Merge pull request #14 from biolink/rtd

Preparing docs for RTD
biolink · May 15, 2017 · d548d93 · d548d93
2 parents 68b1dc4 + f15f640
commit d548d93
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -0,0 +1,4 @@
+CHANGES
+-------
+
+* todo
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
diff --git a/Makefile b/Makefile
@@ -12,7 +12,7 @@ test:
 
 # only run local tests
 travis_test:
-	pytest tests/*local*.py
+	pytest tests/test_*local*.py tests/test_*parser*.py
 
 cleandist:
 	rm dist/*
@@ -24,3 +24,6 @@ release: cleandist
 
 nb:
 	PYTHONPATH=.. jupyter notebook
+
+foo:
+	./bin/flask2marshmallow.pl ../biolink-api/biolink/datamodel/serializers.py 
diff --git a/README.md b/README.md
@@ -1,5 +1,6 @@
-[![Build Status](https://travis-ci.org/biolink/ontobio.svg?branch=master)](https://travis-ci.org/biolink/ontobio)
+<[![Build Status](https://travis-ci.org/biolink/ontobio.svg?branch=master)](https://travis-ci.org/biolink/ontobio)
 [![DOI](https://zenodo.org/badge/13996/biolink/ontobio.svg)](https://zenodo.org/badge/latestdoi/13996/biolink/ontobio)
+[![PyPI](https://img.shields.io/pypi/v/ontobio.svg)](https://pypi.python.org/pypi/ontobio)
 
 # ontobio - a python API for working with ontologies and associations
 
@@ -11,35 +12,12 @@ The ontologies and associations can either be local files or provided
 by remote services (currently the OntoBee SPARQL service for
 ontologies and a Monarch or GO Golr service for associations).
 
-# API Docs
+# Documentation
 
-[ontobio](https://www.pydoc.io/pypi/ontobio-0.1.6/index.html) on pydoc.io
-
-# Command Line
-
-See the README in the [bin](https://github.com/biolink/ontobio/tree/master/bin) directory
+Documentation is on [readthedocs](https://ontobio.readthedocs.io)
 
 # Notebooks
 
 See the [Jupyter Notebooks](http://nbviewer.jupyter.org/github/biolink/ontobio/tree/master/notebooks/) for code examples
 
-# Basics
-
-There are two ways of initiating an ontology object:
-
- * via a local obo-json file
- * via remote connections to OBO PURLs
- * via remote query to a SPARQL service (currently  ontobee, but soon others)
-
-Persistent caching is used (currently cachier) to avoid repeated expensive I/O connections
-
-This is handled via the [ontol_manager.py](ontobio/ontol_manager.py)
-module. This creates an ontology object (see [ontol.py](ontobio/ontol.py) ).
-
-Note that object modeling is lightweight - we use the python networkx
-package for representing the basic graph portion of an ontology. See
-also the [obographs](https://github.com/geneontology/obographs) spec.
-
-# Associations
 
-See the ontobio.golr package
diff --git a/bin/ogr-assoc.py b/bin/ogr-assoc.py
@@ -48,7 +48,9 @@ def main():
     parser.add_argument('-r', '--resource', type=str, required=False,
                         help='Name of ontology')
     parser.add_argument('-f', '--assocfile', type=str, required=False,
-                        help='Name of input file for associations - currently GAF is assumed')
+                        help='Name of input file for associations')
+    parser.add_argument('--assocformat', type=str, default='gaf', required=False,
+                        help='Format of association file, if passed (default: gaf)')
     parser.add_argument('-o', '--outfile', type=str, required=False,
                         help='Path to output file')
     parser.add_argument('-t', '--to', type=str, required=False,
@@ -154,7 +156,8 @@ def main():
     aset = None
     if args.assocfile is not None:
         aset = afactory.create_from_file(file=args.assocfile,
-                                        ontology=ont)
+                                         fmt=args.assocformat,
+                                         ontology=ont)
     else:
         # create using GO/Monarch services
         aset = afactory.create(ontology=ont,

diff --git a/bin/qbiogolr.py b/bin/qbiogolr.py
@@ -5,7 +5,7 @@
 
 Type:
 
