Docfix

docs/.gitignore

@@ -5,3 +5,4 @@ example_snps.vcf
 sims.make
 example_sim.vcf
 .ipynb_checkpoints
+example_sim2.vcf

docs/python_api.md

@@ -49,6 +49,8 @@ Here is a quick reference to some of the methods:
   individuals_alive_at
   mutation_metadata
   next_slim_mutation_id
+  mutation_at
+  nucleotide_at
   nodes_vacant
   population_size
   recapitate
@@ -156,6 +158,14 @@ Additionally, ``pyslim`` contains the following methods:
 .. autofunction::  is_current_version
 ```
 
+```{eval-rst}
+.. autofunction::  nucleotide_at
+```
+
+```{eval-rst}
+.. autofunction::  mutation_at
+```
+
 
 ## Metadata
 

pyslim/slim_metadata.py

@@ -786,10 +786,14 @@ def default_slim_metadata(name, num_chromosomes=1, num_traits=1, **kwargs):
     metadata dictionary: for each such key=value pair the returned dictionary
     has `value` (re)assigned to `key`.
 
+    For top-level ("tree_sequence") metadata, this method does not provide entries
+    for more than one chromosome under the key "chromosomes", since this is
+    considered optional by SLiM.
+
     :param str name: The type of metadata requested.
     :param int num_chromosomes: The number of chromosomes (only relevant for "node").
     :param int num_traits: The number of traits
-        (only relevant for "individual" and "mutation_list_entry").
+        (only relevant for "tree_sequence", "individual" and "mutation_list_entry").
     :rtype dict:
     """
     if name == "tree_sequence":

pyslim/slim_tree_sequence.py

@@ -120,7 +120,7 @@ def nucleotide_at(ts, node, position, time=None, mut_metadata=None):
     mutation IDs in its metadata.
 
     This method uses a dictionary of mutation metadata, computed by
-    :meth:`mut_metadata`. This step can be expensive if there are
+    :meth:`mutation_metadata`. This step can be expensive if there are
     many mutations, so this can be pre-computed and passed in as
     ``mutations``. If not provided, it will be computed.