, replacement, replacement_len);
result_loc += replacement_len;
+ orig_loc += search_len;
+
}
if (bytes_copied < original_len) {
diff --git a/libbdc/bdc_strings/string_substitution.c b/libbdc/bdc_strings/string_substitution.c
new file mode 100644
index 0000000..2ee87c1
--- /dev/null
+++ b/libbdc/bdc_strings/string_substitution.c
@@ -0,0 +1,158 @@
+// SPDX-License-Identifier: GPL-3.0-or-later
+//
+// string_substitution.c
+//
+// 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.
+//
+
+#include <string.h>
+
+#include "bdc_memory/bdc_memory.h"
+#include "bdc_logging/logging.h"
+#include "bdc_hashtable/bdc_hashtable.h"
+#include "bdc_strings.h"
+
+struct string_substitution {
+ struct bdc_hash_table *substitution_strings;
+ struct bdc_hash_table *integer_patterns;
+ struct string_array *keys;
+};
+
+struct string_substitution *new_substituter()
+{
+ struct string_substitution *new = calloc_or_die(1, sizeof(struct string_substitution));
+ new->substitution_strings = new_hash_table();
+ new->integer_patterns = new_hash_table();
+ new->keys = new_string_array();
+ return new;
+}
+
+
+void set_integer_pattern(struct string_substitution *substituter, const char *key, const char *pattern)
+{
+ if (substituter == NULL) {
+ log_message(LOG_ERROR, "%s: substituter == NULL", __func__);
+ exit(EXIT_FAILURE);
+ }
+ bdc_ht_add_string(substituter->integer_patterns, key, pattern);
+}
+
+void add_substitution_integer(struct string_substitution *substituter, const char *key, int32_t initial_value)
+{
+ if (substituter == NULL) {
+ log_message(LOG_ERROR, "%s: substituter == NULL", __func__);
+ exit(EXIT_FAILURE);
+ }
+
+ char *default_pattern = "%d";
+ char *pattern = NULL;
+ char *loaded_pattern = NULL;
+ bdc_ht_get_string_from_key(substituter->integer_patterns, key, &loaded_pattern);
+ if (!loaded_pattern) {
+ pattern = default_pattern;
+
+ } else {
+ pattern = loaded_pattern;
+ }
+
+ char *value = NULL;
+ int rc = asprintf(&value, pattern, initial_value);
+ asprintf_check(rc);
+ add_substitution(substituter, key, value);
+ free(value);
+ free(loaded_pattern);
+}
+
+
+
+
+
+void add_substitution(struct string_substitution *substituter, const char *key, const char *initial_value)
+{
+ if (!bdc_key_in_hash_table(substituter->substitution_strings, key)) {
+ string_array_add(substituter->keys, key);
+ }
+
+ bdc_ht_add_string(substituter->substitution_strings, key, initial_value);
+}
+
+char *substitute_string(const char *string, const struct string_substitution *substituter)
+{
+ if (substituter == NULL) {
+ log_message(LOG_ERROR, "%s: substituter == NULL", __func__);
+ exit(EXIT_FAILURE);
+ }
+ if (substituter->keys == NULL) {
+ log_message(LOG_ERROR, "%s: substituter invalid, keys = NULL", __func__);
+ exit(EXIT_FAILURE);
+ }
+ log_message(LOG_INFO, "substituting string '%s' with %d potential substitutions", string, get_string_count(substituter->keys));
+ const int count = get_string_count(substituter->keys);
+ char *copy = strdup(string);
+ char *result = strdup(string);
+ for (int i = 0; i < count; i++) {
+ const char *key = get_string(substituter->keys, i);
+ char *value = NULL;
+ bool found = bdc_ht_get_string_from_key(substituter->substitution_strings, key, &value);
+ if (! found) {
+ continue;
+ }
+ free(result);
+ result = replace_substring(copy, key, value);
+ free(copy);
+ copy = strdup(result);
+
+
+ }
+ free(copy);
+ return result;
+}
+
+void destroy_substituter(struct string_substitution **substituter)
+{
+ if (substituter == NULL || *substituter == NULL) return;
+ struct string_substitution *s = *substituter;
+ free_string_array(&s->keys);
+ destroy_hash_table(&s->substitution_strings);
+ destroy_hash_table(&s->integer_patterns);
+ free(s);
+ *substituter = NULL;
+
+}
+
+struct string_substitution *copy_substituter(const struct string_substitution *from)
+{
+ if (from == NULL) return NULL;
+ struct string_substitution *to = new_substituter();
+ const struct string_array *keys = from->keys;
+ const int32_t count = get_string_count(keys);
+ for (int32_t i = 0; i< count; i++) {
+ const char *key = get_string(keys, i);
+ char *value = NULL;
+ bdc_ht_get_string_from_key(from->substitution_strings, key, &value);
+ if (value) {
+ add_substitution(to, key, value);
+ }
+ bdc_ht_get_string_from_key(from->integer_patterns, key, &value);
+ if (value) {
+ set_integer_pattern(to, key, value);
+ }
+
+ }
+
+ return to;
+}
\ No newline at end of file
diff --git a/libbdc/bdc_time/bdc_time.c b/libbdc/bdc_time/bdc_time.c
index 41bc4a6..2d7908c 100644
--- a/libbdc/bdc_time/bdc_time.c
+++ b/libbdc/bdc_time/bdc_time.c
@@ -1,25 +1,23 @@
-/*
- * SPDX-License-Identifier: GPL-3.0-or-later
- *
- * bdc_time.c
- *
- * Copyright (C) 2011-2022, 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.
- *
- */
+// SPDX-License-Identifier: GPL-3.0-or-later
+//
+// bdc_time.c
+//
+// 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.
+//
#include <time.h>
#include <stdio.h>
diff --git a/libbdc/bdc_time/bdc_time.h b/libbdc/bdc_time/bdc_time.h
index 68ff826..d8f8227 100644
--- a/libbdc/bdc_time/bdc_time.h
+++ b/libbdc/bdc_time/bdc_time.h
@@ -1,25 +1,23 @@
-/*
- * SPDX-License-Identifier: GPL-3.0-or-later
- *
- * bdc_time.h
- *
- * Copyright (C) 2011-2022, 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.
- *
- */
+// SPDX-License-Identifier: GPL-3.0-or-later
+//
+// bdc_time.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 BDC_TIME_H
#define BDC_TIME_H
diff --git a/libbdc/bdc_time/bdc_timer.c b/libbdc/bdc_time/bdc_timer.c
index 321951d..2a147c2 100644
--- a/libbdc/bdc_time/bdc_timer.c
+++ b/libbdc/bdc_time/bdc_timer.c
@@ -1,3 +1,24 @@
+// SPDX-License-Identifier: GPL-3.0-or-later
+//
+// bdc_timer.c
+//
+// 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.
