Make dump tables operations const.

c/CHANGELOG.rst

@@ -4,6 +4,10 @@
 
 **Breaking changes**
 
+- Removed ``TSK_NO_BUILD_INDEXES``.
+  Not building indexes is now the default behaviour of `tsk_table_collection_dump` and related functions.
+  (:user:`molpopgen`, :issue:`1327`, :pr:`1337`).
+
 **Features**
 
 - Add ``tsk_*_table_extend`` methods to append to a table from another

c/tests/test_tables.c

@@ -5080,11 +5080,11 @@ test_dump_unindexed_with_options(tsk_flags_t tc_options)
     CU_ASSERT_FALSE(tsk_table_collection_has_index(&tables, 0));
     ret = tsk_table_collection_dump(&tables, _tmp_file_name, 0);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
-    CU_ASSERT_TRUE(tsk_table_collection_has_index(&tables, 0));
+    CU_ASSERT_FALSE(tsk_table_collection_has_index(&tables, 0));
 
     ret = tsk_table_collection_load(&loaded, _tmp_file_name, 0);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
-    CU_ASSERT_TRUE(tsk_table_collection_has_index(&loaded, 0));
+    CU_ASSERT_FALSE(tsk_table_collection_has_index(&loaded, 0));
     CU_ASSERT_TRUE(tsk_node_table_equals(&tables.nodes, &loaded.nodes, 0));
     CU_ASSERT_TRUE(tsk_edge_table_equals(&tables.edges, &loaded.edges, 0));
 
@@ -5165,16 +5165,7 @@ test_dump_load_unsorted_with_options(tsk_flags_t tc_options)
     ret = tsk_table_collection_check_integrity(&t1, TSK_CHECK_EDGE_ORDERING);
     CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_EDGES_NOT_SORTED_PARENT_TIME);
 
-    /* Indexing should fail */
-    ret = tsk_table_collection_build_index(&t1, 0);
-    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_EDGES_NOT_SORTED_PARENT_TIME);
-    CU_ASSERT_FALSE(tsk_table_collection_has_index(&t1, 0));
-
-    /* Trying to dump without first sorting should also fail */
     ret = tsk_table_collection_dump(&t1, _tmp_file_name, 0);
-    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_EDGES_NOT_SORTED_PARENT_TIME);
-
-    ret = tsk_table_collection_dump(&t1, _tmp_file_name, TSK_NO_BUILD_INDEXES);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     CU_ASSERT_FALSE(tsk_table_collection_has_index(&t1, 0));
     ret = tsk_table_collection_load(&t2, _tmp_file_name, 0);
@@ -5272,9 +5263,6 @@ test_dump_fail_no_file(void)
     unlink(_tmp_file_name);
     errno = 0;
 
-    /* Trying to dump without first sorting fails */
-    ret = tsk_table_collection_dump(&t1, _tmp_file_name, 0);
-    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_EDGES_NOT_SORTED_PARENT_TIME);
     CU_ASSERT_EQUAL(access(_tmp_file_name, F_OK), -1);
 
     tsk_table_collection_free(&t1);
@@ -5303,7 +5291,7 @@ test_load_reindex(void)
     ret = tsk_table_collection_drop_index(&tables, 0);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     /* Dump the unindexed version */
-    ret = tsk_table_collection_dump(&tables, _tmp_file_name, TSK_NO_BUILD_INDEXES);
+    ret = tsk_table_collection_dump(&tables, _tmp_file_name, 0);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     ret = tsk_table_collection_free(&tables);
     CU_ASSERT_EQUAL_FATAL(ret, 0);

c/tskit/tables.c

@@ -50,7 +50,7 @@ typedef struct {
 
 typedef struct {
     const char *name;
-    void *array;
+    const void *array;
     tsk_size_t len;
     int type;
 } write_table_col_t;
@@ -9325,7 +9325,8 @@ tsk_table_collection_load(
 }
 
 static int TSK_WARN_UNUSED
-tsk_table_collection_write_format_data(tsk_table_collection_t *self, kastore_t *store)
+tsk_table_collection_write_format_data(
+    const tsk_table_collection_t *self, kastore_t *store)
 {
     int ret = 0;
     char format_name[TSK_FILE_FORMAT_NAME_LENGTH];
@@ -9335,7 +9336,7 @@ tsk_table_collection_write_format_data(tsk_table_collection_t *self, kastore_t *
     write_table_col_t write_cols[] = {
         { "format/name", (void *) format_name, sizeof(format_name), KAS_INT8 },
         { "format/version", (void *) version, 2, KAS_UINT32 },
-        { "sequence_length", (void *) &self->sequence_length, 1, KAS_FLOAT64 },
+        { "sequence_length", (const void *) &self->sequence_length, 1, KAS_FLOAT64 },
         { "uuid", (void *) uuid, TSK_UUID_SIZE, KAS_INT8 },
         { "metadata", (void *) self->metadata, self->metadata_length, KAS_INT8 },
         { "metadata_schema", (void *) self->metadata_schema,
@@ -9356,7 +9357,7 @@ tsk_table_collection_write_format_data(tsk_table_collection_t *self, kastore_t *
 
