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May 3, 2022
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Rename int and load flags to common namespace #2224

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7 changes: 5 additions & 2 deletions c/CHANGELOG.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -20,8 +20,11 @@
- Rename several flags:
- All flags to ``simplify`` for example ``TSK_KEEP_INPUT_ROOTS`` becomes ``TSK_SIMPLIFY_KEEP_INPUT_ROOTS``.
- All flags to ``subset`` for example ``TSK_KEEP_UNREFERENCED`` becomes ``TSK_SUBSET_KEEP_UNREFERENCED``.

(:user:`benjeffery`, :issue:`1720`, :pr:`2226`, :pr:`2229`)
- ``TSK_BUILD_INDEXES`` -> ``TSK_TS_INIT_BUILD_INDEXES``
- ``TSK_NO_METADATA`` -> ``TSK_TABLE_NO_METADATA``
- ``TSK_NO_EDGE_METADATA`` -> ``TSK_TC_NO_EDGE_METADATA``

(:user:`benjeffery`, :issue:`1720`, :pr:`2226`, :pr:`2229`, :pr:`2224`)

**Features**

Expand Down
2 changes: 1 addition & 1 deletion c/tests/test_genotypes.c
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Original file line number Diff line number Diff line change
Expand Up @@ -756,7 +756,7 @@ test_single_tree_many_alleles(void)
ret_id = tsk_mutation_table_add_row(&tables.mutations, 0, 0, j - 1,
TSK_UNKNOWN_TIME, alleles, (tsk_size_t) j, NULL, 0);
CU_ASSERT_FATAL(ret_id >= 0);
ret = tsk_treeseq_init(&ts, &tables, TSK_BUILD_INDEXES);
ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
CU_ASSERT_EQUAL_FATAL(ret, 0);

ret = tsk_vargen_init(&vargen, &ts, NULL, 0, NULL, 0);
Expand Down
70 changes: 35 additions & 35 deletions c/tests/test_tables.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1496,7 +1496,7 @@ test_edge_table_with_options(tsk_flags_t options)
CU_ASSERT_EQUAL_FATAL(ret, 0);

for (j = 0; j < (tsk_id_t) num_rows; j++) {
if (options & TSK_NO_METADATA) {
if (options & TSK_TABLE_NO_METADATA) {
ret_id = tsk_edge_table_add_row(&table, (double) j, (double) j, j, j,
test_metadata, test_metadata_length);
CU_ASSERT_EQUAL(ret_id, TSK_ERR_METADATA_DISABLED);
Expand All @@ -1512,7 +1512,7 @@ test_edge_table_with_options(tsk_flags_t options)
CU_ASSERT_EQUAL(table.parent[j], j);
CU_ASSERT_EQUAL(table.child[j], j);
CU_ASSERT_EQUAL(table.num_rows, (tsk_size_t) j + 1);
if (options & TSK_NO_METADATA) {
if (options & TSK_TABLE_NO_METADATA) {
CU_ASSERT_EQUAL(table.metadata_length, 0);
CU_ASSERT_EQUAL(table.metadata, NULL);
CU_ASSERT_EQUAL(table.metadata_offset, NULL);
Expand All @@ -1533,7 +1533,7 @@ test_edge_table_with_options(tsk_flags_t options)
CU_ASSERT_EQUAL(edge.right, j);
CU_ASSERT_EQUAL(edge.parent, j);
CU_ASSERT_EQUAL(edge.child, j);
if (options & TSK_NO_METADATA) {
if (options & TSK_TABLE_NO_METADATA) {
CU_ASSERT_EQUAL(edge.metadata_length, 0);
CU_ASSERT_EQUAL(edge.metadata, NULL);
} else {
Expand Down Expand Up @@ -1568,7 +1568,7 @@ test_edge_table_with_options(tsk_flags_t options)
for (j = 0; j < (tsk_id_t) num_rows + 1; j++) {
metadata_offset[j] = (tsk_size_t) j;
}
if (options & TSK_NO_METADATA) {
if (options & TSK_TABLE_NO_METADATA) {
ret = tsk_edge_table_set_columns(
&table, num_rows, left, right, parent, child, metadata, metadata_offset);
CU_ASSERT_EQUAL(ret, TSK_ERR_METADATA_DISABLED);
Expand All @@ -1583,7 +1583,7 @@ test_edge_table_with_options(tsk_flags_t options)
CU_ASSERT_EQUAL(tsk_memcmp(table.right, right, num_rows * sizeof(double)), 0);
CU_ASSERT_EQUAL(tsk_memcmp(table.parent, parent, num_rows * sizeof(tsk_id_t)), 0);
CU_ASSERT_EQUAL(tsk_memcmp(table.child, child, num_rows * sizeof(tsk_id_t)), 0);
if (options & TSK_NO_METADATA) {
if (options & TSK_TABLE_NO_METADATA) {
CU_ASSERT_EQUAL(table.metadata, NULL);
CU_ASSERT_EQUAL(table.metadata_offset, NULL);
CU_ASSERT_EQUAL(table.metadata_length, 0);
Expand All @@ -1599,7 +1599,7 @@ test_edge_table_with_options(tsk_flags_t options)
CU_ASSERT_EQUAL(table.num_rows, num_rows);

