Merge branch 'master' of https://github.com/KarrLab/wc_rules

.circleci/config.yml

@@ -3,7 +3,7 @@ jobs:
   build:
     working_directory: /root/project
     docker:
-      - image: karrlab/build:0.0.7
+      - image: karrlab/build:0.0.10
     steps:
       - checkout
 

docs/about.rst

@@ -4,6 +4,7 @@ About
 ----------------------
 License
 ----------------------
+
 The software is released under the MIT license
 
 .. literalinclude:: ../LICENSE
@@ -12,9 +13,17 @@ The software is released under the MIT license
 ----------------------
 Development team
 ----------------------
+
 This package was developed by the `Karr Lab <http://www.karrlab.org/>`_ at the Icahn School of Medicine at Mount Sinai in New York, USA.
 
+----------------------
+Acknowledgements
+----------------------
+
+This work was supported by a National Science Foundation INSPIRE award [grant number 1649014].
+
 ----------------------
 Questions and comments
 ----------------------
+
 Please contact the `Karr Lab <http://www.karrlab.org/>`_ with any questions or comments.

docs/conf.py

@@ -32,10 +32,16 @@
 # ones.
 extensions = [
     'sphinx.ext.autodoc',
+    'sphinx.ext.autosectionlabel',
     'sphinx.ext.coverage',
+    'sphinx.ext.imgconverter',
+    'sphinx.ext.linkcode',
+    'sphinx.ext.mathjax',
     'sphinx.ext.napoleon',
-    'sphinx.ext.viewcode',
+    'sphinx.ext.todo',
+    'sphinxcontrib.bibtex',
     'sphinxcontrib.googleanalytics',
+    'sphinxcontrib.spelling',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -121,6 +127,36 @@
 todo_include_todos = False
 
 
+# -- section/figure/table numbering options -------------------------------
+numfig = True
+numfig_format = {
+    'figure': 'Figure %s',
+    'table': 'Table %s',
+    'code-block': 'Listing %s',
+    'section': 'Section %s',
+}
+
+
+# -- image converter options ----------------------------------------------
+image_converter_args = [
+    '-density', '150',
+    '-quality', '00',
+    ]
+
+
+# -- linkcode options -----------------------------------------------------
+def linkcode_resolve(domain, info):
+    if domain != 'py':
+        return None
+    if not info['module']:
+        return None
+    rel_filename = info['module'].replace('.', '/')
+    if os.path.isfile(os.path.join(os.path.dirname(__file__), '..', rel_filename + '.py')):
+        return "https://github.com/KarrLab/wc_rules/blob/master/{}.py".format(rel_filename)
+    else:
+        return "https://github.com/KarrLab/wc_rules/blob/master/{}/__init__.py".format(rel_filename)
+
+
 # -- napoleon options -----------------------------------------------------
 napoleon_google_docstring = True
 napoleon_numpy_docstring = False

docs/index.rst

@@ -8,7 +8,9 @@ Contents
 
 .. toctree::
    :maxdepth: 3
+   :numbered:
 
    installation.rst
    API documentation <source/modules.rst>
    about.rst
+   references.rst

docs/references.rst

@@ -0,0 +1,6 @@
+References
+==========
+
+.. bibliography:: references.bib
+    :encoding: latex+latin
+    :style: unsrt

docs/requirements.txt

@@ -3,5 +3,8 @@ configparser
 networkx
 git+https://github.com/KarrLab/obj_model.git#egg=obj_model
 robpol86-sphinxcontrib-googleanalytics
-Sphinx
+six
+Sphinx >= 1.6
 sphinx_rtd_theme
+sphinxcontrib-bibtex
+sphinxcontrib-spelling