 int TSK_WARN_UNUSED
 tsk_table_collection_dump(
-    tsk_table_collection_t *self, const char *filename, tsk_flags_t options)
+    const tsk_table_collection_t *self, const char *filename, tsk_flags_t options)
 {
     int ret = 0;
     FILE *file = fopen(filename, "wb");
@@ -9386,23 +9387,14 @@ tsk_table_collection_dump(
 }
 
 int TSK_WARN_UNUSED
-tsk_table_collection_dumpf(tsk_table_collection_t *self, FILE *file, tsk_flags_t options)
+tsk_table_collection_dumpf(
+    const tsk_table_collection_t *self, FILE *file, tsk_flags_t TSK_UNUSED(options))
 {
     int ret = 0;
     kastore_t store;
 
     memset(&store, 0, sizeof(store));
 
-    /* By default we build indexes, if they are needed. Note that this will fail if
-     * the tables aren't sorted. */
-    if ((!(options & TSK_NO_BUILD_INDEXES))
-        && (!tsk_table_collection_has_index(self, 0))) {
-        ret = tsk_table_collection_build_index(self, 0);
-        if (ret != 0) {
-            goto out;
-        }
-    }
-
     ret = kastore_openf(&store, file, "w", 0);
     if (ret != 0) {
         ret = tsk_set_kas_error(ret);

c/tskit/tables.h

@@ -727,9 +727,6 @@ typedef struct {
 /* Leave room for more positive check flags */
 #define TSK_NO_CHECK_POPULATION_REFS (1 << 10)
 
-/* Flags for dump tables */
-#define TSK_NO_BUILD_INDEXES (1 << 0)
-
 /* Flags for load tables */
 #define TSK_BUILD_INDEXES (1 << 0)
 
@@ -2712,7 +2709,7 @@ TSK_NO_BUILD_INDEXES
 @return Return 0 on success or a negative value on failure.
 */
 int tsk_table_collection_dump(
-    tsk_table_collection_t *self, const char *filename, tsk_flags_t options);
+    const tsk_table_collection_t *self, const char *filename, tsk_flags_t options);
 
 /**
 @brief Write a table collection to a stream.
@@ -2744,7 +2741,7 @@ TSK_NO_BUILD_INDEXES
 */
 
 int tsk_table_collection_dumpf(
-    tsk_table_collection_t *self, FILE *file, tsk_flags_t options);
+    const tsk_table_collection_t *self, FILE *file, tsk_flags_t options);
 
 /**
 @brief Record the number of rows in each table in the specified tsk_bookmark_t object.

c/tskit/trees.c

@@ -471,13 +471,13 @@ tsk_treeseq_loadf(tsk_treeseq_t *self, FILE *file, tsk_flags_t TSK_UNUSED(option
 }
 
 int TSK_WARN_UNUSED
-tsk_treeseq_dump(tsk_treeseq_t *self, const char *filename, tsk_flags_t options)
+tsk_treeseq_dump(const tsk_treeseq_t *self, const char *filename, tsk_flags_t options)
 {
     return tsk_table_collection_dump(self->tables, filename, options);
 }
 
 int TSK_WARN_UNUSED
-tsk_treeseq_dumpf(tsk_treeseq_t *self, FILE *file, tsk_flags_t options)
+tsk_treeseq_dumpf(const tsk_treeseq_t *self, FILE *file, tsk_flags_t options)
 {
     return tsk_table_collection_dumpf(self->tables, file, options);
 }

c/tskit/trees.h

@@ -226,8 +226,9 @@ int tsk_treeseq_init(
 int tsk_treeseq_load(tsk_treeseq_t *self, const char *filename, tsk_flags_t options);
 int tsk_treeseq_loadf(tsk_treeseq_t *self, FILE *file, tsk_flags_t options);
 
-int tsk_treeseq_dump(tsk_treeseq_t *self, const char *filename, tsk_flags_t options);
-int tsk_treeseq_dumpf(tsk_treeseq_t *self, FILE *file, tsk_flags_t options);
+int tsk_treeseq_dump(
+    const tsk_treeseq_t *self, const char *filename, tsk_flags_t options);
+int tsk_treeseq_dumpf(const tsk_treeseq_t *self, FILE *file, tsk_flags_t options);
 int tsk_treeseq_copy_tables(
     const tsk_treeseq_t *self, tsk_table_collection_t *tables, tsk_flags_t options);
 int tsk_treeseq_free(tsk_treeseq_t *self);