/* Append another num_rows to the end. */
if (options & TSK_NO_METADATA) {
if (options & TSK_TABLE_NO_METADATA) {
ret = tsk_edge_table_append_columns(
&table, num_rows, left, right, parent, child, metadata, metadata_offset);
CU_ASSERT_EQUAL(ret, TSK_ERR_METADATA_DISABLED);
Expand All @@ -1622,7 +1622,7 @@ test_edge_table_with_options(tsk_flags_t options)
CU_ASSERT_EQUAL(tsk_memcmp(table.child, child, num_rows * sizeof(tsk_id_t)), 0);
CU_ASSERT_EQUAL(
tsk_memcmp(table.child + num_rows, child, num_rows * sizeof(tsk_id_t)), 0);
if (options & TSK_NO_METADATA) {
if (options & TSK_TABLE_NO_METADATA) {
CU_ASSERT_EQUAL(table.metadata, NULL);
CU_ASSERT_EQUAL(table.metadata_offset, NULL);
CU_ASSERT_EQUAL(table.metadata_length, 0);
Expand All @@ -1643,7 +1643,7 @@ test_edge_table_with_options(tsk_flags_t options)
CU_ASSERT_EQUAL(tsk_memcmp(table.right, right, num_rows * sizeof(double)), 0);
CU_ASSERT_EQUAL(tsk_memcmp(table.parent, parent, num_rows * sizeof(tsk_id_t)), 0);
CU_ASSERT_EQUAL(tsk_memcmp(table.child, child, num_rows * sizeof(tsk_id_t)), 0);
if (options & TSK_NO_METADATA) {
if (options & TSK_TABLE_NO_METADATA) {
CU_ASSERT_EQUAL(table.metadata, NULL);
CU_ASSERT_EQUAL(table.metadata_offset, NULL);
CU_ASSERT_EQUAL(table.metadata_length, 0);
Expand All @@ -1664,7 +1664,7 @@ test_edge_table_with_options(tsk_flags_t options)
tsk_edge_table_copy(&table, &table2, 0);
CU_ASSERT_TRUE(tsk_edge_table_equals(&table, &table2, 0));
CU_ASSERT_TRUE(tsk_edge_table_equals(&table, &table2, TSK_CMP_IGNORE_METADATA));
if (!(options & TSK_NO_METADATA)) {
if (!(options & TSK_TABLE_NO_METADATA)) {
/* Change the metadata values */
table2.metadata[0] = 0;
CU_ASSERT_FALSE(tsk_edge_table_equals(&table, &table2, 0));
Expand Down Expand Up @@ -1711,7 +1711,7 @@ test_edge_table_with_options(tsk_flags_t options)
CU_ASSERT_EQUAL(tsk_memcmp(table.right, right, num_rows * sizeof(double)), 0);
CU_ASSERT_EQUAL(tsk_memcmp(table.parent, parent, num_rows * sizeof(tsk_id_t)), 0);
CU_ASSERT_EQUAL(tsk_memcmp(table.child, child, num_rows * sizeof(tsk_id_t)), 0);
if (options & TSK_NO_METADATA) {
if (options & TSK_TABLE_NO_METADATA) {
CU_ASSERT_EQUAL(table.metadata, NULL);
CU_ASSERT_EQUAL(table.metadata_offset, NULL);
} else {
Expand All @@ -1736,7 +1736,7 @@ test_edge_table_with_options(tsk_flags_t options)
CU_ASSERT_EQUAL(tsk_memcmp(table.child, child, num_rows * sizeof(tsk_id_t)), 0);
CU_ASSERT_EQUAL(
tsk_memcmp(table.child + num_rows, child, num_rows * sizeof(tsk_id_t)), 0);
if (options & TSK_NO_METADATA) {
if (options & TSK_TABLE_NO_METADATA) {
CU_ASSERT_EQUAL(table.metadata, NULL);
CU_ASSERT_EQUAL(table.metadata_offset, NULL);
} else {
Expand Down Expand Up @@ -1778,7 +1778,7 @@ test_edge_table_with_options(tsk_flags_t options)
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_EDGE_OUT_OF_BOUNDS);

