Remove WrappedTreeSequence (#978)

* Remove deprecated tskit_tools.load function.
* Remove deprecated "wrapped" kwarg for dumping tree sequences

Closes #945

fwdpy11/_types/diploid_population.py

@@ -6,7 +6,6 @@
 import fwdpy11.tskit_tools._dump_tables_to_tskit
 import numpy as np
 import tskit
-from fwdpy11.tskit_tools import WrappedTreeSequence
 
 from .._fwdpy11 import DiploidGenotype, DiploidMetadata, ll_DiploidPopulation
 from .model_params import ModelParams
@@ -208,7 +207,6 @@ def dump_tables_to_tskit(
         seed: Optional[int] = None,
         parameters: Optional[Dict] = None,
         destructive=False,
-        wrapped=False,
     ) -> tskit.TreeSequence:
         """
         Dump the population's TableCollection into
@@ -236,9 +234,6 @@ def dump_tables_to_tskit(
         :param destructive: If `True`, delete data held by the current instance.
         :type destructive: bool
 
-        :param wrapped: If `True`, return `fwdpy11.tskit_tools.WrappedTreeSequence`
-        :type wrapped: bool
-
         :rtype: tskit.TreeSequence
 
         For examples, see :ref:`tskitconvert_vignette`.
@@ -281,13 +276,11 @@ def dump_tables_to_tskit(
 
             The `wrapped` keyword argument is deprecated.
 
+        .. versionadded:: 0.19.0
+
+            Removed deprecated `wrapped` keyword argument.
+
         """
-        if wrapped is True:
-            warnings.warn(
-                FutureWarning(
-                    "the wrapped kwarg is deprecated and will be removed in a future release"
-                )
-            )
         return fwdpy11.tskit_tools._dump_tables_to_tskit._dump_tables_to_tskit(
             self,
             model_params=model_params,
@@ -297,7 +290,6 @@ def dump_tables_to_tskit(
             seed=seed,
             parameters=parameters,
             destructive=destructive,
-            wrapped=wrapped,
         )
 
     def dump_to_file(self, filename: str):

fwdpy11/tskit_tools/__init__.py

@@ -31,9 +31,11 @@
 import tskit
 
 from ._flags import *  # NOQA
-from .metadata import (DiploidMetadata, decode_individual_metadata,
-                       decode_mutation_metadata)
-from .trees import WrappedTreeSequence
+from .metadata import (
+    DiploidMetadata,
+    decode_individual_metadata,
+    decode_mutation_metadata,
+)
 
 
 def get_toplevel_metadata(ts: tskit.TreeSequence, name: str) -> typing.Optional[object]:
@@ -106,28 +108,3 @@ def iterate_timepoints_with_individuals(
         else:
             decoded_individual_metadata = None
         yield utime, node_table_rows, decoded_individual_metadata
-
-
-def load(filename: str):
-    """
-    Load a tree sequence from a file.
-
-    :param filename: Name of the trees file.
-    :type filename: str
-
-    :returns: A wrapped tree sequence
-
-    .. deprecated:: 0.17.0
-
-        Prefer {meth}`tskit.TreeSequence.load`
-    """
-    import tskit
-
-    warnings.warn(
-        FutureWarning(
-            "fwdpy11.tskit_tools.load is deprecated. Please use tskit.load instead."
-        )
-    )
-
-    ts = tskit.load(filename)
-    return WrappedTreeSequence(ts=ts)

fwdpy11/tskit_tools/_dump_tables_to_tskit.py

@@ -27,8 +27,6 @@
 import tskit
 from fwdpy11._types.model_params import ModelParams
 
-from .trees import WrappedTreeSequence
-
 
 def _initializePopulationTable(
     node_view, population_metadata: typing.Optional[typing.Dict[int, object]], tc
@@ -134,8 +132,7 @@ def _dump_tables_to_tskit(
     seed: typing.Optional[int] = None,
     parameters: typing.Optional[typing.Dict] = None,
     destructive=False,
-    wrapped=False,
-) -> typing.Union[tskit.TreeSequence, WrappedTreeSequence]:
+) -> tskit.TreeSequence:
     from .._fwdpy11 import gsl_version, pybind11_version
 
     environment = tskit.provenance.get_environment(
@@ -239,8 +236,6 @@ def _dump_tables_to_tskit(
 
     tc.provenances.add_row(json.dumps(provenance))
 
-    if wrapped is True:
-        return WrappedTreeSequence(ts=tc.tree_sequence())
     return tc.tree_sequence()