master <-- Update/documentation

source/core_tools/index.rst

@@ -0,0 +1,19 @@
+Core Tools
+==========
+
+This section provides a listing of official software tools used by Rxn Rover. These are not plugins, but software components that provide functionality to Rxn Rover itself.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Software
+
+   software/index
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Libraries
+
+   libraries/index
+
+
+

source/core_tools/libraries/DynamicReentrant.rst

@@ -0,0 +1,24 @@
+.. _dynamic-reentrant:
+
+Dynamic Reentrant Library
+=========================
+
+Description
+-----------
+
+The Dynamic Reentrant library facilitates communication between Rxn Rover and its plugins, and helps manage dynamic reentrant VIs. 
+This library is essential for first-party(and likely most other third-party) plugins to work with Rxn Rover, 
+
+Acquisition
+-----------
+
+Download and install from the official GitHub release pages listed below.
+
+**Downloads**
+
+- **Quick Installer via VIPM (.vip file):**  
+  `Dynamic Reentrant – Releases <https://github.com/RxnRover/DynamicReentrant/releases>`_
+
+**Source Code**
+
+- `GitHub Repository <https://github.com/RxnRover/DynamicReentrant>`_

source/core_tools/libraries/index.rst

@@ -0,0 +1,8 @@
+Libraries
+=========
+This section lists libraries created by Rxn Rover's team that are used for the functionality of Rxn Rover. 
+
+.. toctree::
+   :maxdepth: 1
+
+   DynamicReentrant

source/core_tools/software/RxnRover.rst

@@ -0,0 +1,24 @@
+.. _rxnrover-software:
+
+Rxn Rover Software
+==================
+
+Description
+-----------
+
+Rxn Rover is an open-source, modular automation platform for reaction discovery and optimization. 
+Primarily targetting smaller research groups, it is designed using interchangeable plugins to be flexible and easy to integrate into a variety of laboratory environments. 
+
+Acquisition
+-----------
+
+Download and install from the official GitHub release pages listed below. Also ensure you have installed DynamicReentrant which can be found here :ref:`dynamic-reentrant`.
+
+**Downloads**
+
+- **Quick Installer via VIPM (.vip file):**  
+  `Rxn Rover – Releases <https://github.com/RxnRover/RxnRover/releases>`_
+
+**Source Code**
+
+- `GitHub Repository <https://github.com/RxnRover/RxnRover>`_

source/core_tools/software/index.rst

@@ -0,0 +1,7 @@
+Software
+========
+
+.. toctree::
+   :maxdepth: 1
+
+   RxnRover

source/first_party/analyzers/waters_patrol_uplc_report_parser.rst

@@ -1,16 +1,11 @@
 Waters |tm| Patrol |tm| UPLC |tm| Report Parser [#f1]_
 ======================================================
 
-Plugin class: Optimizer
-
-Acquisition
------------
-
-This plugin is available for download at `<https://github.com/RxnRover/plugin_waters_patrol_uplc_report_parser>`_.
-
 Description
 -----------
 
+Plugin class: Optimizer
+
 This plugin parses report files output from Waters |tm| Patrol |tm| program to 
 extract the concentration of an analyte. The plugin will average the results 
 of three injections before reporting a new concentration value to Rxn Rover.
@@ -20,4 +15,19 @@ exactly for the parser to work.
 .. [#f1] The Waters |tm|, Patrol |tm|, UPLC |tm| trademarks are owned by Waters 
    Corporation and its affiliated entities.
 
-.. |tm| unicode:: U+2122 .. TRADEMARK SYMBOL
+.. |tm| unicode:: U+2122 .. TRADEMARK SYMBOL
+
+Acquisition
+-----------
+
+Download and install the plugin from the official GitHub release page listed below.
+
+**Downloads**
+
+- **Plugin (.vip file):**  
+  `MilliGAT Pump Plugin – Releases <https://github.com/RxnRover/plugin_waters_patrol_uplc_report_parser/releases>`_
+
+**Source Code**
+
+- `Plugin Repository <https://github.com/RxnRover/plugin_waters_patrol_uplc_report_parser>`_
+

source/first_party/optimizers/deep_reaction_optimizer.rst

@@ -3,20 +3,31 @@ Deep Reaction Optimizer
 
 Plugin class: Optimizer
 
-Acquisition
------------
-
-This plugin is available for download at 
-`<https://github.com/RxnRover/plugin_dro>`_.
-
 Description
 -----------
 
+Plugin class: Optimizer
+
 This plugin allows Rxn Rover to connect with an instance of the Deep Reaction 
 Optimizer. [#dro]_ A Python program is provided with the plugin to launch an 
 instance of DRO for use with this plugin. This program uses a modified 
 objective function with built-in communication capabilities. The DRO algorithm, 
 along with other aspects of the program, can be configured by specifying a 
 configuration file (example files are provided).
 
