Update documentation (on RTD) and also update docstrings (#116)

* Switch hyperlinks to RST * Separate documentation for `DAT_restraints` by using `@property` * Finish running through restraints documentation. * Make each API a separate restructed text document * Update documentation outline and add side bar links * Remove unused import * Make BaseExceptions more specific * Remove unnecessary OpenMM import * Flesh out the format of the ``results`` dictionary in the documentation * Correctly read in class properties as instance attributes when loading restraints from JSON * Bug fix typo * Remove unnecessary import * Add `tleap` module documentation
GilsonLabUCSD · Nov 4, 2019 · 7114cff · 7114cff
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diff --git a/docs/align.rst b/docs/align.rst
@@ -0,0 +1,7 @@
+Align API
+---------
+
+.. automodule:: paprika.align
+   :members:
+   :undoc-members:
+
diff --git a/docs/amber.rst b/docs/amber.rst
@@ -0,0 +1,7 @@
+AMBER Simulation Wrapper API
+----------------------------
+
+.. automodule:: paprika.amber
+   :members:
+   :undoc-members:
+
diff --git a/docs/analysis.rst b/docs/analysis.rst
@@ -0,0 +1,7 @@
+Analysis API
+------------
+
+.. automodule:: paprika.analysis
+   :members:
+   :undoc-members:
+
diff --git a/docs/index.rst b/docs/index.rst
@@ -28,11 +28,23 @@ Index
 
 **Developer Documentation**
 
-* :doc:`api`
+* :doc:`align`
+* :doc:`analysis`
+* :doc:`amber`
+* :doc:`restraints`
+* :doc:`tleap`
+
 
 .. toctree::
   :maxdepth: 4
   :hidden:
   :caption: Developer Documentation
 
-  api
+  align
+  analysis
+  amber
+  restraints
+  tleap
+
+
+**Write about convenience functions**
diff --git a/docs/install.rst b/docs/install.rst
@@ -5,7 +5,7 @@ We recommend installing pAPRika in a fresh ``conda`` environment if possible. Th
 
 1. The latest release on ``conda-forge``:
     a. ``conda install -c conda-forge paprika``
-    b. To use all features of pAPRika, you must either have [AmberTools](http://ambermd.org/AmberTools.php) in your `$PATH` or separately install AmberTools with `conda install -c http://ambermd.org/downloads/ambertools/conda/ ambertools=18`.
+    b. To use all features of pAPRika, you must either have _AmberTools: http://ambermd.org/AmberTools.php in your `$PATH` or separately install AmberTools with ``conda install -c http://ambermd.org/downloads/ambertools/conda/ ambertools=19``.
     c. To use OpenMM features: ``conda install -c omnia openmm``.
 
 2. The master branch on GitHub:
@@ -16,7 +16,7 @@ We recommend installing pAPRika in a fresh ``conda`` environment if possible. Th
     e. Install ``paprika`` in the environment: ``pip install .``
 
 3. The latest release on GitHub:
-    a. Download [the latest release](https://github.com/slochower/pAPRika/releases), extract it, and change to the ``paprika`` directory:
+    a. Download _the latest release: https://github.com/slochower/pAPRika/releases, extract it, and change to the ``paprika`` directory:
     b. Change the ``name`` field in ``devtools/conda-envs/test_env.yaml`` to be ``paprika``.
     c. Create the environment: ``conda env create -f devtools/conda-envs/test_env.yaml``.
     d. Activate the environment: ``conda activate paprika``

diff --git a/docs/api.rst → docs/restraints.rst b/docs/api.rst → docs/restraints.rst
@@ -1,8 +1,3 @@
-API
-===
-
-A set of API documents for this projects classes and modules.
-
 Restraints API
 ---------------
 
@@ -22,5 +17,4 @@ Restraints API
 
 .. automodule:: paprika.restraints.utils
    :members:
-   :undoc-members:
-
+   :undoc-members:
diff --git a/docs/tleap.rst b/docs/tleap.rst
@@ -0,0 +1,7 @@
+Tleap API
+------------
+
+.. automodule:: paprika.tleap
+   :members:
+   :undoc-members:
+