+//
+
#include <assert.h>
#include <stdlib.h>
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index ee838a3..423f4c7 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,6 +1,5 @@
-add_subdirectory(logging)
+
add_subdirectory(cats)
-add_subdirectory(cats_strings)
add_subdirectory(cats_ini)
add_subdirectory(cats_csv)
add_subdirectory(modules/cats_test_module)
diff --git a/src/cats/CMakeLists.txt b/src/cats/CMakeLists.txt
index 66572ef..ff9fab8 100644
--- a/src/cats/CMakeLists.txt
+++ b/src/cats/CMakeLists.txt
@@ -318,15 +318,15 @@ set(CATS_SOURCES_MPI
)
add_executable(cats cats.c)
-target_link_libraries(libcats cats_logging bdc cats_strings cats_ini cats_csv)
-target_link_libraries(cats libcats cats_logging bdc cats_strings cats_ini cats_csv)
+target_link_libraries(libcats bdc_logging bdc bdc_strings cats_ini cats_csv)
+target_link_libraries(cats libcats bdc_logging bdc bdc_strings cats_ini cats_csv)
if (MSVC)
# target_include_directories(cats PRIVATE ${GDAL_INCLUDE_DIRS})
- # target_link_libraries(cats cats_logging cats_memory cats_strings cats_ini cats_csv ${GDAL_LIBRARIES})
+ # target_link_libraries(cats bdc_logging bdc_memory bdc_strings cats_ini cats_csv ${GDAL_LIBRARIES})
else ()
- target_link_libraries(cats cats_logging bdc cats_strings cats_ini cats_csv)
+ target_link_libraries(cats bdc_logging bdc bdc_strings cats_ini cats_csv)
endif ()
@@ -334,7 +334,7 @@ if (MPI_FOUND)
add_executable(cats-mpi cats.c ${CATS_SOURCES_MPI})
- target_link_libraries(cats-mpi ${MPI_C_LIBRARIES} cats_logging bdc_memory cats_strings cats_ini cats_csv libcats)
+ target_link_libraries(cats-mpi ${MPI_C_LIBRARIES} bdc_logging bdc_memory bdc_strings cats_ini cats_csv libcats)
target_compile_options(cats-mpi PRIVATE -DUSEMPI)
diff --git a/src/cats/actions/setup_actions.c b/src/cats/actions/setup_actions.c
index e3a1539..274d8a6 100644
--- a/src/cats/actions/setup_actions.c
+++ b/src/cats/actions/setup_actions.c
@@ -28,7 +28,7 @@
#include "actions/setup_actions.h"
#include "actions/cats_actions.h"
#include "actions/process_inter_period_survival.h"
-#include "cats_strings/cats_strings.h"
+#include "bdc_strings/bdc_strings.h"
#include "dispersal/dispersal.h"
#include "bdc_memory/bdc_memory.h"
diff --git a/src/cats/cats.c b/src/cats/cats.c
index a0d5a4f..d2c14b3 100644
--- a/src/cats/cats.c
+++ b/src/cats/cats.c
@@ -31,7 +31,7 @@
#include "cats_global.h"
#include <cats_ini/cats_ini.h>
-#include <logging/logging.h>
+#include <bdc_logging/logging.h>
#include "cats/command_line/command_line_info.h"
#include "cats/command_line/command_line_options.h"
diff --git a/src/cats/command_line/command_line_info.c b/src/cats/command_line/command_line_info.c
index 779d32e..fb3b699 100644
--- a/src/cats/command_line/command_line_info.c
+++ b/src/cats/command_line/command_line_info.c
@@ -24,7 +24,7 @@
#include "vital_rates/vital_rates_helper.h"
#include "command_line_options.h"
#include "command_line_info.h"
-#include "logging/logging.h"
+#include "bdc_logging/logging.h"
#include "cats_ini/cats_ini.h"
#include "defaults.h"
#include "cats_global.h"
diff --git a/src/cats/command_line/command_line_options.h b/src/cats/command_line/command_line_options.h
index df6924e..35f4287 100644
--- a/src/cats/command_line/command_line_options.h
+++ b/src/cats/command_line/command_line_options.h
@@ -25,7 +25,7 @@
#include <getopt.h>
#include <stdlib.h>
#include <stdbool.h>
-#include "logging/logging.h"
+#include "bdc_logging/logging.h"
#include "cats_global.h"
@@ -114,7 +114,7 @@ struct program_options {
bool lambda_test;
enum cats_debug_flags debug_flags;
- enum cats_log_level default_log_level;
+ enum bdc_log_level default_log_level;
bool show_unused_config_values;
bool show_unspecified_config_values;
bool have_poisson_dampening_factor;
diff --git a/src/cats/configuration/load_config_spatial.c b/src/cats/configuration/load_config_spatial.c
index 6fed729..fa9ae72 100644
--- a/src/cats/configuration/load_config_spatial.c
+++ b/src/cats/configuration/load_config_spatial.c
@@ -25,7 +25,7 @@
#include "misc/misc.h"
#include "logging.h"
#include "cats_ini/cats_ini.h"
-#include "cats_strings/cats_strings.h"
+#include "bdc_strings/bdc_strings.h"
#include "load_configuration_temporal.h"
#include "paths/paths.h"
#include "grids/gdal_helper.h"
@@ -34,7 +34,7 @@
void load_simulation_geometry_from_initial_population(struct cats_configuration *conf, struct cats_ini *ini)
{
struct string_array *species_sections = get_sections_with_prefix(ini, "species");
- if (species_sections->count == 0) {
+ if (get_string_count(species_sections) == 0) {
log_message(LOG_ERROR, "%s: could not load any species information", __func__);
exit_cats(EXIT_FAILURE);
}
@@ -53,9 +53,9 @@ void load_simulation_geometry_from_initial_population(struct cats_configuration
}
char *file_name = NULL;
bool load_ini_pop = ! conf->command_line_options.no_input_rasters_required;
- for (int32_t i = 0; i < species_sections->count; i++) {
- char *species_section = species_sections->string[i];
-
+ size_t count = get_string_count(species_sections);
+ for (int32_t i = 0; i < count; i++) {
+ const char *species_section = get_string(species_sections, i);
load_conf_value(load_ini_pop, ini, species_section, "initial population filename", &file_name); // VR::ignored::
break;
}
diff --git a/src/cats/configuration/load_configuration.c b/src/cats/configuration/load_configuration.c
index e312c92..7b768ad 100644
--- a/src/cats/configuration/load_configuration.c
+++ b/src/cats/configuration/load_configuration.c
@@ -25,7 +25,7 @@
#include <assert.h>
#include <cats_ini/cats_ini.h>
-#include <logging/logging.h>
+#include <bdc_logging/logging.h>
#ifdef USEMPI
#include "mpi/mpi_cats.h"
@@ -48,6 +48,7 @@
#include "load_configuration_modules.h"
#include "test/test_ini.h"
#include "debug/debug_vital_rates.h"
+#include "bdc_io/bdc_io.h"
void load_configuration_elements(struct cats_configuration *conf, struct cats_ini *ini);
diff --git a/src/cats/configuration/load_configuration_dispersal.c b/src/cats/configuration/load_configuration_dispersal.c
