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Tests and methods for individual parents #1153

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2 changes: 2 additions & 0 deletions c/tests/test_file_format.c
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Original file line number Diff line number Diff line change
Expand Up @@ -319,6 +319,7 @@ test_missing_required_column_pairs(void)
tsk_table_collection_t t;
const char *required_cols[][2] = {
{ "individuals/location", "individuals/location_offset" },
{ "individuals/parents", "individuals/parents_offset" },
{ "individuals/metadata", "individuals/metadata_offset" },
{ "mutations/derived_state", "mutations/derived_state_offset" },
{ "mutations/metadata", "mutations/metadata_offset" },
Expand Down Expand Up @@ -438,6 +439,7 @@ test_bad_offset_columns(void)
"edges/metadata_offset",
"migrations/metadata_offset",
"individuals/location_offset",
"individuals/parents_offset",
"individuals/metadata_offset",
"mutations/derived_state_offset",
"mutations/metadata_offset",
Expand Down
102 changes: 91 additions & 11 deletions c/tests/test_tables.c
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Expand Up @@ -2069,14 +2069,17 @@ test_individual_table(void)
tsk_size_t k;
uint32_t *flags;
double *location;
tsk_id_t *parents;
char *metadata;
tsk_size_t *metadata_offset;
tsk_size_t *parents_offset;
tsk_size_t *location_offset;
tsk_individual_t individual;
const char *test_metadata = "test";
tsk_size_t test_metadata_length = 4;
char metadata_copy[test_metadata_length + 1];
tsk_size_t spatial_dimension = 2;
tsk_size_t num_parents = 2;
double test_location[spatial_dimension];

for (k = 0; k < spatial_dimension; k++) {
Expand Down Expand Up @@ -2165,6 +2168,14 @@ test_individual_table(void)
for (j = 0; j < (tsk_id_t) num_rows + 1; j++) {
location_offset[j] = (tsk_size_t) j * spatial_dimension;
}
parents = malloc(num_parents * num_rows * sizeof(tsk_id_t));
CU_ASSERT_FATAL(parents != NULL);
memset(parents, 0, num_parents * num_rows * sizeof(tsk_id_t));
parents_offset = malloc((num_rows + 1) * sizeof(tsk_size_t));
CU_ASSERT_FATAL(parents_offset != NULL);
for (j = 0; j < (tsk_id_t) num_rows + 1; j++) {
parents_offset[j] = (tsk_size_t) j * num_parents;
}
metadata = malloc(num_rows * sizeof(char));
memset(metadata, 'a', num_rows * sizeof(char));
CU_ASSERT_FATAL(metadata != NULL);
Expand All @@ -2174,7 +2185,7 @@ test_individual_table(void)
metadata_offset[j] = (tsk_size_t) j;
}
ret = tsk_individual_table_set_columns(&table, num_rows, flags, location,
location_offset, NULL, NULL, metadata, metadata_offset);
location_offset, parents, parents_offset, metadata, metadata_offset);
CU_ASSERT_EQUAL(ret, 0);
CU_ASSERT_EQUAL(memcmp(table.flags, flags, num_rows * sizeof(uint32_t)), 0);
CU_ASSERT_EQUAL(
Expand All @@ -2183,18 +2194,24 @@ test_individual_table(void)
CU_ASSERT_EQUAL(memcmp(table.location_offset, location_offset,
(num_rows + 1) * sizeof(tsk_size_t)),
0);
CU_ASSERT_EQUAL(
memcmp(table.parents, parents, num_parents * num_rows * sizeof(tsk_id_t)), 0);
CU_ASSERT_EQUAL(memcmp(table.parents_offset, parents_offset,
(num_rows + 1) * sizeof(tsk_size_t)),
0);
CU_ASSERT_EQUAL(memcmp(table.metadata, metadata, num_rows * sizeof(char)), 0);
CU_ASSERT_EQUAL(memcmp(table.metadata_offset, metadata_offset,
(num_rows + 1) * sizeof(tsk_size_t)),
0);
CU_ASSERT_EQUAL(table.num_rows, num_rows);
CU_ASSERT_EQUAL(table.location_length, spatial_dimension * num_rows);
CU_ASSERT_EQUAL(table.parents_length, num_parents * num_rows);
CU_ASSERT_EQUAL(table.metadata_length, num_rows);
tsk_individual_table_print_state(&table, _devnull);

