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Merged
merged 1 commit into from
Jun 16, 2025
Merged

Remove tsk_diff_iter_t #3221

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9 changes: 9 additions & 0 deletions c/CHANGELOG.rst
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Original file line number Diff line number Diff line change
@@ -1,3 +1,12 @@
--------------------
[1.2.0] - 2025-XX-XX
--------------------

**Breaking changes**

- Remove ``tsk_diff_iter_t`` and associated functions.
(:user:`benjeffery`, :pr:`3221`, :issue:`2797`).

--------------------
[1.1.4] - 2025-03-31
--------------------
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31 changes: 0 additions & 31 deletions c/tests/test_tables.c
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Original file line number Diff line number Diff line change
Expand Up @@ -11505,35 +11505,6 @@ test_table_collection_delete_older(void)
tsk_treeseq_free(&ts);
}

static void
test_table_collection_edge_diffs_errors(void)
{
int ret;
tsk_id_t ret_id;
tsk_table_collection_t tables;
tsk_diff_iter_t iter;

ret = tsk_table_collection_init(&tables, 0);
CU_ASSERT_EQUAL(ret, 0);
tables.sequence_length = 1;
ret_id
= tsk_node_table_add_row(&tables.nodes, TSK_NODE_IS_SAMPLE, 0, -1, -1, NULL, 0);
CU_ASSERT_EQUAL(ret_id, 0);
ret_id = tsk_node_table_add_row(&tables.nodes, 0, 1, -1, -1, NULL, 0);
CU_ASSERT_EQUAL(ret_id, 1);
ret = (int) tsk_edge_table_add_row(&tables.edges, 0., 1., 1, 0, NULL, 0);
CU_ASSERT_EQUAL(ret, 0);

ret = tsk_diff_iter_init(&iter, &tables, -1, 0);
CU_ASSERT_EQUAL(ret, TSK_ERR_TABLES_NOT_INDEXED);

tables.nodes.time[0] = 1;
ret = tsk_diff_iter_init(&iter, &tables, -1, 0);
CU_ASSERT_EQUAL(ret, TSK_ERR_BAD_NODE_TIME_ORDERING);

tsk_table_collection_free(&tables);
}

int
main(int argc, char **argv)
{
Expand Down Expand Up @@ -11670,8 +11641,6 @@ main(int argc, char **argv)
{ "test_table_collection_takeset_indexes",
test_table_collection_takeset_indexes },
{ "test_table_collection_delete_older", test_table_collection_delete_older },
{ "test_table_collection_edge_diffs_errors",
test_table_collection_edge_diffs_errors },
{ NULL, NULL },
};

Expand Down
197 changes: 0 additions & 197 deletions c/tests/test_trees.c
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Original file line number Diff line number Diff line change
Expand Up @@ -534,100 +534,6 @@ verify_tree_next_prev(tsk_treeseq_t *ts)
free(trees);
}

static void
verify_tree_diffs(tsk_treeseq_t *ts, tsk_flags_t options)
{
int ret, valid_tree;
tsk_diff_iter_t iter;
tsk_tree_t tree;
tsk_edge_list_node_t *record;
tsk_edge_list_t records_out, records_in;
tsk_size_t num_nodes = tsk_treeseq_get_num_nodes(ts);
tsk_size_t j, num_trees;
double lft, rgt;
tsk_id_t *parent = tsk_malloc(num_nodes * sizeof(tsk_id_t));
tsk_id_t *child = tsk_malloc(num_nodes * sizeof(tsk_id_t));
tsk_id_t *sib = tsk_malloc(num_nodes * sizeof(tsk_id_t));

CU_ASSERT_FATAL(parent != NULL);
CU_ASSERT_FATAL(child != NULL);
CU_ASSERT_FATAL(sib != NULL);
for (j = 0; j < num_nodes; j++) {
parent[j] = TSK_NULL;
child[j] = TSK_NULL;
sib[j] = TSK_NULL;
}
ret = tsk_diff_iter_init_from_ts(&iter, ts, options);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_tree_init(&tree, ts, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
valid_tree = tsk_tree_first(&tree);
CU_ASSERT_EQUAL_FATAL(valid_tree, TSK_TREE_OK);
tsk_diff_iter_print_state(&iter, _devnull);

num_trees = 0;
while ((ret = tsk_diff_iter_next(&iter, &lft, &rgt, &records_out, &records_in))
== TSK_TREE_OK) {
tsk_diff_iter_print_state(&iter, _devnull);
num_trees++;
/* Update forwards */
for (record = records_out.head; record != NULL; record = record->next) {
parent[record->edge.child] = TSK_NULL;
}
for (record = records_in.head; record != NULL; record = record->next) {
parent[record->edge.child] = record->edge.parent;
}
if (valid_tree) {
/* Now check against the sparse tree iterator. */
for (j = 0; j < num_nodes; j++) {
CU_ASSERT_EQUAL(parent[j], tree.parent[j]);
}
}
/* Update backwards */
for (record = records_out.tail; record != NULL; record = record->prev) {
parent[record->edge.child] = TSK_NULL;
}
for (record = records_in.tail; record != NULL; record = record->prev) {
parent[record->edge.child] = record->edge.parent;
}
if (valid_tree) {
/* Now check against the sparse tree iterator. */
for (j = 0; j < num_nodes; j++) {
CU_ASSERT_EQUAL(parent[j], tree.parent[j]);
}
CU_ASSERT_EQUAL(tree.interval.left, lft);
CU_ASSERT_EQUAL(tree.interval.right, rgt);
valid_tree = tsk_tree_next(&tree);
if (num_trees < tsk_treeseq_get_num_trees(ts)) {
CU_ASSERT_EQUAL(ret, TSK_TREE_OK);
} else {
CU_ASSERT_EQUAL(valid_tree, 0);
}
} else {
CU_ASSERT_TRUE_FATAL(options & TSK_INCLUDE_TERMINAL);
for (j = 0; j < num_nodes; j++) {
CU_ASSERT_EQUAL(parent[j], -1);
}
CU_ASSERT_EQUAL(lft, tsk_treeseq_get_sequence_length(ts));
CU_ASSERT_EQUAL(rgt, tsk_treeseq_get_sequence_length(ts));
}
}
if (options & TSK_INCLUDE_TERMINAL) {
CU_ASSERT_EQUAL(num_trees, tsk_treeseq_get_num_trees(ts) + 1);
} else {
CU_ASSERT_EQUAL(num_trees, tsk_treeseq_get_num_trees(ts));
}
CU_ASSERT_EQUAL_FATAL(valid_tree, 0);
ret = tsk_diff_iter_free(&iter);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_tree_free(&tree);
CU_ASSERT_EQUAL_FATAL(ret, 0);

