Documentation in TableCollection points to ts doc

python/tskit/tables.py

@@ -1481,6 +1481,8 @@ def simplify(
         requirements to specify a valid tree sequence (but the resulting tables
         will).
 
+        This is identical to the :class:`TreeSequence` method of the same
+        name but acts *in place* to alter the data in this :class:`TableCollection`.
         Please see the :meth:`TreeSequence.simplify` method for a description
         of the remaining parameters.
 
@@ -1662,15 +1664,12 @@ def deduplicate_sites(self):
     def delete_sites(self, site_ids, record_provenance=True):
         """
         Remove the specified sites entirely from the sites and mutations tables in this
-        collection. The site IDs do not need to be in any particular order, and
-        specifying the same ID multiple times does not have any effect (i.e., calling
-        ``tables.delete_sites([0, 1, 1])`` has the same effect as calling
-        ``tables.delete_sites([0, 1])``.
+        collection. This is identical to the :class:`TreeSequence` method of the same
+        name but acts *in place* to alter the data in this :class:`TableCollection`.
 
         :param list[int] site_ids: A list of site IDs specifying the sites to remove.
-        :param bool record_provenance: If True, record details of this call to
-            ``delete_sites`` in the this TableCollection's provenance information.
-            (Default: True).
+        :param bool record_provenance: If ``True``, add details of this operation
+            to the provenance table in this TableCollection. (Default: ``True``).
         """
         keep_sites = np.ones(len(self.sites), dtype=bool)
         site_ids = util.safe_np_int_cast(site_ids, np.int32)
@@ -1722,26 +1721,18 @@ def delete_sites(self, site_ids, record_provenance=True):
     def delete_intervals(self, intervals, simplify=True, record_provenance=True):
         """
         Delete all information from this set of tables which lies *within* the
-        specified list of genomic intervals. Edges spanning these intervals
-        are truncated or deleted, and sites and mutations falling within them are
-        discarded.
-
-        Note that node IDs may change as a result of this operation,
-        as by default :meth:`.simplify` is called on this TableCollection to
-        remove redundant nodes. If you wish to map node IDs onto the same
-        nodes before and after this method has been called, specify ``simplify=False``.
-
-        See also :meth:`.keep_intervals`.
+        specified list of genomic intervals. This is identical to the
+        :class:`TreeSequence` method of the same name but acts *in place* to alter
+        the data in this :class:`TableCollection`.
 
         :param array_like intervals: A list (start, end) pairs describing the
             genomic intervals to delete. Intervals must be non-overlapping and
             in increasing order. The list of intervals must be interpretable as a
             2D numpy array with shape (N, 2), where N is the number of intervals.
         :param bool simplify: If True, run simplify on this tables so that nodes
             no longer used are discarded. (Default: True).
-        :param bool record_provenance: If True, record details of this operation
-            in the table collection's provenance information.
-            (Default: True).
+        :param bool record_provenance: If ``True``, add details of this operation
+            to the provenance table in this TableCollection. (Default: ``True``).
         """
         self.keep_intervals(
             util.negate_intervals(intervals, 0, self.sequence_length),
@@ -1757,30 +1748,22 @@ def delete_intervals(self, intervals, simplify=True, record_provenance=True):
     def keep_intervals(self, intervals, simplify=True, record_provenance=True):
         """
         Delete all information from this set of tables which lies *outside* the
-        specified list of genomic intervals. Edges are truncated to lie within
-        these intervals, and sites and mutations falling outside these intervals
-        are discarded.
-
-        Note that node IDs may change as a result of this operation,
-        as by default :meth:`.simplify` is called on this TableCollection to
-        remove redundant nodes. If you wish to map node IDs onto the same
-        nodes before and after this method has been called, specify ``simplify=False``.
-
-        See also :meth:`.delete_intervals`.
+        specified list of genomic intervals. This is identical to the
+        :class:`TreeSequence` method of the same name but acts *in place* to alter
+        the data in this :class:`TableCollection`.
 
         :param array_like intervals: A list (start, end) pairs describing the
             genomic intervals to keep. Intervals must be non-overlapping and
             in increasing order. The list of intervals must be interpretable as a
             2D numpy array with shape (N, 2), where N is the number of intervals.
         :param bool simplify: If True, run simplify on this tables so that nodes
             no longer used are discarded. (Default: True).
-        :param bool record_provenance: If True, record details of this operation
-            in this table collection's provenance information.
-            (Default: True).
+        :param bool record_provenance: If ``True``, add details of this operation
+            to the provenance table in this TableCollection. (Default: ``True``).
         """
         intervals = util.intervals_to_np_array(intervals, 0, self.sequence_length)
         if len(self.migrations) > 0:
-            raise ValueError("Migrations not supported by keep_intervals")
+            raise ValueError("Migrations not supported by keep_ and delete_ intervals")
 
         edges = self.edges.copy()
         self.edges.clear()

python/tskit/trees.py

@@ -3233,9 +3233,8 @@ def delete_intervals(self, intervals, simplify=True, record_provenance=True):
             2D numpy array with shape (N, 2), where N is the number of intervals.
         :param bool simplify: If True, return a simplified tree sequence where nodes
             no longer used are discarded. (Default: True).
-        :param bool record_provenance: If True, record details of this operation
-            in the tree sequence's provenance information.
-            (Default: True).
+        :param bool record_provenance: If ``True``, add details of this operation to the
+            provenance information of the returned tree sequence. (Default: ``True``).
         :rtype: .TreeSequence
         """
         tables = self.dump_tables()
@@ -3262,8 +3261,8 @@ def keep_intervals(self, intervals, simplify=True, record_provenance=True):
             2D numpy array with shape (N, 2), where N is the number of intervals.
         :param bool simplify: If True, return a simplified tree sequence where nodes
             no longer used are discarded. (Default: True).
-        :param bool record_provenance: If True, record details of this operation
-            in the tree sequence's provenance information.
+        :param bool record_provenance: If True, add details of this operation to the
+            provenance information of the returned tree sequence.
             (Default: True).
         :rtype: .TreeSequence
         """