/* Append another num_rows onto the end */
ret = tsk_individual_table_append_columns(&table, num_rows, flags, location,
location_offset, NULL, NULL, metadata, metadata_offset);
location_offset, parents, parents_offset, metadata, metadata_offset);
CU_ASSERT_EQUAL(ret, 0);
CU_ASSERT_EQUAL(memcmp(table.flags, flags, num_rows * sizeof(uint32_t)), 0);
CU_ASSERT_EQUAL(
Expand All @@ -2208,8 +2225,15 @@ test_individual_table(void)
CU_ASSERT_EQUAL(memcmp(table.location + spatial_dimension * num_rows, location,
spatial_dimension * num_rows * sizeof(double)),
0);
CU_ASSERT_EQUAL(
memcmp(table.parents, parents, num_parents * num_rows * sizeof(tsk_id_t)), 0);
CU_ASSERT_EQUAL(memcmp(table.parents + num_parents * num_rows, parents,
num_parents * num_rows * sizeof(tsk_id_t)),
0);
CU_ASSERT_EQUAL(table.num_rows, 2 * num_rows);
CU_ASSERT_EQUAL(table.metadata_length, 2 * num_rows);
CU_ASSERT_EQUAL(table.parents_length, 2 * num_parents * num_rows);
CU_ASSERT_EQUAL(table.location_length, 2 * spatial_dimension * num_rows);
tsk_individual_table_print_state(&table, _devnull);
ret = tsk_individual_table_dump_text(&table, _devnull);
CU_ASSERT_EQUAL_FATAL(ret, 0);
Expand All @@ -2224,36 +2248,48 @@ test_individual_table(void)
CU_ASSERT_EQUAL(memcmp(table.location_offset, location_offset,
(num_rows + 1) * sizeof(tsk_size_t)),
0);
CU_ASSERT_EQUAL(
memcmp(table.parents, parents, num_parents * num_rows * sizeof(tsk_id_t)), 0);
CU_ASSERT_EQUAL(memcmp(table.parents_offset, parents_offset,
(num_rows + 1) * sizeof(tsk_size_t)),
0);
CU_ASSERT_EQUAL(memcmp(table.metadata, metadata, num_rows * sizeof(char)), 0);
CU_ASSERT_EQUAL(memcmp(table.metadata_offset, metadata_offset,
(num_rows + 1) * sizeof(tsk_size_t)),
0);
CU_ASSERT_EQUAL(table.num_rows, num_rows);
CU_ASSERT_EQUAL(table.location_length, spatial_dimension * num_rows);
CU_ASSERT_EQUAL(table.parents_length, num_parents * num_rows);
CU_ASSERT_EQUAL(table.metadata_length, num_rows);
tsk_individual_table_print_state(&table, _devnull);

ret = tsk_individual_table_truncate(&table, num_rows + 1);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_TABLE_POSITION);

// TODO: add tests for parent spec
/* flags can't be NULL */
ret = tsk_individual_table_set_columns(&table, num_rows, NULL, location,
location_offset, NULL, NULL, metadata, metadata_offset);
location_offset, parents, parents_offset, metadata, metadata_offset);
CU_ASSERT_EQUAL(ret, TSK_ERR_BAD_PARAM_VALUE);
/* location and location offset must be simultaneously NULL or not */
ret = tsk_individual_table_set_columns(
&table, num_rows, flags, location, NULL, NULL, NULL, metadata, metadata_offset);
ret = tsk_individual_table_set_columns(&table, num_rows, flags, location, NULL,
parents, parents_offset, metadata, metadata_offset);
CU_ASSERT_EQUAL(ret, TSK_ERR_BAD_PARAM_VALUE);
ret = tsk_individual_table_set_columns(&table, num_rows, flags, NULL,
location_offset, NULL, NULL, metadata, metadata_offset);
CU_ASSERT_EQUAL(ret, TSK_ERR_BAD_PARAM_VALUE);
/* parents and parents offset must be simultaneously NULL or not */
ret = tsk_individual_table_set_columns(&table, num_rows, flags, location,
location_offset, parents, NULL, metadata, metadata_offset);
CU_ASSERT_EQUAL(ret, TSK_ERR_BAD_PARAM_VALUE);
ret = tsk_individual_table_set_columns(&table, num_rows, flags, location,
location_offset, NULL, parents_offset, metadata, metadata_offset);
CU_ASSERT_EQUAL(ret, TSK_ERR_BAD_PARAM_VALUE);
/* metadata and metadata offset must be simultaneously NULL or not */
ret = tsk_individual_table_set_columns(&table, num_rows, flags, location,
location_offset, NULL, NULL, NULL, metadata_offset);
location_offset, parents, parents_offset, NULL, metadata_offset);
CU_ASSERT_EQUAL(ret, TSK_ERR_BAD_PARAM_VALUE);
ret = tsk_individual_table_set_columns(
&table, num_rows, flags, location, location_offset, NULL, NULL, metadata, NULL);
ret = tsk_individual_table_set_columns(&table, num_rows, flags, location,
location_offset, parents, parents_offset, metadata, NULL);
CU_ASSERT_EQUAL(ret, TSK_ERR_BAD_PARAM_VALUE);