/* Copy rows in order if index NULL */
if (options & TSK_NO_METADATA) {
if (options & TSK_TABLE_NO_METADATA) {
ret = tsk_edge_table_set_columns(
&table2, num_rows, left, right, parent, child, NULL, NULL);
} else {
Expand All @@ -1804,7 +1804,7 @@ test_edge_table_with_options(tsk_flags_t options)
ret = tsk_edge_table_truncate(&table2, num_rows / 2);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_TRUE(tsk_edge_table_equals(&table, &table2, 0));
if (options & TSK_NO_METADATA) {
if (options & TSK_TABLE_NO_METADATA) {
ret = tsk_edge_table_set_columns(
&table2, num_rows, left, right, parent, child, NULL, NULL);
} else {
Expand Down Expand Up @@ -1880,7 +1880,7 @@ static void
test_edge_table(void)
{
test_edge_table_with_options(0);
test_edge_table_with_options(TSK_NO_METADATA);
test_edge_table_with_options(TSK_TABLE_NO_METADATA);
}

static void
Expand Down Expand Up @@ -1974,7 +1974,7 @@ test_edge_table_update_row_no_metadata(void)
tsk_edge_t row;
const char *metadata = "ABC";

ret = tsk_edge_table_init(&table, TSK_NO_METADATA);
ret = tsk_edge_table_init(&table, TSK_TABLE_NO_METADATA);
CU_ASSERT_EQUAL_FATAL(ret, 0);

ret_id = tsk_edge_table_add_row(&table, 0, 1.0, 2, 3, NULL, 0);
Expand Down Expand Up @@ -2036,7 +2036,7 @@ test_edge_table_takeset_with_options(tsk_flags_t table_options)
ret = tsk_edge_table_init(&source_table, table_options);
CU_ASSERT_EQUAL_FATAL(ret, 0);
for (j = 0; j < (tsk_id_t) num_rows; j++) {
if (table_options & TSK_NO_METADATA) {
if (table_options & TSK_TABLE_NO_METADATA) {
ret_id = tsk_edge_table_add_row(
&source_table, (double) j, (double) j + 1, j + 2, j + 3, NULL, 0);

