Add tsk_bool_t and change keep_rows signature

Author: jeromekelleher

c/tests/test_tables.c

@@ -1499,7 +1499,7 @@ test_node_table_keep_rows(void)
     tsk_size_t j;
     tsk_node_table_t source, t1, t2;
     tsk_node_t row;
-    bool keep[3] = { 1, 1, 1 };
+    tsk_bool_t keep[3] = { 1, 1, 1 };
     tsk_id_t id_map[3];
     const char *metadata = "ABC";
     tsk_id_t indexes[] = { 0, 1, 2 };
@@ -2142,7 +2142,7 @@ test_edge_table_keep_rows(void)
     tsk_size_t j;
     tsk_edge_table_t source, t1, t2;
     tsk_edge_t row;
-    bool keep[3] = { 1, 1, 1 };
+    tsk_bool_t keep[3] = { 1, 1, 1 };
     tsk_id_t id_map[3];
     const char *metadata = "ABC";
     tsk_id_t indexes[] = { 0, 1, 2 };
@@ -2242,7 +2242,7 @@ test_edge_table_keep_rows_no_metadata(void)
     tsk_size_t j;
     tsk_edge_table_t source, t1, t2;
     tsk_edge_t row;
-    bool keep[3] = { 1, 1, 1 };
+    tsk_bool_t keep[3] = { 1, 1, 1 };
     tsk_id_t id_map[3];
     tsk_id_t indexes[] = { 0, 1, 2 };
 
@@ -3265,7 +3265,7 @@ test_site_table_keep_rows(void)
     tsk_site_t row;
     const char *ancestral_state = "XYZ";
     const char *metadata = "ABC";
-    bool keep[3] = { 1, 1, 1 };
+    tsk_bool_t keep[3] = { 1, 1, 1 };
     tsk_id_t id_map[3];
     tsk_id_t indexes[] = { 0, 1, 2 };
 
@@ -4051,7 +4051,7 @@ test_mutation_table_keep_rows(void)
     tsk_mutation_t row;
     const char *derived_state = "XYZ";
     const char *metadata = "ABC";
-    bool keep[3] = { 1, 1, 1 };
+    tsk_bool_t keep[3] = { 1, 1, 1 };
     tsk_id_t id_map[3];
     tsk_id_t indexes[] = { 0, 1, 2 };
 
@@ -4154,7 +4154,7 @@ test_mutation_table_keep_rows_parent_references(void)
     int ret;
     tsk_id_t ret_id;
     tsk_mutation_table_t source, t;
-    bool keep[4] = { 1, 1, 1, 1 };
+    tsk_bool_t keep[4] = { 1, 1, 1, 1 };
     tsk_id_t id_map[4];
 
     ret = tsk_mutation_table_init(&source, 0);
@@ -4844,7 +4844,7 @@ test_migration_table_keep_rows(void)
     tsk_migration_table_t source, t1, t2;
     tsk_migration_t row;
     const char *metadata = "ABC";
-    bool keep[3] = { 1, 1, 1 };
+    tsk_bool_t keep[3] = { 1, 1, 1 };
     tsk_id_t id_map[3];
     tsk_id_t indexes[] = { 0, 1, 2 };
 
@@ -5671,7 +5671,7 @@ test_individual_table_keep_rows(void)
     double location[] = { 0, 1, 2 };
     tsk_id_t parents[] = { -1, 1, -1 };
     const char *metadata = "ABC";
-    bool keep[3] = { 1, 1, 1 };
+    tsk_bool_t keep[3] = { 1, 1, 1 };
     tsk_id_t indexes[] = { 0, 1, 2 };
     tsk_id_t id_map[3];
     tsk_individual_table_t source, t1, t2;
@@ -5776,7 +5776,7 @@ test_individual_table_keep_rows_parent_references(void)
     int ret;
     tsk_id_t ret_id;
     tsk_individual_table_t source, t;
-    bool keep[] = { 1, 1, 1, 1 };
+    tsk_bool_t keep[] = { 1, 1, 1, 1 };
     tsk_id_t parents[] = { -1, 1, 2 };
     tsk_id_t id_map[4];
 
