Merge pull request #39 from Carreau/test-dendrolink

Example Crosslink documentation with Dendropy.
McTavishLab · Dec 1, 2018 · a55ed37 · a55ed37
2 parents e5a06e6 + 0dd762f
commit a55ed37
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diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -202,4 +202,5 @@
 # -- Options for intersphinx extension ---------------------------------------
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {'py': ('https://docs.python.org/',None),
+                       'dp': ('https://dendropy.org/', None)}
diff --git a/physcraper/__init__.py b/physcraper/__init__.py
@@ -563,7 +563,7 @@ class AlignTreeTax(object):
 
           * **newick**: dendropy.tre.as_string(schema=schema_trf) object
           * **otu_dict**: json file including the otu_dict information generated earlier
-          * **alignment**: dendropy DNACharacterMatrix object
+          * **alignment**: dendropy :class:`DnaCharacterMatrix <dendropy.datamodel.charmatrixmodel.DnaCharacterMatrix>` object
           * **ingroup_mrca**: OToL identifier of the group of interest, either subclade as defined by user or of all tiplabels in the phylogeny
           * **workdir**: the path to the corresponding working directory
           * **schema**: optional argument to define tre file schema, if different from "newick"