docs: Update the online documentation (#196)

Author: paloma-martinez

docs/geos-ats.rst

@@ -1,16 +1,16 @@
 
-GEOS ATS
+ATS
 ==========
 
 The `geos-ats` python package includes tools for managing integrated tests for GEOS.
 It is built using the `Automated Test System <https://ats.readthedocs.io/en/latest/>`_ (ATS) package.
 The available console scripts for this package and its API are described below.
 
 
-run_geos_ats
-----------------
+Usage
+--------
 
-Primary entry point for running integrated tests.
+`run_geos_ats` is the primary entry point for running integrated tests.
 
 .. argparse::
    :module: geos.ats.command_line_parsers

docs/geos-geomechanics.rst

@@ -2,5 +2,44 @@
 Time History Tools
 --------------------------
 
+The `geos-timehistory` package contains tools to treat and plot time-history data from GEOS output.
+
+Usage
+^^^^^^^^
+
+.. code-block:: bash
+
+    $ python plot_time_history.py --help
+
+    usage: plot_time_history.py [-h] [--sets name [name ...]]
+                            [--indices index [index ...]]
+                            [--components int [int ...]]
+                            history_file variable_name
+
+    A script that parses geosx HDF5 time-history files and produces time-history
+    plots using matplotlib
+
+    positional arguments:
+    history_file          The time history file to parse
+    variable_name         Which time-history variable collected by GEOSX to
+                            generate a plot file for.
+
+    options:
+    -h, --help            show this help message and exit
+    --sets name [name ...]
+                            Which index set of time-history data collected by GEOS
+                            to generate a plot file for, may be specified multiple
+                            times with different indices/components for each set.
+    --indices index [index ...]
+                            An optional list of specific indices in the most-
+                            recently specified set.
+    --components int [int ...]
+                            An optional list of specific variable components
+
+
+API
+^^^^
+
 .. automodule:: geos.timehistory.plot_time_history
     :members:
+

docs/geos-processing.rst

@@ -1,73 +1,72 @@
-
-GEOS Utilities
+Utilities
 ===============
 
 The `geos-utils` python package defines utilities for all GEOS python packages including a logger, GEOS constants, basic functions, and unit management tools.
 
 
-API
-^^^
-
-geos.utils.ConnectionSet module
+ConnectionSet module
 --------------------------------
 
 .. automodule:: geos.utils.ConnectionSet
    :members:
    :undoc-members:
    :show-inheritance:
 
-geos.utils.enumUnits module
+enumUnits module
 --------------------------------
 
 .. automodule:: geos.utils.enumUnits
    :members:
    :undoc-members:
    :show-inheritance:
-   
-geos.utils.geometryFunctions module
+
+geometryFunctions module
 ------------------------------------
 
 .. automodule:: geos.utils.geometryFunctions
    :members:
    :undoc-members:
    :show-inheritance:
 
-geos.utils.GeosOutputsConstants module
+
+GeosOutputsConstants module
 -------------------------------------------
 
 .. automodule:: geos.utils.GeosOutputsConstants
    :members:
    :undoc-members:
    :show-inheritance:
 
-geos.utils.algebraFunctions module
+algebraFunctions module
 -------------------------------------------
 
 .. automodule:: geos.utils.algebraFunctions
    :members:
    :undoc-members:
    :show-inheritance:
 
-geos.utils.Logger module
+Logger module
 ------------------------------
 
 .. automodule:: geos.utils.Logger
    :members:
    :undoc-members:
    :show-inheritance:
 
-geos.utils.PhysicalConstants module
+.. _output-constant:
+
+PhysicalConstants module
 -----------------------------------------
 
 .. automodule:: geos.utils.PhysicalConstants
    :members:
    :undoc-members:
    :show-inheritance:
 
-geos.utils.UnitRepository module
+UnitRepository module
 -------------------------------------
 
 .. automodule:: geos.utils.UnitRepository
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:

docs/geos-pv.rst

@@ -0,0 +1,12 @@
+GEOS Geomechanics tools
+=============================
+
+This package contains geomechanics functions and data models.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   model
+
+   processing

docs/geos-timehistory.rst

@@ -1,18 +1,18 @@
-Geomechanics models
-======================
+Models
+=============
 
 This module defines data structures for geomechanics calculations.
 
-geos.geomechanics.model.MohrCircle module
-------------------------------------------
+Mohr circle
+-----------------
 
 .. automodule:: geos.geomechanics.model.MohrCircle
    :members:
    :undoc-members:
    :show-inheritance:
 
-geos.geomechanics.model.MohrCoulomb module
--------------------------------------------
+Mohr-Coulomb failure envelop
+-------------------------------
 
 .. automodule:: geos.geomechanics.model.MohrCoulomb
    :members: