Added docs and generalized to multiple species

docs/source/_static/css/baselines_theme.css

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+/* Main colors from https://color.adobe.com/fr/Copy-of-NOUEBO-Original-color-theme-11116609 */
+:root{
+  --main-bg-color: #324D5C;
+  --link-color: #14B278;
+}
+
+/* Header fonts y */
+h1, h2, .rst-content .toctree-wrapper p.caption, h3, h4, h5, h6, legend, p.caption {
+    font-family: "Lato","proxima-nova","Helvetica Neue",Arial,sans-serif;
+}
+
+
+/* Docs background */
+.wy-side-nav-search{
+  background-color: var(--main-bg-color);
+}
+
+/* Mobile version */
+.wy-nav-top{
+  background-color: var(--main-bg-color);
+}
+
+/* Change link colors (except for the menu) */
+a {
+    color: var(--link-color);
+}
+
+a:hover {
+    color: #4F778F;
+}
+
+.wy-menu a {
+    color: #b3b3b3;
+}
+
+.wy-menu a:hover {
+    color: #b3b3b3;
+}
+
+a.icon.icon-home {
+    color: #b3b3b3;
+}
+
+.version{
+    color: var(--link-color) !important;
+}
+
+
+/* Make code blocks have a background */
+.codeblock,pre.literal-block,.rst-content .literal-block,.rst-content pre.literal-block,div[class^='highlight'] {
+        background: #f8f8f8;;
+}

docs/source/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath('../../'))
+
+# -- Project information -----------------------------------------------------
+
+project = 'reeps'
+copyright = '2020, Titus Quah, Nwike Iloeje'
+author = 'Titus Quah, Nwike Iloeje'
+
+# The full version, including alpha/beta/rc tags
+release = '1.0.0'
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+
+import sphinx_rtd_theme
+
+extensions = ["sphinx_rtd_theme",
+              'sphinx.ext.autodoc',
+              'sphinx.ext.autosummary',
+              'sphinx.ext.mathjax',
+              'sphinx.ext.ifconfig',
+              'sphinx.ext.viewcode',
+              ]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = 'python'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+html_logo = '_static/img/logo.png'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

docs/source/guide/install.rst

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+.. _install:
+
+************
+Installation
+************
+
+
+Prerequisites
+=============
+
+REEPS requires python3 (>=3.5) with the development headers. 
+
+
+Stable Release
+==============
+
+There is currently no stable release
+
+
+Bleeding-edge version
+=====================
+
+To install the latest master version:
+
+.. code-block:: bash
+
+	pip install git+https://xgitlab.cels.anl.gov/summer-2020/parameter-estimation.git
+
+
+Development version
+===================
+
+To contribute to Stable-Baselines, with support for running tests and building the documentation.
+
+.. code-block:: bash
+
+    git clone https://xgitlab.cels.anl.gov/summer-2020/parameter-estimation.git && cd parameter-estimation
+    pip install -e .[docs,tests]
+
+
+Using Docker Images
+===================
+
+Not set up yet.

docs/source/guide/quickstart.rst

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+.. _quickstart:
+
+***************
+Getting Started
+***************
+
+Here is a quick example of how to fit an xml thermodynamic model to experimental data.
+
+This code fits Nd standard enthalpy in the "twophase.xml" cantera file to the 
+experimental data in "Nd_exp_data.csv".
+
+The code then produces a parity plot of the measured and predicted concentrations of Nd 3+ in the 
+aqueous phase.
+
+.. code-block:: python
+
+	from reeps import REEPS
+
+	searcher_parameters = {'exp_csv_filename': 'Nd_exp_data.csv',
+						   'phases_xml_filename': 'twophase.xml',
+						   'opt_dict': {'Nd(H(A)2)3(org)': {'h0': -4.7e6}},
+						   'phase_names': ['HCl_electrolyte', 'PC88A_liquid'],
+						   'aq_solvent_name': 'H2O(L)',
+						   'extractant_name': '(HA)2(org)',
+						   'diluant_name': 'dodecane',
+						   'complex_names': ['Nd(H(A)2)3(org)'],
+						   'rare_earth_ion_names': ['Nd+++'],
+						   'aq_solvent_rho': 1000.0,
+						   'extractant_rho': 960.0,
+						   'diluant_rho': 750.0}
+	searcher = REEPS(**searcher_parameters)
+	est_enthalpy = searcher.fit()
+	searcher.update_xml(est_enthalpy)
+	searcher.parity_plot(print_r_squared=True)
+	
+The code should return something like this

docs/source/index.rst

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+.. reeps documentation master file, created by Titus Quah
+   sphinx-quickstart on Tue Jun  9 10:13:23 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to reeps's docs! - the Rare earth element parameter searcher
+====================================================================
+REEPS is a package for thermodynamic parameter estimation specifically 
+for rare earth element extraction modeling. 
+
+REEPS takes experimental data in a csv and system data in a xml.
+
+The package then uses Cantera, another python package, to simulate equilibrium.
+
+Error between predicted and experimental data is then minimized.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: User Guide
+   
+   guide/install
+   guide/quickstart
+   
+.. toctree::
+   :maxdepth: 1
+   :caption: Searchers
+   
+   modules/reeps
+   
+
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/modules/reeps.rst

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+.. _reeps:
+
+.. automodule:: reeps
+
+REEPS
+=====
+
+
+
+Parameters
+----------
+
+.. autoclass:: REEPS
+  :members:
+  :inherited-members: