Remove _offset accessors

Author: benjeffery

python/tests/test_highlevel.py

@@ -2592,33 +2592,25 @@ def test_individual_properties(self, n):
         "array",
         [
             "individuals_flags",
-            "individuals_metadata_offset",
             "nodes_time",
             "nodes_flags",
             "nodes_population",
             "nodes_individual",
-            "nodes_metadata_offset",
             "edges_left",
             "edges_right",
             "edges_parent",
             "edges_child",
-            "edges_metadata_offset",
             "sites_position",
-            "sites_metadata_offset",
             "mutations_site",
             "mutations_node",
             "mutations_parent",
             "mutations_time",
-            "mutations_metadata_offset",
             "migrations_left",
             "migrations_right",
             "migrations_node",
             "migrations_source",
             "migrations_dest",
             "migrations_time",
-            "migrations_metadata_offset",
-            "individuals_metadata_offset",
-            "populations_metadata_offset",
             "indexes_edge_insertion_order",
             "indexes_edge_removal_order",
         ],
@@ -2639,46 +2631,30 @@ def test_arrays_equal_to_tables(self, ts_fixture):
         tables = ts.tables
 
         assert_array_equal(ts.individuals_flags, tables.individuals.flags)
-        assert_array_equal(
-            ts.individuals_metadata_offset, tables.individuals.metadata_offset
-        )
 
         assert_array_equal(ts.nodes_flags, tables.nodes.flags)
         assert_array_equal(ts.nodes_population, tables.nodes.population)
         assert_array_equal(ts.nodes_time, tables.nodes.time)
         assert_array_equal(ts.nodes_individual, tables.nodes.individual)
-        assert_array_equal(ts.nodes_metadata_offset, tables.nodes.metadata_offset)
 
         assert_array_equal(ts.edges_left, tables.edges.left)
         assert_array_equal(ts.edges_right, tables.edges.right)
         assert_array_equal(ts.edges_parent, tables.edges.parent)
         assert_array_equal(ts.edges_child, tables.edges.child)
-        assert_array_equal(ts.edges_metadata_offset, tables.edges.metadata_offset)
 
         assert_array_equal(ts.sites_position, tables.sites.position)
-        assert_array_equal(ts.sites_metadata_offset, tables.sites.metadata_offset)
 
         assert_array_equal(ts.mutations_site, tables.mutations.site)
         assert_array_equal(ts.mutations_node, tables.mutations.node)
         assert_array_equal(ts.mutations_parent, tables.mutations.parent)
         assert_array_equal(ts.mutations_time, tables.mutations.time)
-        assert_array_equal(
-            ts.mutations_metadata_offset, tables.mutations.metadata_offset
-        )
 
         assert_array_equal(ts.migrations_left, tables.migrations.left)
         assert_array_equal(ts.migrations_right, tables.migrations.right)
         assert_array_equal(ts.migrations_node, tables.migrations.node)
         assert_array_equal(ts.migrations_source, tables.migrations.source)
         assert_array_equal(ts.migrations_dest, tables.migrations.dest)
         assert_array_equal(ts.migrations_time, tables.migrations.time)
-        assert_array_equal(
-            ts.migrations_metadata_offset, tables.migrations.metadata_offset
-        )
-
-        assert_array_equal(
-            ts.populations_metadata_offset, tables.populations.metadata_offset
-        )
 
         assert_array_equal(
             ts.indexes_edge_insertion_order, tables.indexes.edge_insertion_order

python/tskit/trees.py

@@ -4122,38 +4122,31 @@ def __init__(self, ll_tree_sequence):
         llts = self._ll_tree_sequence
         self._individuals_flags = llts.individuals_flags
         self._individuals_metadata = llts.individuals_metadata
-        self._individuals_metadata_offset = llts.individuals_metadata_offset
         self._nodes_time = llts.nodes_time
         self._nodes_flags = llts.nodes_flags
         self._nodes_population = llts.nodes_population
         self._nodes_individual = llts.nodes_individual
         self._nodes_metadata = llts.nodes_metadata
-        self._nodes_metadata_offset = llts.nodes_metadata_offset
         self._edges_left = llts.edges_left
         self._edges_right = llts.edges_right
         self._edges_parent = llts.edges_parent
         self._edges_child = llts.edges_child
         self._edges_metadata = llts.edges_metadata
-        self._edges_metadata_offset = llts.edges_metadata_offset
         self._sites_position = llts.sites_position
         self._sites_metadata = llts.sites_metadata
-        self._sites_metadata_offset = llts.sites_metadata_offset
         self._mutations_site = llts.mutations_site
         self._mutations_node = llts.mutations_node
         self._mutations_parent = llts.mutations_parent
         self._mutations_time = llts.mutations_time
         self._mutations_metadata = llts.mutations_metadata
-        self._mutations_metadata_offset = llts.mutations_metadata_offset
         self._migrations_left = llts.migrations_left
         self._migrations_right = llts.migrations_right
         self._migrations_node = llts.migrations_node
         self._migrations_source = llts.migrations_source
         self._migrations_dest = llts.migrations_dest
         self._migrations_time = llts.migrations_time
         self._migrations_metadata = llts.migrations_metadata
-        self._migrations_metadata_offset = llts.migrations_metadata_offset
         self._populations_metadata = llts.populations_metadata
-        self._populations_metadata_offset = llts.populations_metadata_offset
         self._indexes_edge_insertion_order = llts.indexes_edge_insertion_order
         self._indexes_edge_removal_order = llts.indexes_edge_removal_order
 