Expand All @@ -2060,7 +2060,7 @@ test_edge_table_takeset_with_options(tsk_flags_t table_options)
child = tsk_malloc(num_rows * sizeof(tsk_id_t));
CU_ASSERT_FATAL(child != NULL);
tsk_memcpy(child, source_table.child, num_rows * sizeof(tsk_id_t));
if (table_options & TSK_NO_METADATA) {
if (table_options & TSK_TABLE_NO_METADATA) {
metadata = NULL;
metadata_offset = NULL;
test_metadata = NULL;
Expand Down Expand Up @@ -2103,7 +2103,7 @@ test_edge_table_takeset_with_options(tsk_flags_t table_options)
ret = tsk_edge_table_takeset_columns(
&table, num_rows, left, right, parent, NULL, metadata, metadata_offset);
CU_ASSERT_EQUAL(ret, TSK_ERR_BAD_PARAM_VALUE);
if (table_options & TSK_NO_METADATA) {
if (table_options & TSK_TABLE_NO_METADATA) {
/* It isn't used, so any pointer does for testing that presence of metadata
fails */
ret = tsk_edge_table_takeset_columns(
Expand Down Expand Up @@ -2132,7 +2132,7 @@ test_edge_table_takeset_with_options(tsk_flags_t table_options)
static void
test_edge_table_takeset(void)
{
test_edge_table_takeset_with_options(TSK_NO_METADATA);
test_edge_table_takeset_with_options(TSK_TABLE_NO_METADATA);
test_edge_table_takeset_with_options(0);
}

Expand All @@ -2157,7 +2157,7 @@ test_edge_table_copy_semantics(void)
tsk_table_collection_free(&t2);

/* We should not be able to copy into a table with no metadata */
ret = tsk_table_collection_copy(&t1, &t2, TSK_NO_EDGE_METADATA);
ret = tsk_table_collection_copy(&t1, &t2, TSK_TC_NO_EDGE_METADATA);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_METADATA_DISABLED);
tsk_table_collection_free(&t2);

Expand All @@ -2172,7 +2172,7 @@ test_edge_table_copy_semantics(void)
CU_ASSERT_TRUE(tsk_table_collection_equals(&t1, &t2, 0));
tsk_table_collection_free(&t2);

ret = tsk_table_collection_copy(&t1, &t2, TSK_NO_EDGE_METADATA);
ret = tsk_table_collection_copy(&t1, &t2, TSK_TC_NO_EDGE_METADATA);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_TRUE(tsk_table_collection_equals(&t1, &t2, 0));
tsk_table_collection_free(&t2);
Expand Down Expand Up @@ -2332,7 +2332,7 @@ test_edge_table_squash_bad_intervals(void)
const char *edges_ex = "0 0.6 1 0\n"
"0.4 1 1 0\n";

ret = tsk_table_collection_init(&tables, TSK_NO_EDGE_METADATA);
ret = tsk_table_collection_init(&tables, TSK_TC_NO_EDGE_METADATA);
CU_ASSERT_EQUAL_FATAL(ret, 0);
tables.sequence_length = 1;

Expand Down Expand Up @@ -2366,7 +2366,7 @@ test_edge_table_squash_metadata(void)

tsk_table_collection_free(&tables);

ret = tsk_table_collection_init(&tables, TSK_NO_EDGE_METADATA);
ret = tsk_table_collection_init(&tables, TSK_TC_NO_EDGE_METADATA);
CU_ASSERT_EQUAL_FATAL(ret, 0);
tables.sequence_length = 10;
ret_id = tsk_edge_table_add_row(&tables.edges, 0, 0, 1, 1, NULL, 0);
Expand Down Expand Up @@ -7726,7 +7726,7 @@ static void
test_sort_tables_drops_indexes(void)
{
test_sort_tables_drops_indexes_with_options(0);
test_sort_tables_drops_indexes_with_options(TSK_NO_EDGE_METADATA);
test_sort_tables_drops_indexes_with_options(TSK_TC_NO_EDGE_METADATA);
}

static void
Expand Down Expand Up @@ -7764,12 +7764,12 @@ test_sort_tables_no_edge_metadata(void)