index 045df97..d180881 100644
--- a/src/cats/configuration/load_configuration_dispersal.c
+++ b/src/cats/configuration/load_configuration_dispersal.c
@@ -26,8 +26,8 @@
#include <string.h>
#include <stdbool.h>
-#include <logging/logging.h>
-#include <cats_strings/cats_strings.h>
+#include <bdc_logging/logging.h>
+#include <bdc_strings/bdc_strings.h>
#include "data/species_parameters.h"
#include "load_configuration_helper.h"
@@ -42,10 +42,13 @@ bool load_dispersal_info(struct cats_configuration *conf, struct cats_ini *ini,
struct string_array *prob_min = get_char_array_from_conf2(ini, dispersal_section, "minimum weights");
struct string_array *prob_max = get_char_array_from_conf2(ini, dispersal_section, "maximum weights");
- if (!((file_names->count == prob_min->count) && (file_names->count == prob_max->count))) {
+ if (!((get_string_count(file_names) == get_string_count(prob_min)) &&
+ (get_string_count(file_names) == get_string_count(prob_max)))) {
log_message(LOG_ERROR, "CONF: count mismatch: %d file names, %d minimum weights, "
- "%d maximum weights. Expected all counts to be equal.", file_names->count,
- prob_min->count, prob_max->count);
+ "%d maximum weights. Expected all counts to be equal.",
+ get_string_count(file_names),
+ get_string_count(prob_min),
+ get_string_count(prob_max));
exit(EXIT_FAILURE);
}
@@ -64,20 +67,20 @@ bool load_dispersal_info(struct cats_configuration *conf, struct cats_ini *ini,
dispersal->long_range_enabled = true;
}
- for (int32_t i = 0; i < file_names->count; i++) {
+ for (int32_t i = 0; i <get_string_count(file_names); i++) {
dispersal->types[i] = DISPERSAL_KERNEL;
- bool pmin_succ = string_to_long_double(prob_min->string[i], &pmin);
- bool pmax_succ = string_to_long_double(prob_max->string[i], &pmax);
+ bool pmin_succ = string_to_long_double(get_string(prob_min, i), &pmin);
+ bool pmax_succ = string_to_long_double(get_string(prob_min, i), &pmax);
if (pmin_succ == false || pmax_succ == false) {
log_message(LOG_ERROR, "CONF: error reading minimum and maximum probability: "
"'%s' and '%s'",
- prob_min->string[i], prob_max->string[i]);
+ get_string(prob_min, i), get_string(prob_min, i));
exit(EXIT_FAILURE);
}
- if (file_names->count > i && file_names->string[i]) {
- dispersal->filenames[i] = strdup(file_names->string[i]);
+ if (get_string_count(file_names) > i && get_string(file_names, i)) {
+ dispersal->filenames[i] = strdup(get_string(file_names, i));
}
if ((pmax >= 0 && pmax <= 1.0 && pmin >= 0 && pmin <= 1.0 && pmax >= pmin) ||
diff --git a/src/cats/configuration/load_configuration_environments.c b/src/cats/configuration/load_configuration_environments.c
index 08f0f70..94cc25e 100644
--- a/src/cats/configuration/load_configuration_environments.c
+++ b/src/cats/configuration/load_configuration_environments.c
@@ -42,7 +42,7 @@ enum environment_variable_type get_environment_variable_type_from_string(const c
}
-void add_environment_variable_from_conf(struct cats_configuration *conf, struct cats_ini *ini, char *environment_section)
+void add_environment_variable_from_conf(struct cats_configuration *conf, struct cats_ini *ini, const char *environment_section)
{
struct array_dimension *dimension = &conf->geometry.dimension;
char *name = remove_0th_token(environment_section, ":");
@@ -126,14 +126,16 @@ void load_environments_configuration(struct cats_configuration *conf, struct cat
//struct string_array *suitability_variables = get_sections_with_prefix(ini, "suitability");
struct string_array *glms = get_sections_with_prefix(ini, "glm");
+ size_t count = get_string_count(env_variables);
+ for (int32_t i = 0; i < count; i++) {
- for (int32_t i = 0; i < env_variables->count; i++) {
- add_environment_variable_from_conf(conf, ini, env_variables->string[i]);
+ add_environment_variable_from_conf(conf, ini, get_string(env_variables, i));
}
-
- for (int32_t i = 0; i < glms->count; i++) {
- add_glm_from_conf(conf, ini, glms->string[i]);
+ count = get_string_count(glms);
+ for (int32_t i = 0; i < count; i++) {
+ char *name = strdup(get_string(glms, i)); // FIXME, make add_glm_from_conf argument const
+ add_glm_from_conf(conf, ini, name);
}
diff --git a/src/cats/configuration/load_configuration_glm.c b/src/cats/configuration/load_configuration_glm.c
index d5d1745..3c234a3 100644
--- a/src/cats/configuration/load_configuration_glm.c
+++ b/src/cats/configuration/load_configuration_glm.c
@@ -115,14 +115,14 @@ void add_glm_from_conf(struct cats_configuration *conf, struct cats_ini *ini, ch
}
struct glm_params glm = {0};
struct string_array *predictors = get_char_array_from_conf2(ini, environment_section, "predictors");
- if (predictors->count == 0) {
+ if (get_string_count(predictors) == 0) {
log_message(LOG_ERROR, "%s: section [%s] does not contain any predictor names", __func__, environment_section);
exit_cats(EXIT_FAILURE);
}
- if (predictors->count > MAX_ENVIRONMENTS) {
+ if (get_string_count(predictors) > MAX_ENVIRONMENTS) {
log_message(LOG_ERROR, "%s: section [%s]: more predictors (%d) found than the allowed maximum %d",
__func__, environment_section,
- predictors->count, MAX_ENVIRONMENTS);
+ get_string_count(predictors), MAX_ENVIRONMENTS);
exit_cats(EXIT_FAILURE);
}
enum environment_type type = get_environment_glm_type(type_name);
@@ -142,15 +142,15 @@ void add_glm_from_conf(struct cats_configuration *conf, struct cats_ini *ini, ch
free(family_name);
- for (int32_t i = 0; i < predictors->count; i++) {
- get_environment_from_registry(&conf->environment_registry, predictors->string[i]);
- char *predictor_linear = compound_string(predictors->string[i], "linear", " ");
+ for (int32_t i = 0; i < get_string_count(predictors); i++) {
+ get_environment_from_registry(&conf->environment_registry, get_string(predictors,i));
+ char *predictor_linear = compound_string(get_string(predictors, i), "linear", " ");
load_conf_value(true, ini, environment_section, predictor_linear, &glm.linear[i]);
free(predictor_linear);
glm.count += 1;
if (glm.type == GLM_QUADRATIC) {
- char *predictor_quadratic = compound_string(predictors->string[i], "quadratic", " ");