/* if location and location_offset are both null, all locations are zero length */
Expand Down Expand Up @@ -2282,6 +2318,32 @@ test_individual_table(void)
ret = tsk_individual_table_dump_text(&table, _devnull);
CU_ASSERT_EQUAL_FATAL(ret, 0);

/* if parents and parents_offset are both null, all parents are zero length */
num_rows = 10;
memset(parents_offset, 0, (num_rows + 1) * sizeof(tsk_size_t));
ret = tsk_individual_table_set_columns(
&table, num_rows, flags, NULL, NULL, NULL, NULL, NULL, NULL);
CU_ASSERT_EQUAL(ret, 0);
CU_ASSERT_EQUAL(memcmp(table.parents_offset, parents_offset,
(num_rows + 1) * sizeof(tsk_size_t)),
0);
CU_ASSERT_EQUAL(table.num_rows, num_rows);
CU_ASSERT_EQUAL(table.parents_length, 0);
ret = tsk_individual_table_append_columns(
&table, num_rows, flags, NULL, NULL, NULL, NULL, NULL, NULL);
CU_ASSERT_EQUAL(ret, 0);
CU_ASSERT_EQUAL(memcmp(table.parents_offset, parents_offset,
(num_rows + 1) * sizeof(tsk_size_t)),
0);
CU_ASSERT_EQUAL(memcmp(table.parents_offset + num_rows, parents_offset,
num_rows * sizeof(uint32_t)),
0);
CU_ASSERT_EQUAL(table.num_rows, 2 * num_rows);
CU_ASSERT_EQUAL(table.parents_length, 0);
tsk_individual_table_print_state(&table, _devnull);
ret = tsk_individual_table_dump_text(&table, _devnull);
CU_ASSERT_EQUAL_FATAL(ret, 0);

/* if metadata and metadata_offset are both null, all metadatas are zero length */
num_rows = 10;
memset(metadata_offset, 0, (num_rows + 1) * sizeof(tsk_size_t));
Expand All @@ -2297,15 +2359,20 @@ test_individual_table(void)
0);
CU_ASSERT_EQUAL(table.num_rows, num_rows);
CU_ASSERT_EQUAL(table.metadata_length, 0);
ret = tsk_individual_table_append_columns(
&table, num_rows, flags, location, location_offset, NULL, NULL, NULL, NULL);
ret = tsk_individual_table_append_columns(&table, num_rows, flags, location,
location_offset, parents, parents_offset, NULL, NULL);
CU_ASSERT_EQUAL(ret, 0);
CU_ASSERT_EQUAL(
memcmp(table.location, location, spatial_dimension * num_rows * sizeof(double)),
0);
CU_ASSERT_EQUAL(memcmp(table.location + spatial_dimension * num_rows, location,
spatial_dimension * num_rows * sizeof(double)),
0);
CU_ASSERT_EQUAL(
memcmp(table.parents, parents, num_parents * num_rows * sizeof(tsk_id_t)), 0);
CU_ASSERT_EQUAL(memcmp(table.parents + num_parents * num_rows, parents,
num_parents * num_rows * sizeof(tsk_id_t)),
0);
CU_ASSERT_EQUAL(memcmp(table.metadata_offset, metadata_offset,
(num_rows + 1) * sizeof(tsk_size_t)),
0);
Expand Down Expand Up @@ -2352,6 +2419,8 @@ test_individual_table(void)
free(flags);
free(location);
free(location_offset);
free(parents);
free(parents_offset);
free(metadata);
free(metadata_offset);
}
Expand Down Expand Up @@ -2766,6 +2835,10 @@ test_table_size_increments(void)
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_EQUAL_FATAL(
tables.individuals.max_location_length_increment, default_size);
ret = tsk_individual_table_set_max_parents_length_increment(
&tables.individuals, new_size);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_EQUAL_FATAL(tables.individuals.max_parents_length_increment, default_size);

