Merge pull request #481 from GavinHuttley/develop

DOC: tidied some docstrings

src/cogent3/core/alignment.py

@@ -2035,28 +2035,19 @@ def _get_moltype(self):
 
     moltype = property(_get_moltype)
 
-    def copy(self, memo=None, _nil=None, constructor="ignored"):
+    def copy(self):
         """Returns a shallow copy of self
-
-        WARNING: cogent3.core.sequence.Sequence does NOT implement a copy method,
-        as such, the data member variable of the copied object will maintain
-        reference to the original object.
-
-        WARNING: cogent3.core.location.Map does NOT implement a copy method, as
-        such, the data member variable of the copied object will maintain
-        reference to the original object.
         """
-        _nil = _nil or []
         return self.__class__(self.map, self.data)
 
     def deepcopy(self, sliced=True):
         """
-        does a proper slice on the copied sequence when sliced is True and returns a deep copy of self
         Parameters
         -----------
         sliced : bool
-            Slices underlying sequence with start/end of self coordinates. This has the effect of breaking the connection
-            to any longer parent sequence.
+            Slices underlying sequence with start/end of self coordinates. This
+            has the effect of breaking the connection to any longer parent sequence.
+
         Returns
         -------
         a copy of self
@@ -2337,12 +2328,16 @@ def probs_per_pos(
         )
         return counts.to_freq_array()
 
-    def entropy_per_pos(self, motif_length=1, include_ambiguity=False, allow_gap=False, alert=False):
+    def entropy_per_pos(
+        self, motif_length=1, include_ambiguity=False, allow_gap=False, alert=False
+    ):
         """returns shannon entropy per position"""
-        probs = self.probs_per_pos(motif_length=motif_length,
-                                   include_ambiguity=include_ambiguity,
-                                   allow_gap=allow_gap,
-                                   alert=alert)
+        probs = self.probs_per_pos(
+            motif_length=motif_length,
+            include_ambiguity=include_ambiguity,
+            allow_gap=allow_gap,
+            alert=alert,
+        )
         return probs.entropy()
 
     def probs_per_seq(