+ char *predictor_quadratic = compound_string(get_string(predictors, i), "quadratic", " ");
load_conf_value(true, ini, environment_section, predictor_quadratic, &glm.quadratic[i]);
free(predictor_quadratic);
}
@@ -160,9 +160,9 @@ void add_glm_from_conf(struct cats_configuration *conf, struct cats_ini *ini, ch
struct cats_environment *set = add_environment(conf, name, type, &glm);
load_conf_value(false, ini, environment_section, "save environment", &set->save_environment);
- for (int32_t i = 0; i < predictors->count; i++) {
+ for (int32_t i = 0; i < get_string_count(predictors); i++) {
struct cats_environment_variable *env = get_environment_from_registry(&conf->environment_registry,
- predictors->string[i]);
+ get_string(predictors, i));
add_to_environment(set, env);
}
diff --git a/src/cats/configuration/load_configuration_helper.c b/src/cats/configuration/load_configuration_helper.c
index 2e93757..ee3c452 100644
--- a/src/cats/configuration/load_configuration_helper.c
+++ b/src/cats/configuration/load_configuration_helper.c
@@ -60,7 +60,7 @@ void reset_same_dispersals(bool all_same, struct cats_configuration_counts *coun
}
-int32_t count_kernel_dispersal_for_species(struct cats_ini *ini, char *species_section)
+int32_t count_kernel_dispersal_for_species(struct cats_ini *ini, const char *species_section)
{
int32_t dispersal_count = 0;
char *dispersal_name = NULL;
@@ -77,14 +77,14 @@ int32_t count_kernel_dispersal_for_species(struct cats_ini *ini, char *species_s
struct string_array *dispersal_kernel_filenames = get_char_array_from_conf2(ini, dispersal_section_name,
"kernel filenames");
- if (!dispersal_kernel_filenames->count) {
+ if (!get_string_count(dispersal_kernel_filenames)) {
log_message(LOG_ERROR,
"Error creating configuration structures: could not load dispersal information for species '%s': '%s' [%s]",
species_section, dispersal_name, dispersal_section_name);
exit_cats(EXIT_FAILURE);
}
- dispersal_count = dispersal_kernel_filenames->count;
+ dispersal_count = get_string_count(dispersal_kernel_filenames);
free(dispersal_section_name);
free_string_array(&dispersal_kernel_filenames);
@@ -100,13 +100,13 @@ struct cats_configuration_counts get_counts_from_config(struct cats_ini *ini)
// required
struct string_array *species = get_sections_with_prefix(ini, "species");
- counts.species = species->count;
+ counts.species = get_string_count(species);
counts.dispersals = new_raw_1d_array(counts.species, sizeof(int));
for (int i = 0; i < counts.species; i++) {
- counts.dispersals[i] = count_kernel_dispersal_for_species(ini, species->string[i]);
+ counts.dispersals[i] = count_kernel_dispersal_for_species(ini, get_string(species, i));
}
free_string_array(&species);
diff --git a/src/cats/configuration/load_configuration_modules.c b/src/cats/configuration/load_configuration_modules.c
index 281d1eb..bd3c3d7 100644
--- a/src/cats/configuration/load_configuration_modules.c
+++ b/src/cats/configuration/load_configuration_modules.c
@@ -29,9 +29,9 @@
void load_configuration_modules(struct cats_configuration *conf, struct cats_ini *ini)
{
struct string_array *modules = get_sections_with_prefix(ini, "module");
- for (int32_t i = 0; i < modules->count; i++) {
+ for (int32_t i = 0; i < get_string_count(modules); i++) {
- char *module_section = modules->string[i];
+ const char *module_section = get_string(modules, i);
char *name = remove_0th_token(module_section, ":");
if (i >= MAX_MODULES) {
log_message(LOG_ERROR, "too many modules, limit is %d", MAX_MODULES);
diff --git a/src/cats/configuration/load_configuration_overlays.c b/src/cats/configuration/load_configuration_overlays.c
index 31fe1d7..f48163d 100644
--- a/src/cats/configuration/load_configuration_overlays.c
+++ b/src/cats/configuration/load_configuration_overlays.c
@@ -24,8 +24,8 @@
#include <string.h>
#include <math.h>
-#include <logging/logging.h>
-#include <cats_strings/cats_strings.h>
+#include <bdc_logging/logging.h>
+#include <bdc_strings/bdc_strings.h>
#include "load_configuration_overlays.h"
#include "overlays/overlay_habitat_type_cc.h"
#include "grids/grid_setup.h"
@@ -36,15 +36,15 @@ void load_overlay_configuration(struct cats_configuration *conf, struct cats_ini
if (conf->command_line_options.no_input_rasters_required) return;
struct string_array *overlay_names = get_sections_with_prefix(ini, "overlay");
- for (int32_t i = 0; i < overlay_names->count; i++) {
- char *overlay_section = overlay_names->string[i];
+ for (int32_t i = 0; i < get_string_count(overlay_names); i++) {
+ const char *overlay_section = get_string(overlay_names, i);
bool enabled = true;
load_conf_value(false, ini, overlay_section, "enabled", &enabled);
if (enabled == false) {
continue;
}
- char *overlay_name = remove_0th_token(overlay_names->string[i], ":");
+ char *overlay_name = remove_0th_token(get_string(overlay_names, i), ":");
char *type_name = NULL;
diff --git a/src/cats/configuration/load_configuration_species_params.c b/src/cats/configuration/load_configuration_species_params.c
index a7418dd..ec3ce4e 100644
--- a/src/cats/configuration/load_configuration_species_params.c
+++ b/src/cats/configuration/load_configuration_species_params.c
@@ -30,7 +30,7 @@
#include "bdc_memory/bdc_memory.h"
#include <cats_ini/cats_ini.h>
-#include <logging/logging.h>
+#include <bdc_logging/logging.h>
#include "configuration/configuration.h"
#include "load_configuration_dispersal.h"
@@ -46,7 +46,7 @@ enum sexuality_type get_sexuality_from_string(const char *string)
}
-void preload_default_vital_rates_for_presets(struct cats_configuration *conf, struct cats_ini *ini, char *species_section,
+void preload_default_vital_rates_for_presets(struct cats_configuration *conf, struct cats_ini *ini, const char *species_section,
struct cats_species_param *p)
{
// load values that could be used for presets -- e.g. some presets could depend on these values
@@ -62,7 +62,7 @@ void preload_default_vital_rates_for_presets(struct cats_configuration *conf, st
}
