Merge pull request #439 from u6052029/api-documentation

add api class documentation
cogent3 · Dec 6, 2019 · 5d87551 · 5d87551
2 parents 187fcc8 + 9dfe197
commit 5d87551
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diff --git a/doc/api/alignment/alignment.rst b/doc/api/alignment/alignment.rst
@@ -0,0 +1,14 @@
+:mod:`alignment`
+===============================
+
+.. currentmodule:: cogent3.core.alignment
+
+Class overview
+--------------
+.. autosummary::
+    :toctree: classes
+    :template: class.rst
+
+    SequenceCollection
+    Alignment
+    ArrayAlignment
diff --git a/doc/api/alignment/classes/cogent3.core.alignment.Alignment.rst b/doc/api/alignment/classes/cogent3.core.alignment.Alignment.rst
@@ -0,0 +1,9 @@
+Alignment
+========= 
+
+.. currentmodule:: cogent3.core.alignment
+
+.. autoclass:: Alignment
+    :members:
+    :undoc-members:
+    :inherited-members:
diff --git a/doc/api/alignment/classes/cogent3.core.alignment.ArrayAlignment.rst b/doc/api/alignment/classes/cogent3.core.alignment.ArrayAlignment.rst
@@ -0,0 +1,9 @@
+ArrayAlignment
+============== 
+
+.. currentmodule:: cogent3.core.alignment
+
+.. autoclass:: ArrayAlignment
+    :members:
+    :undoc-members:
+    :inherited-members:
diff --git a/doc/api/alignment/classes/cogent3.core.alignment.SequenceCollection.rst b/doc/api/alignment/classes/cogent3.core.alignment.SequenceCollection.rst
@@ -0,0 +1,9 @@
+SequenceCollection
+================== 
+
+.. currentmodule:: cogent3.core.alignment
+
+.. autoclass:: SequenceCollection
+    :members:
+    :undoc-members:
+    :inherited-members:
diff --git a/doc/api/index.rst b/doc/api/index.rst
@@ -0,0 +1,14 @@
+###########
+API
+###########
+
+
+**Contents**
+
+.. toctree::
+    :maxdepth: 1
+
+    alignment/alignment
+    sequence/sequence
+    tree/tree
+    table/table
diff --git a/doc/api/sequence/classes/cogent3.core.sequence.DnaSequence.rst b/doc/api/sequence/classes/cogent3.core.sequence.DnaSequence.rst
@@ -0,0 +1,9 @@
+DnaSequence
+=========== 
+
+.. currentmodule:: cogent3.core.sequence
+
+.. autoclass:: DnaSequence
+    :members:
+    :undoc-members:
+    :inherited-members:
diff --git a/doc/api/sequence/classes/cogent3.core.sequence.RnaSequence.rst b/doc/api/sequence/classes/cogent3.core.sequence.RnaSequence.rst
@@ -0,0 +1,9 @@
+RnaSequence
+=========== 
+
+.. currentmodule:: cogent3.core.sequence
+
+.. autoclass:: RnaSequence
+    :members:
+    :undoc-members:
+    :inherited-members:
diff --git a/doc/api/sequence/sequence.rst b/doc/api/sequence/sequence.rst
@@ -0,0 +1,13 @@
+:mod:`sequence`
+===============================
+
+.. currentmodule:: cogent3.core.sequence
+
+Class overview
+--------------
+.. autosummary::
+    :toctree: classes
+    :template: class.rst
+
+    DnaSequence
+    RnaSequence
diff --git a/doc/api/table/classes/cogent3.util.table.Table.rst b/doc/api/table/classes/cogent3.util.table.Table.rst
@@ -0,0 +1,9 @@
+Table
+===== 
+
+.. currentmodule:: cogent3.util.table
+
+.. autoclass:: Table
+    :members:
+    :undoc-members:
+    :inherited-members:
diff --git a/doc/api/table/table.rst b/doc/api/table/table.rst
@@ -0,0 +1,12 @@
+:mod:`table`
+===============================
+
+.. currentmodule:: cogent3.util.table
+
+Class overview
+--------------
+.. autosummary::
+    :toctree: classes
+    :template: class.rst
+
+    Table
diff --git a/doc/api/tree/classes/cogent3.core.tree.PhyloNode.rst b/doc/api/tree/classes/cogent3.core.tree.PhyloNode.rst
@@ -0,0 +1,9 @@
+PhyloNode
+========= 
+
+.. currentmodule:: cogent3.core.tree
+
+.. autoclass:: PhyloNode
+    :members:
+    :undoc-members:
+    :inherited-members:
diff --git a/doc/api/tree/tree.rst b/doc/api/tree/tree.rst
@@ -0,0 +1,12 @@
+:mod:`tree`
+===============================
+
+.. currentmodule:: cogent3.core.tree
+
+Class overview
+--------------
+.. autosummary::
+    :toctree: classes
+    :template: class.rst
+
+    PhyloNode
diff --git a/doc/conf.py b/doc/conf.py
@@ -1,13 +1,20 @@
 import os
 
 
+# Allow autosummary to generate stub files
+autosummary_generate = True
+
+# Prevent numpydoc from requiring stub files for methods
+numpydoc_class_members_toctree = False
+
 extensions = [
     "numpydoc",
     "sphinx.ext.todo",
     "sphinx.ext.doctest",
     "nbsphinx",
     "sphinx.ext.mathjax",
     "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
     "sphinxcontrib.bibtex",
 ]
 

diff --git a/doc/library.rst b/doc/library.rst
@@ -12,3 +12,4 @@ This section is for those users comfortable with Python programming.
     examples/index
     cookbook/index
     data_file_links
+    api/index
diff --git a/doc/templates/class.rst b/doc/templates/class.rst
@@ -0,0 +1,8 @@
+{{ name | escape | underline }} 
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ name }}
+    :members:
+    :undoc-members:
+    :inherited-members: