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Feb 2, 2021
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Bump versions for individual parents and add LWT tests #1177

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5 changes: 5 additions & 0 deletions c/CHANGELOG.rst
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Expand Up @@ -4,8 +4,13 @@

**Features**

- Add ``parents`` to the individual table to enable recording of pedigrees
(:user:`ivan-krukov`, :user:`benjeffery`, :issue:`852`, :pr:`1125`, :pr:`866`, :pr:`1153`, :pr:`1177`).

**Breaking changes**

- Method ``tsk_individual_table_add_row`` has an extra arguments ``parents`` and ``parents_length``.

**Bugfixes**

----------------------
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2 changes: 1 addition & 1 deletion c/tskit/core.h
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Expand Up @@ -144,7 +144,7 @@ to the API or ABI are introduced, i.e., internal refactors of bugfixes.
#define TSK_FILE_FORMAT_NAME "tskit.trees"
#define TSK_FILE_FORMAT_NAME_LENGTH 11
#define TSK_FILE_FORMAT_VERSION_MAJOR 12
#define TSK_FILE_FORMAT_VERSION_MINOR 3
#define TSK_FILE_FORMAT_VERSION_MINOR 4

/**
@defgroup GENERAL_ERROR_GROUP General errors.
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3 changes: 3 additions & 0 deletions python/CHANGELOG.rst
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Expand Up @@ -4,6 +4,9 @@

**Features**

- Add ``parents`` column to the individual table to allow recording of pedigrees
(:user:`ivan-krukov`, :user:`benjeffery`, :issue:`852`, :pr:`1125`, :pr:`866`, :pr:`1153`, :pr:`1177`).

- Added ``Tree.generate_random_binary`` static method to create random
binary trees (:user:`hyanwong`, :user:`jeromekelleher`, :pr:`1037`).

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6 changes: 6 additions & 0 deletions python/lwt_interface/CHANGELOG.rst
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@@ -1,3 +1,9 @@
--------------------
[0.1.3] - 2021-02-01
--------------------

- Added optional ``parents`` to individual table.

--------------------
[0.1.2] - 2020-10-22
--------------------
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17 changes: 15 additions & 2 deletions python/lwt_interface/dict_encoding_testlib.py
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Expand Up @@ -114,7 +114,7 @@ def test_check_ts_full(tmp_path, full_ts):
class TestEncodingVersion:
def test_version(self):
lwt = lwt_module.LightweightTableCollection()
assert lwt.asdict()["encoding_version"] == (1, 2)
assert lwt.asdict()["encoding_version"] == (1, 3)


class TestRoundTrip:
Expand All @@ -141,7 +141,9 @@ def test_individuals(self):
ts = msprime.simulate(n, mutation_rate=1, random_seed=2)
tables = ts.dump_tables()
for j in range(n):
tables.individuals.add_row(flags=j, location=(j, j), metadata=b"x" * j)
tables.individuals.add_row(
flags=j, location=(j, j), parents=(j, j), metadata=b"x" * j
)
self.verify(tables)

def test_sequence_length(self):
Expand Down Expand Up @@ -473,10 +475,21 @@ def test_individuals(self, tables):
self.verify_offset_pair(
tables, len(tables.individuals), "individuals", "location"
)
self.verify_offset_pair(
tables, len(tables.individuals), "individuals", "parents"
)
self.verify_offset_pair(
tables, len(tables.individuals), "individuals", "metadata"
)
self.verify_metadata_schema(tables, "individuals")
# Verify optional parents column
d = tables.asdict()
d["individuals"]["parents"] = None
d["individuals"]["parents_offset"] = None
lwt = lwt_module.LightweightTableCollection()
lwt.fromdict(d)
out = lwt.asdict()
assert all(val == [] for val in out["individuals"]["parents"])

def test_nodes(self, tables):
self.verify_offset_pair(tables, len(tables.nodes), "nodes", "metadata")
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2 changes: 1 addition & 1 deletion python/lwt_interface/tskit_lwt_interface.h
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Expand Up @@ -1695,7 +1695,7 @@ dump_tables_dict(tsk_table_collection_t *tables)
}

/* Dict representation version */
val = Py_BuildValue("ll", 1, 2);
val = Py_BuildValue("ll", 1, 3);
if (val == NULL) {
goto out;
}
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2 changes: 1 addition & 1 deletion python/tests/test_file_format.py
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Expand Up @@ -41,7 +41,7 @@


CURRENT_FILE_MAJOR = 12
CURRENT_FILE_MINOR = 3
CURRENT_FILE_MINOR = 4

test_data_dir = os.path.join(os.path.dirname(__file__), "data")

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2 changes: 1 addition & 1 deletion python/tskit/tables.py
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Expand Up @@ -2233,7 +2233,7 @@ def asdict(self):
map of table names to the tables themselves was returned.
"""
ret = {
"encoding_version": (1, 2),
"encoding_version": (1, 3),
"sequence_length": self.sequence_length,
"metadata_schema": repr(self.metadata_schema),
"metadata": self.metadata_schema.encode_row(self.metadata),
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