-.. [#dro] Zhou, Z.;  Li, X.; Zare, R. N., Optimizing Chemical Reactions with Deep Reinforcement Learning. ACS Central Science 2017, 3 (12), 1337-1344.; DOI: 10.1021/acscentsci.7b00492; Code available at: https://github.com/lightingghost/chemopt.
+.. [#dro] Zhou, Z.;  Li, X.; Zare, R. N., Optimizing Chemical Reactions with Deep Reinforcement Learning. ACS Central Science 2017, 3 (12), 1337-1344.; DOI: 10.1021/acscentsci.7b00492; Code available at: https://github.com/lightingghost/chemopt.
+
+
+Aqcquisition
+------------
+
+Download and install the plugin from the official GitHub release page listed below.
+
+**Downloads**
+
+- **Plugin (.vip file):**  
+  `CyRxnOpt Plugin – Releases <https://github.com/RxnRover/plugin_dro/releases>`_
+
+**Source Code**
+
+- `Plugin Repository <https://github.com/RxnRover/plugin_dro>`_

source/first_party/optimizers/rxn_q_timing.rst

@@ -1,5 +1,5 @@
-Rxn Queue With Timing (in-development)
-======================================
+Rxn Q With Timing (in-development)
+==================================
 
 .. warning::
 
@@ -23,11 +23,11 @@ Download and install the plugin from the official GitHub release page listed bel
 **Downloads**
 
 - **Plugin (.vip file):**  
-  `Rxn Queue With Timing – Releases <https://github.com/RxnRover/>`_
+  `Rxn Queue With Timing – Releases <https://github.com/RxnRover/plugin_rxn_q_timing/releases>`_
 
 - **Drivers:**  
   This plugin does not require any additional drivers.
 
 **Source Code**
 
-- `Plugin Repository <https://github.com/RxnRover/>`_
+- `Plugin Repository <https://github.com/RxnRover/plugin_rxn_q_timing>`_

source/first_party/optimizers/rxn_queue.rst

@@ -1,5 +1,5 @@
-Rxn Queue (in-development)
-==========================
+Rxn Q (in-development)
+======================
 
 .. warning::
 

source/first_party/reactor_components/milligat_pump.rst

@@ -22,11 +22,11 @@ Download and install the plugin from the official GitHub release page listed bel
 **Downloads**
 
 - **Plugin (.vip file):**  
-  `MilliGAT Pump Plugin – Releases <https://github.com/RxnRover/>`_
+  `MilliGAT Pump Plugin – Releases <https://github.com/RxnRover/plugin_milligat_pump/releases>`_
 
 - **Drivers:**  
   MilliGAT pump drivers are required to communicate with the pumps. These drivers can be obtained from GlobalFIA using their information email, **[email protected]**. Once the drivers are downloaded, extract the files into your <labview>/instr.lib directory, where <labview> is the location of your LabVIEW installation.
 
 **Source Code**
 
-- `Plugin Repository <https://github.com/RxnRover/>`_
+- `Plugin Repository <https://github.com/RxnRover/plugin_milligat_pump>`_

source/first_party/reactor_components/polar_bear_plus.rst

@@ -21,11 +21,12 @@ Download and install the plugin from the official GitHub release page listed bel
 **Downloads**
 
 - **Plugin (.vip file):**  
-  `Polar Bear Plus Plugin – Releases <https://github.com/RxnRover/>`_
+  `Polar Bear Plus Plugin – Releases <https://github.com/RxnRover/plugin_polar_bear_plus/releases>`_
 
 - **Drivers:**  
-  This plugin does not require any additional drivers.  
+  `Polar Bear Plus Drivers - Releases <https://github.com/RxnRover/driver_polar_bear_plus/releases>`_
+  `Eurotherm nanodac Controller Drivers <https://sine.ni.com/apps/utf8/niid_web_display.download_page?p_id_guid=CDE89C1186CB633BE0440021287E6E02>`
 
 **Source Code**
 
-- `Plugin Repository <https://github.com/RxnRover/>`_         
+- `Plugin Repository <https://github.com/RxnRover/plugin_polar_bear_plus>`_         

source/index.rst

@@ -17,13 +17,19 @@ plugin, or learn a little bit about us!
    :caption: Third-Party Plugins
 
    Plugin Classes <third_party/index>
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Core Tools
+
+   core_tools/index
 
 .. toctree::
    :maxdepth: 1
    :caption: Submissions
 
    submissions/index
-   
+
 .. toctree::
    :maxdepth: 1
    :caption: The Rxn Rover Team

source/submissions/getting_started.rst

@@ -1,5 +1,5 @@
 Getting Started
-===============
+================
 
 Creating a Plugin
 -----------------

source/submissions/index.rst

@@ -1,3 +1,6 @@
+Submissions
+===========
+
 .. toctree::
    :maxdepth: 1
 

source/submissions/plugin_submission_form.rst

@@ -1,5 +1,5 @@
 Plugin Submission Form
-======================
+=======================
 
 This plugin submission form will serve as both a request to have your plugin
 added to the `Rxn Rover Plugin Catalog GitHub Repository <https://github.com/

source/submissions/submission_form.rst

@@ -1,5 +1,5 @@
 Name of the Plugin
-==================
+===================
 
 Description
 -----------

source/submissions/submit_a_plugin.rst

@@ -1,5 +1,5 @@
 Submit a Plugin
-===================
+================
 
 .. note::
    This page assumes that you have already read and completed the tasks in