@@ -5814,16 +5807,6 @@ def individuals_metadata(self):
             self._individuals_metadata
         )
 
-    @property
-    def individuals_metadata_offset(self):
-        """
-        Efficient access to the ``metadata_offset`` column in the
-        :ref:`sec_individual_table_definition` as a numpy array (dtype=np.int32).
-        Equivalent to ``ts.tables.individuals.metadata_offset`` (but avoiding the
-        full copy of the table data that accessing ``ts.tables`` currently entails).
-        """
-        return self._individuals_metadata_offset
-
     @property
     def nodes_metadata(self):
         """
@@ -5837,16 +5820,6 @@ def nodes_metadata(self):
             self._nodes_metadata
         )
 
-    @property
-    def nodes_metadata_offset(self):
-        """
-        Efficient access to the ``metadata_offset`` column in the
-        :ref:`sec_node_table_definition` as a numpy array (dtype=np.int32).
-        Equivalent to ``ts.tables.nodes.metadata_offset`` (but avoiding the full copy
-        of the table data that accessing ``ts.tables`` currently entails).
-        """
-        return self._nodes_metadata_offset
-
     @property
     def nodes_time(self):
         """
@@ -5940,16 +5913,6 @@ def edges_metadata(self):
             self._edges_metadata
         )
 
-    @property
-    def edges_metadata_offset(self):
-        """
-        Efficient access to the ``metadata_offset`` column in the
-        :ref:`sec_edge_table_definition` as a numpy array (dtype=np.int32).
-        Equivalent to ``ts.tables.edges.metadata_offset`` (but avoiding the full copy
-        of the table data that accessing ``ts.tables`` currently entails).
-        """
-        return self._edges_metadata_offset
-
     @property
     def sites_position(self):
         """
@@ -5973,16 +5936,6 @@ def sites_metadata(self):
             self._sites_metadata
         )
 
-    @property
-    def sites_metadata_offset(self):
-        """
-        Efficient access to the ``metadata_offset`` column in the
-        :ref:`sec_site_table_definition` as a numpy array (dtype=np.int32).
-        Equivalent to ``ts.tables.sites.metadata_offset`` (but avoiding the full copy
-        of the table data that accessing ``ts.tables`` currently entails).
-        """
-        return self._sites_metadata_offset
-
     @property
     def mutations_site(self):
         """
@@ -6036,16 +5989,6 @@ def mutations_metadata(self):
             self._mutations_metadata
         )
 
-    @property
-    def mutations_metadata_offset(self):
-        """
-        Efficient access to the ``metadata_offset`` column in the
-        :ref:`sec_mutation_table_definition` as a numpy array (dtype=np.int32).
-        Equivalent to ``ts.tables.mutations.metadata_offset`` (but avoiding the full copy
-        of the table data that accessing ``ts.tables`` currently entails).
-        """
-        return self._mutations_metadata_offset
-
     @property
     def migrations_left(self):
         """
@@ -6119,17 +6062,6 @@ def migrations_metadata(self):
             self._migrations_metadata
         )
 
-    @property
-    def migrations_metadata_offset(self):
-        """
-        Efficient access to the ``metadata_offset`` column in the
-        :ref:`sec_migration_table_definition` as a numpy array (dtype=np.int32).
-        Equivalent to ``ts.tables.migrations.metadata_offset``
-        (but avoiding the full copy of the table data that accessing
-        ``ts.tables`` currently entails).
-        """
-        return self._migrations_metadata_offset
-
     @property
     def populations_metadata(self):
         """
@@ -6143,17 +6075,6 @@ def populations_metadata(self):
             self._populations_metadata
         )
 
-    @property
-    def populations_metadata_offset(self):
-        """
-        Efficient access to the ``metadata_offset`` column in the
-        :ref:`sec_population_table_definition` as a numpy array (dtype=np.int32).
-        Equivalent to ``ts.tables.populations.metadata_offset``
-        (but avoiding the full copy of the table data that accessing
-        ``ts.tables`` currently entails).
-        """
-        return self._populations_metadata_offset
-
     @property
     def indexes_edge_insertion_order(self):
         """