@@ -6243,7 +6243,7 @@ test_population_table_keep_rows(void)
     tsk_population_table_t source, t1, t2;
     tsk_population_t row;
     const char *metadata = "ABC";
-    bool keep[3] = { 1, 1, 1 };
+    tsk_bool_t keep[3] = { 1, 1, 1 };
     tsk_id_t id_map[3];
     tsk_id_t indexes[] = { 0, 1, 2 };
 
@@ -6779,7 +6779,7 @@ test_provenance_table_keep_rows(void)
     tsk_provenance_t row;
     const char *timestamp = "XYZ";
     const char *record = "ABC";
-    bool keep[3] = { 1, 1, 1 };
+    tsk_bool_t keep[3] = { 1, 1, 1 };
     tsk_id_t indexes[] = { 0, 1, 2 };
     tsk_id_t id_map[3];
 

c/tskit/core.h

@@ -123,6 +123,15 @@ specify options to API functions.
 typedef uint32_t tsk_flags_t;
 #define TSK_FLAGS_STORAGE_TYPE KAS_UINT32
 
+/**
+@brief Boolean type.
+
+@rst
+Fixed-size (1 byte) boolean values.
+@endrst
+*/
+typedef uint8_t tsk_bool_t;
+
 // clang-format off
 /**
 @defgroup API_VERSION_GROUP API version macros.

c/tskit/tables.c

@@ -735,7 +735,7 @@ write_metadata_schema_header(
 /* Utilities for in-place subsetting columns */
 
 static tsk_size_t
-count_true(tsk_size_t num_rows, const bool *restrict keep)
+count_true(tsk_size_t num_rows, const tsk_bool_t *restrict keep)
 {
     tsk_size_t j;
     tsk_size_t count = 0;
@@ -750,7 +750,7 @@ count_true(tsk_size_t num_rows, const bool *restrict keep)
 
 static void
 keep_mask_to_id_map(
-    tsk_size_t num_rows, const bool *restrict keep, tsk_id_t *restrict id_map)
+    tsk_size_t num_rows, const tsk_bool_t *restrict keep, tsk_id_t *restrict id_map)
 {
     tsk_size_t j;
     tsk_id_t next_id = 0;
@@ -766,7 +766,7 @@ keep_mask_to_id_map(
 
 static tsk_size_t
 subset_remap_id_column(tsk_id_t *restrict column, tsk_size_t num_rows,
-    const bool *restrict keep, const tsk_id_t *restrict id_map)
+    const tsk_bool_t *restrict keep, const tsk_id_t *restrict id_map)
 {
     tsk_size_t j, k;
     tsk_id_t value;
@@ -792,7 +792,7 @@ subset_remap_id_column(tsk_id_t *restrict column, tsk_size_t num_rows,
 
 static tsk_size_t
 subset_id_column(
-    tsk_id_t *restrict column, tsk_size_t num_rows, const bool *restrict keep)
+    tsk_id_t *restrict column, tsk_size_t num_rows, const tsk_bool_t *restrict keep)
 {
     tsk_size_t j, k;
 
@@ -808,7 +808,7 @@ subset_id_column(
 
 static tsk_size_t
 subset_flags_column(
-    tsk_flags_t *restrict column, tsk_size_t num_rows, const bool *restrict keep)
+    tsk_flags_t *restrict column, tsk_size_t num_rows, const tsk_bool_t *restrict keep)
 {
     tsk_size_t j, k;
 
@@ -824,7 +824,7 @@ subset_flags_column(
 
 static tsk_size_t
 subset_double_column(
-    double *restrict column, tsk_size_t num_rows, const bool *restrict keep)
+    double *restrict column, tsk_size_t num_rows, const tsk_bool_t *restrict keep)
 {
     tsk_size_t j, k;
 
@@ -840,7 +840,7 @@ subset_double_column(
 
 static tsk_size_t
 subset_ragged_char_column(char *restrict data, tsk_size_t *restrict offset_col,
-    tsk_size_t num_rows, const bool *restrict keep)
+    tsk_size_t num_rows, const tsk_bool_t *restrict keep)
 {
     tsk_size_t j, k, i, offset;
 
@@ -864,7 +864,7 @@ subset_ragged_char_column(char *restrict data, tsk_size_t *restrict offset_col,
 
 static tsk_size_t
 subset_ragged_double_column(double *restrict data, tsk_size_t *restrict offset_col,
-    tsk_size_t num_rows, const bool *restrict keep)
+    tsk_size_t num_rows, const tsk_bool_t *restrict keep)
 {
     tsk_size_t j, k, i, offset;
 