-void preload_default_vital_ages_for_presets(struct cats_configuration *conf, struct cats_ini *ini, char *species_section,
+void preload_default_vital_ages_for_presets(struct cats_configuration *conf, struct cats_ini *ini, const char *species_section,
struct cats_species_param *p)
{
for (enum cats_vital_age_id age_id = VA_MIN + 1; age_id < VA_MAX; age_id++) {
@@ -73,7 +73,7 @@ void preload_default_vital_ages_for_presets(struct cats_configuration *conf, str
}
-void load_conf_vital_ages(struct cats_configuration *conf, struct cats_ini *ini, char *species_section,
+void load_conf_vital_ages(struct cats_configuration *conf, struct cats_ini *ini, const char *species_section,
struct cats_species_param *p)
{
for (enum cats_vital_age_id age_id = VA_MIN + 1; age_id < VA_MAX; age_id++) {
@@ -125,7 +125,7 @@ void load_conf_vital_rate(struct cats_vital_rate *vr, struct cats_configuration
void load_plant_species_parameter(struct cats_configuration *conf, struct cats_ini *ini,
- char *species_name, struct cats_species_param *p)
+ const char *species_name, struct cats_species_param *p)
{
char *preset_string = NULL;
@@ -182,7 +182,7 @@ void load_plant_species_parameter(struct cats_configuration *conf, struct cats_i
void load_config_species_parameter(struct cats_configuration *conf, struct cats_ini *ini, int species_idx,
- char *species_section)
+ const char *species_section)
{
struct cats_species_param *p = &conf->param[species_idx];
@@ -290,7 +290,7 @@ void load_config_species_parameter(struct cats_configuration *conf, struct cats_
}
-void load_parameter_sets_all_same(struct cats_configuration *conf, struct cats_ini *ini, int species_idx, char *name)
+void load_parameter_sets_all_same(struct cats_configuration *conf, struct cats_ini *ini, int species_idx, const char *name)
{
assert(species_idx >= 0);
char *species_name = strdup(conf->param[0].species_name);
@@ -313,8 +313,8 @@ void load_all_species(struct cats_configuration *conf, struct cats_ini *ini)
{
struct string_array *species = get_sections_with_prefix(ini, "species");
- for (int32_t i = 0; i < species->count; i++) {
- char *species_section = species->string[i];
+ for (int32_t i = 0; i < get_string_count(species); i++) {
+ const char *species_section = get_string(species, i);
load_config_species_parameter(conf, ini, i, species_section);
if (conf->all_species_same && i == 0) {
diff --git a/src/cats/data/cats_datatypes.c b/src/cats/data/cats_datatypes.c
index c311e40..06624c3 100644
--- a/src/cats/data/cats_datatypes.c
+++ b/src/cats/data/cats_datatypes.c
@@ -35,7 +35,7 @@ const char *false_values[] = {"0", "n", "f"};
const int true_counts = (int) (sizeof(true_values) / sizeof(char *));
const int false_counts = (int) (sizeof(false_values) / sizeof(char *));
-
+/*
bool string_to_double(char *string, double *value)
{
if (string == NULL || strlen(string) == 0) return false;
@@ -149,5 +149,5 @@ bool string_to_integer(char *string, int32_t *value)
}
return false;
}
-
+*/
diff --git a/src/cats/data/cats_datatypes.h b/src/cats/data/cats_datatypes.h
index d2bba54..eea7454 100644
--- a/src/cats/data/cats_datatypes.h
+++ b/src/cats/data/cats_datatypes.h
@@ -58,6 +58,6 @@ struct cats_coordinates {
// conversion functions
-#include <cats_strings/string_converters.h>
+#include <bdc_strings/bdc_strings.h>
#endif
\ No newline at end of file
diff --git a/src/cats/data/cats_global.c b/src/cats/data/cats_global.c
index d3a5749..977f3e3 100644
--- a/src/cats/data/cats_global.c
+++ b/src/cats/data/cats_global.c
@@ -24,7 +24,7 @@
#include "misc/misc.h"
#include "defaults.h"
#include "bdc_memory/bdc_memory.h"
-#include <logging/logging.h>
+#include <bdc_logging/logging.h>
#include <stdlib.h>
diff --git a/src/cats/data/simulation_geometry.c b/src/cats/data/simulation_geometry.c
index ed9e0b1..9959d15 100644
--- a/src/cats/data/simulation_geometry.c
+++ b/src/cats/data/simulation_geometry.c
@@ -23,7 +23,7 @@
#include "cats_global.h"
#include <math.h>
#include "simulation_geometry.h"
-#include <logging/logging.h>
+#include <bdc_logging/logging.h>
void init_simulation_geometry(struct simulation_geometry *geo)
{
diff --git a/src/cats/debug/debug.c b/src/cats/debug/debug.c
index ebe381a..b924064 100644
--- a/src/cats/debug/debug.c
+++ b/src/cats/debug/debug.c
@@ -24,8 +24,9 @@
#include "bdc_memory/bdc_memory.h"
#include "debug/debug.h"
#include "threading/threading-helpers.h"
-#include <cats_strings/cats_strings.h>
+#include <bdc_strings/bdc_strings.h>
#include "misc/misc.h"
+#include "bdc_io/bdc_io.h"
#define DEBUG_DIR "debug"
diff --git a/src/cats/debug/debug_vital_rates.c b/src/cats/debug/debug_vital_rates.c
index ca9da40..996e31e 100644
--- a/src/cats/debug/debug_vital_rates.c
+++ b/src/cats/debug/debug_vital_rates.c
@@ -26,6 +26,7 @@
#include "inline_carrying_capacity.h"
#include "grids/grid_setup.h"
#include "paths/directory_helper.h"
+#include "bdc_io/bdc_io.h"
struct cats_environment *minimal_suitability_environment(void)
diff --git a/src/cats/environment/environment.c b/src/cats/environment/environment.c
index 353a797..04d0ae3 100644
--- a/src/cats/environment/environment.c
+++ b/src/cats/environment/environment.c
@@ -26,7 +26,7 @@
#endif
#include <assert.h>
-#include <logging/logging.h>
+#include <bdc_logging/logging.h>
#include "configuration/configuration.h"
#include "memory.h"
diff --git a/src/cats/environment/environment_registry.c b/src/cats/environment/environment_registry.c
index fa1f606..d2208b7 100644
--- a/src/cats/environment/environment_registry.c
+++ b/src/cats/environment/environment_registry.c
@@ -25,7 +25,7 @@
#include <limits.h>
#include "environment/environment_structures.h"
#include "bdc_memory/bdc_memory.h"
-#include <logging/logging.h>
+#include <bdc_logging/logging.h>
void reset_environment_registry(struct cats_environment_registry *reg)
{
@@ -125,10 +125,10 @@ add_environment_to_registry(struct cats_environment_registry *registry, const ch
}
-struct cats_environment_variable *get_environment_from_registry(struct cats_environment_registry *reg, char *name)