ret = tsk_node_table_set_max_rows_increment(&tables.nodes, new_size);
CU_ASSERT_EQUAL_FATAL(ret, 0);
Expand Down Expand Up @@ -4362,6 +4435,7 @@ test_column_overflow(void)
tsk_size_t too_big = ((tsk_size_t) UINT32_MAX);
double zero = 0;
char zeros[] = { 0, 0, 0, 0, 0, 0, 0, 0 };
tsk_id_t id_zeros[] = { 0, 0, 0, 0, 0, 0, 0, 0 };

ret = tsk_table_collection_init(&tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
Expand All @@ -4380,6 +4454,12 @@ test_column_overflow(void)
ret = tsk_individual_table_add_row(
&tables.individuals, 0, NULL, 0, NULL, 0, NULL, too_big);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_COLUMN_OVERFLOW);
ret = tsk_individual_table_add_row(
&tables.individuals, 0, NULL, 0, id_zeros, 1, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, 2);
ret = tsk_individual_table_add_row(
&tables.individuals, 0, NULL, 0, NULL, too_big, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_COLUMN_OVERFLOW);

ret = tsk_node_table_add_row(&tables.nodes, 0, 0, 0, 0, zeros, 1);
CU_ASSERT_EQUAL_FATAL(ret, 0);
Expand Down
5 changes: 3 additions & 2 deletions c/tests/testlib.c
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Expand Up @@ -730,6 +730,7 @@ caterpillar_tree(tsk_size_t n, tsk_size_t num_sites, tsk_size_t num_mutations)
tsk_id_t j, k, last_node, u;
int state, m;
double position[2];
tsk_id_t parents[2] = { -1, -1 };
const char *states[] = { "0", "1" };
const char *metadata[] = { "This", "is", "some", "metadata" };
const int num_metadatas = sizeof(metadata) / sizeof(*metadata);
Expand Down Expand Up @@ -772,8 +773,8 @@ caterpillar_tree(tsk_size_t n, tsk_size_t num_sites, tsk_size_t num_mutations)
ret = tsk_population_table_add_row(
&tables.populations, metadata[m], strlen(metadata[m]));
CU_ASSERT_EQUAL_FATAL(ret, j);
ret = tsk_individual_table_add_row(&tables.individuals, 0, position, 2, NULL, 0,
metadata[m], strlen(metadata[m]));
ret = tsk_individual_table_add_row(&tables.individuals, 0, position, 2, parents,
2, metadata[m], strlen(metadata[m]));
CU_ASSERT_EQUAL_FATAL(ret, j);
ret = tsk_node_table_add_row(&tables.nodes, TSK_NODE_IS_SAMPLE, 0, j, j,
metadata[m], strlen(metadata[m]));
Expand Down
4 changes: 4 additions & 0 deletions python/tests/test_file_format.py
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Expand Up @@ -589,6 +589,10 @@ def verify_dump_format(self, ts):
assert np.array_equal(
tables.individuals.location_offset, store["individuals/location_offset"]
)
assert np.array_equal(tables.individuals.parents, store["individuals/parents"])
assert np.array_equal(
tables.individuals.parents_offset, store["individuals/parents_offset"]
)
assert np.array_equal(
tables.individuals.metadata, store["individuals/metadata"]
)
Expand Down
2 changes: 2 additions & 0 deletions python/tests/test_highlevel.py
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Expand Up @@ -948,6 +948,7 @@ def test_individuals(self):
assert inds[j] == ts.individual(j)
assert inds[j].id == j
assert isinstance(inds[j].metadata, bytes)
assert isinstance(inds[j].parents, np.ndarray)
assert isinstance(inds[j].location, np.ndarray)
assert isinstance(inds[j].nodes, np.ndarray)
assert ind_node_map[j] == list(inds[j].nodes)
Expand Down Expand Up @@ -2969,6 +2970,7 @@ def get_instances(self, n):
id_=j,
flags=j,
location=[j],
parents=[j],
nodes=[j],
encoded_metadata=b"x" * j,
metadata_decoder=lambda m: m.decode() + "decoded",
Expand Down
19 changes: 11 additions & 8 deletions python/tests/test_metadata.py
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Expand Up @@ -209,26 +209,29 @@ class TestLoadTextMetadata:
def test_individuals(self):
individuals = io.StringIO(
"""\
id flags location metadata
0 1 0.0,1.0,0.0 abc
1 1 1.0,2.0 XYZ+
2 0 2.0,3.0,0.0 !@#$%^&*()
id flags location parents metadata
0 1 0.0,1.0,0.0 -1,-1 abc
1 1 1.0,2.0 0,0 XYZ+
2 0 2.0,3.0,0.0 0,1 !@#$%^&*()
"""
)
i = tskit.parse_individuals(
individuals, strict=False, encoding="utf8", base64_metadata=False
)
expected = [
(1, [0.0, 1.0, 0.0], "abc"),
(1, [1.0, 2.0], "XYZ+"),
(0, [2.0, 3.0, 0.0], "!@#$%^&*()"),
(1, [0.0, 1.0, 0.0], [-1, -1], "abc"),
(1, [1.0, 2.0], [0, 0], "XYZ+"),
(0, [2.0, 3.0, 0.0], [0, 1], "!@#$%^&*()"),
]
for a, b in zip(expected, i):
assert a[0] == b.flags
assert len(a[1]) == len(b.location)
for x, y in zip(a[1], b.location):
assert x == y
assert a[2].encode("utf8") == b.metadata
assert len(a[2]) == len(b.parents)
for x, y in zip(a[2], b.parents):
assert x == y
assert a[3].encode("utf8") == b.metadata

def test_nodes(self):
nodes = io.StringIO(
Expand Down
23 changes: 18 additions & 5 deletions python/tests/test_tables.py
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Original file line number Diff line number Diff line change
Expand Up @@ -866,19 +866,21 @@ class TestIndividualTable(CommonTestsMixin, MetadataTestsMixin):

def test_simple_example(self):
t = tskit.IndividualTable()
t.add_row(flags=0, location=[], metadata=b"123")
t.add_row(flags=1, location=(0, 1, 2, 3), metadata=b"\xf0")
t.add_row(flags=2, parents=[0, 1])
t.add_row(flags=0, location=[], parents=[], metadata=b"123")
t.add_row(
flags=1, location=(0, 1, 2, 3), parents=(4, 5, 6, 7), metadata=b"\xf0"
)
s = str(t)
assert len(s) > 0
assert len(t) == 3
assert len(t) == 2
assert t[0].flags == 0
assert list(t[0].location) == []
assert list(t[0].parents) == []
assert t[0].metadata == b"123"
assert t[1].flags == 1
assert list(t[1].location) == [0, 1, 2, 3]
assert list(t[1].parents) == [4, 5, 6, 7]
assert t[1].metadata == b"\xf0"
assert list(t[2].parents) == [0, 1]
with pytest.raises(IndexError):
t.__getitem__(-4)

Expand Down Expand Up @@ -915,6 +917,17 @@ def test_packset_location(self):
assert list(t[0].location) == [0]
assert list(t[1].location) == [1, 2, 3]

def test_packset_parents(self):
t = tskit.IndividualTable()
t.add_row(flags=0)
t.packset_parents([[0, 2]])
assert list(t[0].parents) == [0, 2]
t.add_row(flags=1)
assert list(t[1].parents) == []
t.packset_parents([[0], [1, 2, 3]])
assert list(t[0].parents) == [0]
assert list(t[1].parents) == [1, 2, 3]

def test_missing_time_equal_to_self(self):
t = tskit.TableCollection(sequence_length=10)
t.sites.add_row(position=1, ancestral_state="0")
Expand Down
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