free(parent);
free(child);
free(sib);
}

static void
verify_edge_array_single_tree(
tsk_tree_t *tree, tsk_edge_table_t *edge_table, tsk_size_t num_nodes)
Expand Down Expand Up @@ -5918,71 +5824,6 @@ test_convenience_arrays_multi_tree(void)
tsk_treeseq_free(&ts);
}

/*=======================================================
* Diff iter tests.
*======================================================*/

static void
test_simple_diff_iter(void)
{
int ret;
tsk_treeseq_t ts;

tsk_treeseq_from_text(&ts, 10, paper_ex_nodes, paper_ex_edges, NULL, NULL, NULL,
paper_ex_individuals, NULL, 0);

verify_tree_diffs(&ts, 0);
verify_tree_diffs(&ts, TSK_INCLUDE_TERMINAL);

ret = tsk_treeseq_free(&ts);
CU_ASSERT_EQUAL(ret, 0);
}

static void
test_nonbinary_diff_iter(void)
{
int ret;
tsk_treeseq_t ts;

tsk_treeseq_from_text(&ts, 100, nonbinary_ex_nodes, nonbinary_ex_edges, NULL, NULL,
NULL, NULL, NULL, 0);
verify_tree_diffs(&ts, 0);
verify_tree_diffs(&ts, TSK_INCLUDE_TERMINAL);

ret = tsk_treeseq_free(&ts);
CU_ASSERT_EQUAL(ret, 0);
}

static void
test_unary_diff_iter(void)
{
int ret;
tsk_treeseq_t ts;

tsk_treeseq_from_text(
&ts, 10, unary_ex_nodes, unary_ex_edges, NULL, NULL, NULL, NULL, NULL, 0);
verify_tree_diffs(&ts, 0);
verify_tree_diffs(&ts, TSK_INCLUDE_TERMINAL);

ret = tsk_treeseq_free(&ts);
CU_ASSERT_EQUAL(ret, 0);
}

static void
test_internal_sample_diff_iter(void)
{
int ret;
tsk_treeseq_t ts;

tsk_treeseq_from_text(&ts, 10, internal_sample_ex_nodes, internal_sample_ex_edges,
NULL, NULL, NULL, NULL, NULL, 0);
verify_tree_diffs(&ts, 0);
verify_tree_diffs(&ts, TSK_INCLUDE_TERMINAL);

ret = tsk_treeseq_free(&ts);
CU_ASSERT_EQUAL(ret, 0);
}

static void
test_multiroot_mrca(void)
{
Expand Down Expand Up @@ -6012,36 +5853,6 @@ test_multiroot_mrca(void)
tsk_treeseq_free(&ts);
}

static void
test_multiroot_diff_iter(void)
{
int ret;
tsk_treeseq_t ts;

tsk_treeseq_from_text(&ts, 10, multiroot_ex_nodes, multiroot_ex_edges, NULL, NULL,
NULL, NULL, NULL, 0);
verify_tree_diffs(&ts, 0);
verify_tree_diffs(&ts, TSK_INCLUDE_TERMINAL);

ret = tsk_treeseq_free(&ts);
CU_ASSERT_EQUAL(ret, 0);
}

static void
test_empty_diff_iter(void)
{
int ret;
tsk_treeseq_t ts;

tsk_treeseq_from_text(
&ts, 10, empty_ex_nodes, empty_ex_edges, NULL, NULL, NULL, NULL, NULL, 0);
verify_tree_diffs(&ts, 0);
verify_tree_diffs(&ts, TSK_INCLUDE_TERMINAL);

ret = tsk_treeseq_free(&ts);
CU_ASSERT_EQUAL(ret, 0);
}

/*=======================================================
* Sample sets
*======================================================*/
Expand Down Expand Up @@ -8840,14 +8651,6 @@ main(int argc, char **argv)

/* multiroot tests */
{ "test_multiroot_mrca", test_multiroot_mrca },
{ "test_multiroot_diff_iter", test_multiroot_diff_iter },

/* Diff iter tests */
{ "test_simple_diff_iter", test_simple_diff_iter },
{ "test_nonbinary_diff_iter", test_nonbinary_diff_iter },
{ "test_unary_diff_iter", test_unary_diff_iter },
{ "test_internal_sample_diff_iter", test_internal_sample_diff_iter },
{ "test_empty_diff_iter", test_empty_diff_iter },

/* Sample sets */
{ "test_simple_sample_sets", test_simple_sample_sets },
Expand Down
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