tsk_treeseq_from_text(&ts, 1, single_tree_ex_nodes, single_tree_ex_edges, NULL, NULL,
NULL, NULL, NULL, 0);
ret = tsk_treeseq_copy_tables(&ts, &t1, TSK_NO_EDGE_METADATA);
ret = tsk_treeseq_copy_tables(&ts, &t1, TSK_TC_NO_EDGE_METADATA);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_FATAL(t1.edges.options & TSK_NO_EDGE_METADATA);
CU_ASSERT_FATAL(t1.edges.options & TSK_TABLE_NO_METADATA);
ret = tsk_table_collection_copy(&t1, &t2, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_FALSE(t2.edges.options & TSK_NO_EDGE_METADATA);
CU_ASSERT_FALSE(t2.edges.options & TSK_TABLE_NO_METADATA);
CU_ASSERT_TRUE(tsk_table_collection_equals(&t1, &t2, 0));
reverse_edges(&t1);
CU_ASSERT_FALSE(tsk_table_collection_equals(&t1, &t2, 0));
Expand All @@ -7778,10 +7778,10 @@ test_sort_tables_no_edge_metadata(void)
CU_ASSERT_TRUE(tsk_table_collection_equals(&t1, &t2, 0));
tsk_table_collection_free(&t2);

ret = tsk_table_collection_copy(&t1, &t2, TSK_NO_EDGE_METADATA);
ret = tsk_table_collection_copy(&t1, &t2, TSK_TC_NO_EDGE_METADATA);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_TRUE(t1.edges.options & TSK_NO_EDGE_METADATA);
CU_ASSERT_TRUE(t2.edges.options & TSK_NO_EDGE_METADATA);
CU_ASSERT_TRUE(t1.edges.options & TSK_TABLE_NO_METADATA);
CU_ASSERT_TRUE(t2.edges.options & TSK_TABLE_NO_METADATA);
CU_ASSERT_TRUE(tsk_table_collection_equals(&t1, &t2, 0));
reverse_edges(&t1);
CU_ASSERT_FALSE(tsk_table_collection_equals(&t1, &t2, 0));
Expand Down Expand Up @@ -8359,7 +8359,7 @@ static void
test_dump_unindexed(void)
{
test_dump_unindexed_with_options(0);
test_dump_unindexed_with_options(TSK_NO_EDGE_METADATA);
test_dump_unindexed_with_options(TSK_TC_NO_EDGE_METADATA);
}

static void
Expand All @@ -8385,7 +8385,7 @@ static void
test_dump_load_empty(void)
{
test_dump_load_empty_with_options(0);
test_dump_load_empty_with_options(TSK_NO_EDGE_METADATA);
test_dump_load_empty_with_options(TSK_TC_NO_EDGE_METADATA);
}

static void
Expand Down Expand Up @@ -8445,7 +8445,7 @@ static void
test_dump_load_unsorted(void)
{
test_dump_load_unsorted_with_options(0);
test_dump_load_unsorted_with_options(TSK_NO_EDGE_METADATA);
test_dump_load_unsorted_with_options(TSK_TC_NO_EDGE_METADATA);
}

static void
Expand Down Expand Up @@ -9323,7 +9323,7 @@ static void
test_table_collection_check_integrity(void)
{
test_table_collection_check_integrity_with_options(0);
test_table_collection_check_integrity_with_options(TSK_NO_EDGE_METADATA);
test_table_collection_check_integrity_with_options(TSK_TC_NO_EDGE_METADATA);
}

static void
Expand Down Expand Up @@ -9500,7 +9500,7 @@ static void
test_table_collection_subset(void)
{
test_table_collection_subset_with_options(0);
test_table_collection_subset_with_options(TSK_NO_EDGE_METADATA);
test_table_collection_subset_with_options(TSK_TC_NO_EDGE_METADATA);
}

static void
Expand Down
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