.

Author: petrelharp

stdpopsim/dfe.py

@@ -9,7 +9,7 @@
 from traits import MultivariateMutationType
 
 
-#TODO: need to add trait index to get passed up to MultivariateMutationType
+# TODO: need to add trait index to get passed up to MultivariateMutationType
 # and also do all of the subclassing stuff.
 # Default index should probably be 0 to keep
 class MutationType(MultivariateMutationType):
@@ -49,7 +49,7 @@ class MutationType(MultivariateMutationType):
     list of dominance coefficients.
 
     :ivar distribution_type: A str abbreviation for the distribution of
-        fitness effects that each new mutation of this type draws from (see below).
+        fitness effects that each new mutation of this type draws from (see above).
     :vartype distribution_type: str
     :ivar distribution_args: Arguments for the distribution type.
     :vartype distribution_type: list
@@ -76,13 +76,13 @@ class MutationType(MultivariateMutationType):
     def __init__(self, **kwargs):
         super_kwargs = {}
         for k, v in kwargs.items():
-            if k != 'convert_to_substitution':
-                super_kwargs['fitness_' + k] = v
+            if k != "convert_to_substitution":
+                super_kwargs["fitness_" + k] = v
             else:
                 super_kwargs[k] = v
         super().__init__(**super_kwargs)
 
-    #TODO: we have broken everything in here by appending fitness_ in front of
+    # TODO: we have broken everything in here by appending fitness_ in front of
     # the name in the superclass (MultivariateMutationType) maybe we can add
     # accessors here to keep back compatibility
 

stdpopsim/traits.py

@@ -375,7 +375,28 @@ class MultivariateMutationType(object):
     fitness and/or trait(s). This design closely mirrors SLiM's MutationType
     class.
 
-    TODO: write a good docstring
+    :ivar distribution_type: A str abbreviation for the distribution of
+        effects that each new mutation of this type draws from (see above).
+    :vartype distribution_type: str
+    :ivar distribution_args: Arguments for the distribution type.
+    :vartype distribution_type: list
+    :ivar dominance_coeff: The dominance coefficient (negative = underdominance,
+        0 = recessive, 0.5 = additive, 1.0 = completely dominant, > 1.0 = overdominant)
+        Default: 0.5.
+    :vartype dominance_coeff: float
+    :ivar convert_to_substitution: Whether to retain any fixed mutations in the
+        simulation: if not, we cannot ask about their frequency once fixed.
+        (Either way, they will remain in the tree sequence).
+    :vartype convert_to_substitution: bool
+    :ivar dominance_coeff_list: Either None (the default) or a list of floats describing
+        a list of dominance coefficients, to apply to different selection coefficients
+        (see details). Cannot be specified along with dominance_coeff.
+    :vartype dominance_coeff_list: list of floats
+    :ivar dominance_coeff_breaks: Either None (the default) or a list of floats
+        describing the intervals of selection coefficient over which each of the entries
+        of dominance_coeff_list applies (see details). Must be of length one shorter than
+        dominance_coeff_list.
+    :vartype dominance_coeff_breaks: list of floats
     """
 
     trait_distribution_type = attr.ib(default=None, type=str)