@@ -888,7 +888,8 @@ subset_ragged_double_column(double *restrict data, tsk_size_t *restrict offset_c
 
 static tsk_size_t
 subset_remap_ragged_id_column(tsk_id_t *restrict data, tsk_size_t *restrict offset_col,
-    tsk_size_t num_rows, const bool *restrict keep, const tsk_id_t *restrict id_map)
+    tsk_size_t num_rows, const tsk_bool_t *restrict keep,
+    const tsk_id_t *restrict id_map)
 {
     tsk_size_t j, k, i, offset;
     tsk_id_t di;
@@ -1804,7 +1805,7 @@ tsk_individual_table_equals(const tsk_individual_table_t *self,
 }
 
 int
-tsk_individual_table_keep_rows(tsk_individual_table_t *self, const bool *keep,
+tsk_individual_table_keep_rows(tsk_individual_table_t *self, const tsk_bool_t *keep,
     tsk_flags_t TSK_UNUSED(options), tsk_id_t *ret_id_map)
 {
     int ret = 0;
@@ -2518,7 +2519,7 @@ tsk_node_table_get_row(const tsk_node_table_t *self, tsk_id_t index, tsk_node_t
 }
 
 int
-tsk_node_table_keep_rows(tsk_node_table_t *self, const bool *keep,
+tsk_node_table_keep_rows(tsk_node_table_t *self, const tsk_bool_t *keep,
     tsk_flags_t TSK_UNUSED(options), tsk_id_t *id_map)
 {
     int ret = 0;
@@ -3210,7 +3211,7 @@ tsk_edge_table_equals(
 }
 
 int
-tsk_edge_table_keep_rows(tsk_edge_table_t *self, const bool *keep,
+tsk_edge_table_keep_rows(tsk_edge_table_t *self, const tsk_bool_t *keep,
     tsk_flags_t TSK_UNUSED(options), tsk_id_t *id_map)
 {
     int ret = 0;
@@ -3968,7 +3969,7 @@ tsk_site_table_dump_text(const tsk_site_table_t *self, FILE *out)
 }
 
 int
-tsk_site_table_keep_rows(tsk_site_table_t *self, const bool *keep,
+tsk_site_table_keep_rows(tsk_site_table_t *self, const tsk_bool_t *keep,
     tsk_flags_t TSK_UNUSED(options), tsk_id_t *id_map)
 {
     int ret = 0;
@@ -4733,7 +4734,7 @@ tsk_mutation_table_dump_text(const tsk_mutation_table_t *self, FILE *out)
 }
 
 int
-tsk_mutation_table_keep_rows(tsk_mutation_table_t *self, const bool *keep,
+tsk_mutation_table_keep_rows(tsk_mutation_table_t *self, const tsk_bool_t *keep,
     tsk_flags_t TSK_UNUSED(options), tsk_id_t *ret_id_map)
 {
     int ret = 0;
@@ -5437,7 +5438,7 @@ tsk_migration_table_equals(const tsk_migration_table_t *self,
 }
 
 int
-tsk_migration_table_keep_rows(tsk_migration_table_t *self, const bool *keep,
+tsk_migration_table_keep_rows(tsk_migration_table_t *self, const tsk_bool_t *keep,
     tsk_flags_t TSK_UNUSED(options), tsk_id_t *id_map)
 {
     int ret = 0;
@@ -6031,7 +6032,7 @@ tsk_population_table_equals(const tsk_population_table_t *self,
 }
 
 int
-tsk_population_table_keep_rows(tsk_population_table_t *self, const bool *keep,
+tsk_population_table_keep_rows(tsk_population_table_t *self, const tsk_bool_t *keep,
     tsk_flags_t TSK_UNUSED(options), tsk_id_t *id_map)
 {
     int ret = 0;
@@ -6661,7 +6662,7 @@ tsk_provenance_table_equals(const tsk_provenance_table_t *self,
 }
 
 int
-tsk_provenance_table_keep_rows(tsk_provenance_table_t *self, const bool *keep,
+tsk_provenance_table_keep_rows(tsk_provenance_table_t *self, const tsk_bool_t *keep,
     tsk_flags_t TSK_UNUSED(options), tsk_id_t *id_map)
 {
     int ret = 0;