+struct cats_environment_variable *get_environment_from_registry(struct cats_environment_registry *reg, const char *name)
{
- int32_t idx = string_array_index(reg->name, name);
+ int32_t idx = string_array_string_index(reg->name, name);
if (idx < 0) {
log_message(LOG_ERROR, "%s: could not find environment '%s' in registry.", __func__, name);
exit(EXIT_FAILURE);
@@ -148,7 +148,7 @@ void cleanup_environment_registry(struct cats_environment_registry *reg)
{
for (int32_t i = 0; i < reg->count; i++) {
- log_message(LOG_INFO, "%s: cleaning up %s", __func__, reg->name->string[i]);
+ log_message(LOG_INFO, "%s: cleaning up %s", __func__, get_string(reg->name, i));
cleanup_cats_environment_variable(®->environment[i]);
}
diff --git a/src/cats/environment/environment_registry.h b/src/cats/environment/environment_registry.h
index 1d4680f..e5a810d 100644
--- a/src/cats/environment/environment_registry.h
+++ b/src/cats/environment/environment_registry.h
@@ -38,7 +38,7 @@ add_environment_to_registry(struct cats_environment_registry *registry, const ch
enum environment_variable_type type, const char *file_name_pattern, int32_t reload_interval,
int32_t interpolation, const struct array_dimension *dimension);
-struct cats_environment_variable *get_environment_from_registry(struct cats_environment_registry *reg, char *name);
+struct cats_environment_variable *get_environment_from_registry(struct cats_environment_registry *reg, const char *name);
void cleanup_environment_registry(struct cats_environment_registry *reg);
diff --git a/src/cats/environment/environment_set.c b/src/cats/environment/environment_set.c
index 7e5f6b0..c0d34ea 100644
--- a/src/cats/environment/environment_set.c
+++ b/src/cats/environment/environment_set.c
@@ -177,12 +177,12 @@ void add_to_environment(struct cats_environment *environment, struct cats_enviro
void failed_to_find_environment(const struct cats_configuration *conf, const char *name)
{
log_message(LOG_ERROR, "%s: could not find environment set '%s' in registry", __func__, name);
- if (conf->environment.names == NULL || conf->environment.names->count == 0) {
+ if (conf->environment.names == NULL || get_string_count(conf->environment.names) == 0) {
log_message(LOG_ERROR, "%s: registry empty ('%s')", __func__, name);
} else {
- for (int32_t i = 0; i < conf->environment.names->count; i++) {
+ for (int32_t i = 0; i < get_string_count(conf->environment.names); i++) {
log_message(LOG_INFO, "%s: have registry entry: '%s'", __func__,
- conf->environment.names->string[i]);
+ get_string(conf->environment.names, i));
}
}
@@ -193,10 +193,10 @@ void failed_to_find_environment(const struct cats_configuration *conf, const cha
struct cats_environment *get_environment(const struct cats_configuration *conf, const char *name)
{
- if (conf->environment.names == NULL || conf->environment.names->count == 0) {
+ if (conf->environment.names == NULL || get_string_count(conf->environment.names) == 0) {
failed_to_find_environment(conf, name);
}
- int32_t idx = string_array_index(conf->environment.names, name);
+ int32_t idx = string_array_string_index(conf->environment.names, name);
if (idx < 0) failed_to_find_environment(conf, name);
diff --git a/src/cats/environment/load_environment.c b/src/cats/environment/load_environment.c
index c1324c5..f9119cf 100644
--- a/src/cats/environment/load_environment.c
+++ b/src/cats/environment/load_environment.c
@@ -76,7 +76,7 @@ enum action_status update_environment_warmup(struct cats_configuration *conf, in
time);
} else if (time == start) {
log_message(LOG_INFO, " ENV: loading environment %s for year %d as static predictor",
- conf->environment_registry.name->string[i],
+ get_string(conf->environment_registry.name, i),
time);
load_environment_raster(conf, &conf->environment_registry.environment[i], INTERPOLATION_CURRENT,
time);
diff --git a/src/cats/grids/cats_grid.c b/src/cats/grids/cats_grid.c
index 9665728..882fe5f 100644
--- a/src/cats/grids/cats_grid.c
+++ b/src/cats/grids/cats_grid.c
@@ -55,6 +55,7 @@
#include "paths/output_paths.h"
#include "stats/global_stats.h"
#include "actions/setup.h"
+#include "bdc_io/bdc_io.h"
struct cats_grid **create_and_initialize_grids(struct cats_configuration *conf, const int32_t count)
diff --git a/src/cats/grids/gdal_helper.c b/src/cats/grids/gdal_helper.c
index 403df56..3ac7221 100644
--- a/src/cats/grids/gdal_helper.c
+++ b/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 {
diff --git a/src/cats/hybrid/scalefactor.c b/src/cats/hybrid/scalefactor.c
index 040be9f..f1c8563 100644
--- a/src/cats/hybrid/scalefactor.c
+++ b/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"
diff --git a/src/cats/inline_population.h b/src/cats/inline_population.h
index 20937d8..d52ced9 100644
--- a/src/cats/inline_population.h
+++ b/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"
diff --git a/src/cats/lambda/eigen.c b/src/cats/lambda/eigen.c
index 5933034..360d208 100644
--- a/src/cats/lambda/eigen.c
+++ b/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"
diff --git a/src/cats/lambda/leslie_matrix.c b/src/cats/lambda/leslie_matrix.c
index e1a8582..491e7ed 100644
--- a/src/cats/lambda/leslie_matrix.c
+++ b/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"
diff --git a/src/cats/lambda/matrix_helpers.c b/src/cats/lambda/matrix_helpers.c
index c054e99..e5694b8 100644
--- a/src/cats/lambda/matrix_helpers.c
+++ b/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"
diff --git a/src/cats/misc/debug.c b/src/cats/misc/debug.c
index f86e57b..5a92ff6 100644
--- a/src/cats/misc/debug.c
+++ b/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
diff --git a/src/cats/misc/filesystem.c b/src/cats/misc/filesystem.c
index 88de2fc..94b6313 100644
--- a/src/cats/misc/filesystem.c
+++ b/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
diff --git a/src/cats/misc/misc.h b/src/cats/misc/misc.h
index 2d377fd..6194c37 100644
--- a/src/cats/misc/misc.h
+++ b/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
diff --git a/src/cats/modules/load_module.c b/src/cats/modules/load_module.c
index 6e6d9bf..7859124 100644
--- a/src/cats/modules/load_module.c
+++ b/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"
diff --git a/src/cats/modules/modules.c b/src/cats/modules/modules.c
index b18d538..92ee7f9 100644
--- a/src/cats/modules/modules.c
+++ b/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)
{
diff --git a/src/cats/mpi/mpi_debug.c b/src/cats/mpi/mpi_debug.c
index 1570c2c..b6b423a 100644
--- a/src/cats/mpi/mpi_debug.c
+++ b/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)
diff --git a/src/cats/overlays/overlays.c b/src/cats/overlays/overlays.c
index a89b27a..c08d061 100644
--- a/src/cats/overlays/overlays.c
+++ b/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;
}
}
diff --git a/src/cats/paths/directory_helper.c b/src/cats/paths/directory_helper.c
index 80d8c5b..6c33840 100644
--- a/src/cats/paths/directory_helper.c
+++ b/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);
diff --git a/src/cats/paths/output_paths.c b/src/cats/paths/output_paths.c
index 08e0fc9..47ad4df 100644
--- a/src/cats/paths/output_paths.c
+++ b/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)
diff --git a/src/cats/paths/paths.c b/src/cats/paths/paths.c
index 53310ab..56b95de 100644
--- a/src/cats/paths/paths.c
+++ b/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, ".");
diff --git a/src/cats/paths/paths.h b/src/cats/paths/paths.h
index b2cfdbc..583ada1 100644
--- a/src/cats/paths/paths.h
+++ b/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;
diff --git a/src/cats/paths/paths_suitability.c b/src/cats/paths/paths_suitability.c
index d3360fa..37739e6 100644
--- a/src/cats/paths/paths_suitability.c
+++ b/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 *
diff --git a/src/cats/stats/global_stats.c b/src/cats/stats/global_stats.c
index a412a82..c7aee12 100644
--- a/src/cats/stats/global_stats.c
+++ b/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"
diff --git a/src/cats/stats/lambda_stats.c b/src/cats/stats/lambda_stats.c
index 7f02b8b..ee5f5a3 100644
--- a/src/cats/stats/lambda_stats.c
+++ b/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 *
diff --git a/src/cats/stats/statistics.c b/src/cats/stats/statistics.c
index c1ed496..1834bfd 100644
--- a/src/cats/stats/statistics.c
+++ b/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"
diff --git a/src/cats/threading/threading-helpers.c b/src/cats/threading/threading-helpers.c
index 0877f6b..cdf3e7a 100644
--- a/src/cats/threading/threading-helpers.c
+++ b/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)
{
diff --git a/src/cats/vital_ages/default_vital_ages.c b/src/cats/vital_ages/default_vital_ages.c
index bbff02c..f9ce195 100644
--- a/src/cats/vital_ages/default_vital_ages.c
+++ b/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)
{
diff --git a/src/cats/vital_rates/setup_rates.c b/src/cats/vital_rates/setup_rates.c
index 7b738d9..02883ad 100644
--- a/src/cats/vital_rates/setup_rates.c
+++ b/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"
diff --git a/src/cats/vital_rates/vital_rate_ranges.c b/src/cats/vital_rates/vital_rate_ranges.c
index 44451ee..82635a8 100644
--- a/src/cats/vital_rates/vital_rate_ranges.c
+++ b/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)
diff --git a/src/cats_csv/CMakeLists.txt b/src/cats_csv/CMakeLists.txt
index d3afbbe..5f055d7 100644
--- a/src/cats_csv/CMakeLists.txt
+++ b/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
diff --git a/src/cats_csv/cats_csv.c b/src/cats_csv/cats_csv.c
index db8cf59..c3d4c2e 100644
--- a/src/cats_csv/cats_csv.c
+++ b/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));
}
diff --git a/src/cats_csv/cats_csv.h b/src/cats_csv/cats_csv.h
index 08e79fc..774183f 100644
--- a/src/cats_csv/cats_csv.h
+++ b/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 {
diff --git a/src/cats_ini/CMakeLists.txt b/src/cats_ini/CMakeLists.txt
index 8b03aec..3aa7adc 100644
--- a/src/cats_ini/CMakeLists.txt
+++ b/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)
diff --git a/src/cats_ini/cats_ini.c b/src/cats_ini/cats_ini.c
index 96f1de8..abc937a 100644
--- a/src/cats_ini/cats_ini.c
+++ b/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"
diff --git a/src/cats_ini/cats_ini_helpers.c b/src/cats_ini/cats_ini_helpers.c
index 89c1643..4a14df0 100644
--- a/src/cats_ini/cats_ini_helpers.c
+++ b/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)
{
diff --git a/src/cats_ini/cats_ini_read_values.c b/src/cats_ini/cats_ini_read_values.c
index b12be68..fcc777a 100644
--- a/src/cats_ini/cats_ini_read_values.c
+++ b/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>
diff --git a/src/cats_ini/cats_ini_write_values.c b/src/cats_ini/cats_ini_write_values.c
index b99d1be..aa461bb 100644
--- a/src/cats_ini/cats_ini_write_values.c
+++ b/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>
diff --git a/src/cats_strings/CMakeLists.txt b/src/cats_strings/CMakeLists.txt
deleted file mode 100644
index 1414340..0000000
--- a/src/cats_strings/CMakeLists.txt
+++ /dev/null
@@ -1,17 +0,0 @@
-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 bdc_time)
\ No newline at end of file
diff --git a/src/cats_strings/io_text.h b/src/cats_strings/io_text.h
deleted file mode 100644
index 224a71a..0000000
--- a/src/cats_strings/io_text.h
+++ /dev/null
@@ -1,26 +0,0 @@
-// SPDX-License-Identifier: GPL-3.0-or-later
-//
-// io_text.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_IO_TEXT_H
-#define CATS_IO_TEXT_H
-
-
-#endif
diff --git a/src/cats_strings/pretty_print.h b/src/cats_strings/pretty_print.h
deleted file mode 100644
index be12b63..0000000
--- a/src/cats_strings/pretty_print.h
+++ /dev/null
@@ -1,25 +0,0 @@
-// 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
diff --git a/src/cats_strings/string_converters.h b/src/cats_strings/string_converters.h
deleted file mode 100644
index b2a8082..0000000
--- a/src/cats_strings/string_converters.h
+++ /dev/null
@@ -1,39 +0,0 @@
-// SPDX-License-Identifier: GPL-3.0-or-later
-//
-// string_converters.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.