-    qbiogorl -h
+    qbiogolr -h
 
 For instructions
 
@@ -14,7 +14,7 @@
 import argparse
 from ontobio.golr.golr_associations import search_associations_compact
 from ontobio.ontol_factory import OntologyFactory
-from ontobio.graph_io import *
+from ontobio.io.ontol_renderers import *
 import networkx as nx
 from networkx.algorithms.dag import ancestors, descendants
 from networkx.drawing.nx_pydot import write_dot

diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = ontobio
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/analyses.rst b/docs/analyses.rst
@@ -0,0 +1,34 @@
+.. _analyses:
+
+Ontology-Based Analyses
+=======================
+
+.. warning ::
+
+    In the future the analysis methods may migrate from the `Ontology`
+    class to dedicated analysis engine classes.
+
+Enrichment
+----------
+
+See the `Notebook example <http://nbviewer.jupyter.org/github/biolink/ontobio/blob/master/notebooks/Phenotype_Enrichment.ipynb>`_
+
+Semantic Similarity
+-------------------
+
+**TODO**
+
+Slimming
+--------
+
+**TODO**
+
+Graph Reduction
+---------------
+
+**TODO**
+
+Lexical Analyses
+----------------
+
+**TODO**
diff --git a/docs/api.rst b/docs/api.rst
@@ -0,0 +1,100 @@
+.. _api:
+
+API
+===
+
+.. currentmodule:: ontobio
+
+Ontology Access
+---------------
+
+Factory
+^^^^^^^
+
+The OntologyFactory class provides a means of creating an ontology
+object backed by either local files or remote services. See
+:ref:`inputs` for more details.
+
+.. currentmodule:: ontobio.ontol_factory
+
+.. autoclass:: OntologyFactory
+    :members:
+
+Ontology Object Model
+^^^^^^^^^^^^^^^^^^^^^
+
+.. currentmodule:: ontobio.ontol
+
+.. autoclass:: Ontology
+    :members:
+    :inherited-members:
+
+.. autoclass:: Synonym
+    :members:
+    :inherited-members:
+
+.. autoclass:: LogicalDefinition
+    :members:        
+    :inherited-members:
+
+
+Assocation Access
+-----------------
+
+Factory
+^^^^^^^
+
+.. currentmodule:: ontobio.assoc_factory
+
+.. autoclass:: AssociationSetFactory
+    :members:
+
+Assocation Object Model
+^^^^^^^^^^^^^^^^^^^^^^^
+
+.. currentmodule:: ontobio.assocmodel
+
+.. autoclass:: AssociationSet
+    :members:
+
+**TODO** - detailed association modeling
+
+Association File Parsers
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. currentmodule:: ontobio.io.gafparser
+
+.. autoclass:: AssocParser
+    :members:
+    :inherited-members:
+
+
+.. autoclass:: GafParser
+    :members:
+    :inherited-members:
+
+
+.. autoclass:: GpadParser
+    :members:
+    :inherited-members:
+
+.. autoclass:: HpoaParser
+    :members:
+    :inherited-members:
+
+.. autoclass:: AssocParserConfig
+    :members:
+
+
+GOlr Queries
+------------
+
+.. currentmodule:: ontobio.golr.golr_query
+
+.. autoclass:: GolrAssociationQuery
+    :members:
+
+.. autoclass:: GolrSearchQuery
+    :members:
+
+
diff --git a/docs/biolink.rst b/docs/biolink.rst
@@ -0,0 +1,10 @@
+:: _biolink:
+
+Biolink
+=======
+
+Biolink is a REST API layer that leverages ontobio
+
+https://github.com/biolink/biolink-api
+
+
diff --git a/docs/changelog.rst b/docs/changelog.rst
@@ -0,0 +1 @@
+.. include:: ../CHANGELOG.rst