GilsonLabUCSD · jeff231li · Oct 8, 2020 · Sep 24, 2020 · Sep 24, 2020 · Sep 25, 2020
diff --git a/docs/README.md b/docs/README.md
@@ -5,7 +5,7 @@ To compile the docs, first ensure that Sphinx and the ReadTheDocs theme are inst
 
 
 ```bash
-conda install sphinx sphinx_rtd_theme 
+conda install sphinx nbsphinx sphinx_rtd_theme 
 ```
 
 

diff --git a/docs/_static/css/theme_overrides.css b/docs/_static/css/theme_overrides.css
@@ -0,0 +1,76 @@
+/* override table width restrictions */
+@media screen and (min-width: 1000px) {
+
+   .wy-table-responsive table td {
+      /* !important prevents the common CSS stylesheets from overriding
+         this as on RTD they are loaded after this stylesheet */
+      white-space: normal !important;
+   }
+
+   .wy-table-responsive {
+      overflow: visible !important;
+   }
+}
+
+table.docutils.clean-table {
+    border: 0 solid #e1e4e5;
+}
+table.docutils.clean-table thead {
+    border-top: 2px solid #e1e4e5;
+    border-bottom: 2px solid #e1e4e5;
+}
+table.docutils.clean-table thead th {
+    border: 0 solid #e1e4e5;
+}
+
+table.clean-table div.line-block {
+    margin-bottom: 0;
+    line-height: normal;
+}
+table.clean-table.docutils td {
+     border-bottom: 0 solid #e1e4e5;
+     border-left: 0 solid #e1e4e5;
+}
+table.clean-table.docutils:not(.field-list) tr:nth-child(2n-1) td {
+    background-color: initial
+}
+
+table.clean-table.property-table th:not(:first-child) {
+    text-align: center;
+}
+table.clean-table.property-table td:not(:first-child) {
+    text-align: center;
+}
+
+ul.spaced-list li {
+    margin-bottom: 10px;
+}
+
+.green-font {
+    color: mediumseagreen;
+}
+.red-font {
+    color: red;
+}
+
+.ignore-width {
+  display: inline-block;
+  width: 0;
+}
+
+.rst-content div.figure p.caption {
+    margin-top: 14px;
+}
+
+.rst-content code.xref {
+    font-weight: normal;
+    color: #9B59B6;
+}
+
+/* override math equation align */
+.math {
+    text-align: left;
+}
+.eqno {
+    float: right;
+}
diff --git a/docs/_static/images/flowchart.png b/docs/_static/images/flowchart.png
diff --git a/docs/_static/images/paprika.png b/docs/_static/images/paprika.png
diff --git a/docs/_static/images/pmf.png b/docs/_static/images/pmf.png
diff --git a/docs/_static/images/restraints.png b/docs/_static/images/restraints.png
diff --git a/docs/align.rst b/docs/align.rst
diff --git a/docs/amber.rst b/docs/amber.rst
diff --git a/docs/api.rst b/docs/api.rst
@@ -0,0 +1,25 @@
+API
+===
+This page provides links to the documentation for classes and modules available in `paprika`.
+
+* :doc:`source/align`
+* :doc:`source/analysis`
+* :doc:`source/dummy`
+* :doc:`source/evaluator`
+* :doc:`source/restraints`
+* :doc:`source/simulation`
+* :doc:`source/tleap`
+* :doc:`source/utils`
+
+.. toctree::
+   :maxdepth: 10
+   :hidden:
+
+   source/align
+   source/analysis
+   source/dummy
+   source/evaluator
+   source/restraints
+   source/simulation
+   source/tleap
+   source/utils
diff --git a/docs/build_docs.rst b/docs/build_docs.rst
@@ -0,0 +1,15 @@
+******************
+Compiling the Docs
+******************
+
+The docs for this project are built with [Sphinx](http://www.sphinx-doc.org/en/master/).
+To compile the docs, first ensure that Sphinx, and the ReadTheDocs theme are installed.::
+
+    conda install sphinx nbsphinx sphinx_rtd_theme
+
+Once installed, you can use the ``Makefile`` in this directory to compile static HTML pages by::
+
+    make html
+
+The compiled docs will be in the ``_build`` directory and can be viewed by opening ``index.html`` (which may itself
+be inside a directory called ``html/`` depending on what version of Sphinx is installed).
diff --git a/docs/conf.py b/docs/conf.py
@@ -22,10 +22,10 @@
 
 project = "pAPRika"
 copyright = (
-    "2020, Niel M. Henriksen, David R. Slochower, Simon Boothroyd, Jeff Setiadi, and Willa Wang. "
+    "2020, Niel M. Henriksen, David R. Slochower, Simon Boothroyd, Jeffry Setiadi, and Willa Wang. "
     "Project structure based on the Computational Molecular Science Python Cookiecutter version 1.0"
 )
-author = "Niel M. Henriksen, David R. Slochower, Simon Boothroyd, Jeff Setiadi, and Willa Wang"
+author = "Niel M. Henriksen, David R. Slochower, Simon Boothroyd, Jeffry Setiadi, and Willa Wang"
 
 # The short X.Y version
 version = ""
@@ -53,6 +53,7 @@
     "sphinx.ext.mathjax",
     "sphinx.ext.viewcode",
     "sphinx.ext.intersphinx",
+    "sphinxcontrib.bibtex",
     "nbsphinx",
 ]
 
@@ -61,7 +62,12 @@
 autodoc_default_flags = ["members", "inherited-members"]
 autodoc_member_order = "bysource"  # preserve ordering in source
 
-autodoc_mock_imports = ["pytraj"]
+autodoc_mock_imports = [
+    "pydantic",
+    "pytraj",
+    "scipy",
+    "typing_extensions",
+]
 
 # Autolabel settings
 autosectionlabel_maxdepth = 3
@@ -119,6 +125,12 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
 
+html_context = {
+    "css_files": [
+        "_static/css/theme_overrides.css",  # override wide tables in RTD theme
+    ],
+}
+
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
 #

diff --git a/docs/environment.yml b/docs/environment.yml
@@ -11,9 +11,11 @@ dependencies:
 
   # Sphinx specific
   - numpydoc
+  - pandoc
   - sphinx
   - nbsphinx
   - sphinx_rtd_theme
+  - sphinxcontrib-bibtex
 
   # Standard dependencies
   - pip
-Original file line number
+Diff line change
@@ Expand Up @@
     ```bash
-    conda install sphinx sphinx_rtd_theme
+    conda install sphinx nbsphinx sphinx_rtd_theme
     ```
@@ Expand Down @@