-//
-
-
-#include <stdint.h>
-
-
-
-
-#ifndef CATS_STRING_CONVERTERS_H
-#define CATS_STRING_CONVERTERS_H
-bool string_to_float(char *string, float *value);
-
-bool string_to_bool(char *string, bool *value);
-
-bool string_to_double(char *string, double *value);
-
-bool string_to_integer(char *string, int32_t *value);
-
-bool string_to_long_double(char *string, long double *value);
-#endif //CATS_STRING_CONVERTERS_H
diff --git a/src/cats_strings/string_helpers.h b/src/cats_strings/string_helpers.h
deleted file mode 100644
index 10671ce..0000000
--- a/src/cats_strings/string_helpers.h
+++ /dev/null
@@ -1,26 +0,0 @@
-// SPDX-License-Identifier: GPL-3.0-or-later
-//
-// string_helpers.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_STRING_HELPERS_H
-#define CATS_STRING_HELPERS_H
-
-
-#endif //CATS_STRING_HELPERS_H
diff --git a/src/logging/CMakeLists.txt b/src/logging/CMakeLists.txt
deleted file mode 100644
index 872a70e..0000000
--- a/src/logging/CMakeLists.txt
+++ /dev/null
@@ -1,12 +0,0 @@
-add_library(cats_logging STATIC "" ../cats_windows.h)
-
-target_sources(cats_logging
- PRIVATE
- ../cats_defs.h
- logging.c
- PUBLIC
- logging.h
- )
-
-target_include_directories(cats_logging PUBLIC ".")
-set_property(TARGET cats_logging PROPERTY POSITION_INDEPENDENT_CODE ON)
\ No newline at end of file
diff --git a/src/modules/butterflies/CMakeLists.txt b/src/modules/butterflies/CMakeLists.txt
index c20a250..538918b 100644
--- a/src/modules/butterflies/CMakeLists.txt
+++ b/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)
diff --git a/src/modules/butterflies/butterflies_main.c b/src/modules/butterflies/butterflies_main.c
index e8e0b29..28b3fb1 100644
--- a/src/modules/butterflies/butterflies_main.c
+++ b/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)
diff --git a/src/modules/butterflies/butterflies_paths.c b/src/modules/butterflies/butterflies_paths.c
index ba749c2..7cc158d 100644
--- a/src/modules/butterflies/butterflies_paths.c
+++ b/src/modules/butterflies/butterflies_paths.c
@@ -30,6 +30,8 @@
#include "actions/cats_actions.h"
#include "butterflies_paths.h"
#include "module.h"
+#include "bdc_io/bdc_io.h"
+
void bf_add_directories(struct cats_configuration *conf)
{
diff --git a/src/modules/butterflies/butterflies_stats.c b/src/modules/butterflies/butterflies_stats.c
index 567a20f..d711dcc 100644
--- a/src/modules/butterflies/butterflies_stats.c
+++ b/src/modules/butterflies/butterflies_stats.c
@@ -32,6 +32,7 @@
#include "butterflies_paths.h"
#include "temporal/phase_names.h"
#include "temporal/years.h"
+#include "bdc_io/bdc_io.h"
const char *bf_get_stats_field_name(enum butterfly_stats which)
diff --git a/src/modules/cats_test_module/CMakeLists.txt b/src/modules/cats_test_module/CMakeLists.txt
index 6ebb9e8..68caf04 100644
--- a/src/modules/cats_test_module/CMakeLists.txt
+++ b/src/modules/cats_test_module/CMakeLists.txt
@@ -8,4 +8,4 @@ target_sources(cats-test-module PRIVATE
target_include_directories(cats-test-module PUBLIC ".")
set_property(TARGET cats-test-module PROPERTY POSITION_INDEPENDENT_CODE ON)
-target_link_libraries(cats-test-module cats_logging libcats)
+target_link_libraries(cats-test-module bdc_logging libcats)
diff --git a/src/tests/CMakeLists.txt b/src/tests/CMakeLists.txt
index 237b15d..b205a80 100644
--- a/src/tests/CMakeLists.txt
+++ b/src/tests/CMakeLists.txt
@@ -9,5 +9,5 @@ add_executable(vital_rate_test vital_rate_test.c)
add_executable(csv_test csv_test.c )
configure_file("test.csv" "test.csv")
-target_link_libraries(vital_rate_test cmocka cats_logging bdc cats_strings cats_ini cats_csv libcats)
-target_link_libraries(csv_test cmocka cats_strings cats_csv cats_strings cats_logging bdc)
+target_link_libraries(vital_rate_test cmocka bdc_logging bdc bdc_strings cats_ini cats_csv libcats)
+target_link_libraries(csv_test cmocka bdc_strings cats_csv bdc_strings bdc_logging bdc)
diff --git a/src/tests/csv_test.c b/src/tests/csv_test.c
index 1375ec1..467a7a4 100644
--- a/src/tests/csv_test.c
+++ b/src/tests/csv_test.c
@@ -24,8 +24,9 @@
#include <cmocka.h>
#include <stdio.h>
#include "bdc_memory/bdc_memory.h"
-#include "cats_strings/cats_strings.h"
+#include "bdc_strings/bdc_strings.h"
#include "cats_csv/cats_csv.h"
+#include "bdc_io/bdc_io.h"
struct csv_test {
--
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