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/dynamic_reentrant.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
+
+   dynamic_reentrant

source/core_tools/software/index.rst

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

source/core_tools/software/rxn_rover.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/first_party/analyzers/index.rst

@@ -9,6 +9,7 @@ submit any questions as new issues tagged with "question".
    :maxdepth: 1
    :caption: Infrared Spectroscopy
 
+   reactir_report_parser
 
 .. toctree::
    :maxdepth: 1

source/first_party/analyzers/mock_lc_parser.rst

@@ -1,17 +1,28 @@
 Mock LC Parser
 ==============
 
+Description
+-----------
+
 Plugin class: Analyzer
 
+This plugin generates and parses report files as if they were generated from a 
+liquid chromatograph (LC). The data generated is random and this plugin is only
+meant to be used as a demonstration of a file parser as an analyzer plugin.
+
 Acquisition
 -----------
 
-This plugin is available for download at 
-`<https://github.com/RxnRover/plugin_mock_lc_parser>`_.
+Download and install the plugin and required drivers from the official GitHub release pages listed below.
 
-Description
------------
+**Downloads**
 
-This plugin generates and parses report files as if they were generated from a 
-liquid chromatograph (LC). The data generated is random and this plugin is only
-meant to be used as a demonstration of a file parser as an analyzer plugin.
+- **Plugin (.vip file):**  
+  `Mock LC Parser Plugin – Releases <https://github.com/RxnRover/plugin_mock_lc_parser/releases>`_
+
+- **Drivers:**  
+  This plugin does not require any additional drivers.
+
+**Source Code**
+
+- `Plugin Repository <https://github.com/RxnRover/plugin_mock_lc_parser>`_

source/first_party/analyzers/reactir_report_parser.rst

@@ -0,0 +1,33 @@
+React IR Report Parser (in-development)
+=======================================
+
+.. warning::
+
+   This plugin is currently in development and is **not publicly accessible at this time**.
+
+Description
+-----------
+
+Plugin class: Analyzer
+
+This plugin parses report files output from a ReactIR(TM) to extract the peak intensity of an analyte. The plugin will average the results of any number of scans before reporting a new concentration value to Rxn Rover. A sample report is included with the plugin, whose format must be matched exactly for the parser to work.
+
+Note: The ReactIR trademark is owned by Mettler Toledo and its affiliated entities.
+
+
+Acquisition
+-----------
+
+Download and install the plugin from the official GitHub release page listed below.
+
+**Downloads**
+
+- **Plugin (.vip file):**  
+  `React IR Report Parser Plugin – Releases <https://github.com/RxnRover/plugin_reactir_report_parser/releases>`_
+
+- **Drivers:**  
+  This plugin does not require any additional drivers.
+
+**Source Code**
+
+- `Plugin Repository <https://github.com/RxnRover/plugin_reactir_report_parser>`_

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: Analyzer
+
 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 +15,21 @@ 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):**  
+  `Waters Patrol UPLC Report Parser – Releases <https://github.com/RxnRover/plugin_waters_patrol_uplc_report_parser/releases>`_
+
+- **Drivers**: This plugin does not require any additional drivers.  
+
+**Source Code**
+
+- `Plugin Repository <https://github.com/RxnRover/plugin_waters_patrol_uplc_report_parser>`_
+

source/first_party/optimizers/cyrxnopt.rst

@@ -0,0 +1,33 @@
+CyRxnOpt (in-development)
+=========================
+
+.. warning::
+
+   This plugin is currently in development and is **not publicly accessible at this time**.
+
+Description
+-----------
+
+Plugin class: Optimizer
+
+CyRxnOpt is an advanced optimizer plugin which provides a singular interface to use many reaction optimization algorithms, AMLRO, EDBO+, SQSnobFit, and Nelder Mead Simplex.
+
+
+Acquisition
+-----------
+
+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_cyrxnopt/releases>`_
+
+- **Drivers:**  
+  `CyRxnOpt Bindings – Releases <https://github.com/RxnRover/cyrxnopt_bindings/releases>`_
+
+**Source Code**
+
+- `Plugin Repository <https://github.com/RxnRover/plugin_cyrxnopt>`_
+- `Bindings Repository <https://github.com/RxnRover/cyrxnopt_bindings>`_
+- `CyRxnOpt Python <https://github.com/RxnRover/CyRxnOpt>`_

source/first_party/optimizers/deep_reaction_optimizer.rst

@@ -3,20 +3,28 @@ 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.
+
+
+Acquisition
+------------
+
+Download and install the plugin from the official GitHub release page listed below.
+
+**Downloads**
+
+**Source Code**
+
+- `Plugin Repository <https://github.com/RxnRover/plugin_dro>`_

source/first_party/optimizers/index.rst

@@ -11,9 +11,11 @@ submit any questions as new issues tagged with "question".
 
    deep_reaction_optimizer
    sqsnobfit
+   cyrxnopt
 
 .. toctree::
    :maxdepth: 1
    :caption: Manual Control
 
-   rxn_queue
+   rxn_q
+   rxn_q_timing

source/first_party/optimizers/rxn_q.rst

@@ -0,0 +1,33 @@
+Rxn Q (in-development)
+======================
+
+.. warning::
+
+   This plugin is currently in development and is **not publicly accessible at this time**.
+
+Description
+-----------
+
+Plugin class: Optimizer
+
+Rxn Q is a Rxn Rover plugin and stand-alone LabVIEW program that performs a sequence of reaction conditions in the given order. A user can create a queue of reaction conditions using the Rxn Q user interface, or load the reaction queue from a formatted file (see CSV File Format section below). This sequence can be paused, modified or added to, and resumed during an experiment, although changes on the current or previous lines will not take effect!
+
+Note: No timing element is built into Rxn Q. The queue will proceed to the next set of reaction conditions immediately upon submitting the result for the current reaction conditions, or when the current line is skipped.
+
+
+Acquisition
+-----------
+
+Download and install the plugin from the official GitHub release page listed below.
+
+**Downloads**
+
+- **Plugin (.vip file):**  
+  `Rxn Q Plugin – Releases <https://github.com/RxnRover/plugin_rxn_q/releases>`_
+
+- **Drivers:**  
+  This plugin does not require any additional drivers.
+
+**Source Code**
+
+- `Plugin Repository <https://github.com/RxnRover/plugin_rxn_q>`_

source/first_party/optimizers/rxn_q_timing.rst

@@ -0,0 +1,33 @@
+Rxn Q With Timing (in-development)
+==================================
+
+.. warning::
+
+   This plugin is currently in development and is **not publicly accessible at this time**.
+
+Description
+-----------
+
+Plugin class: Optimizer
+
+Rxn Q is a Rxn Rover plugin and stand-alone LabVIEW program that performs a sequence of reaction conditions in the given order. A user can create a queue of reaction conditions using the Rxn Q user interface, or load the reaction queue from a formatted file (see CSV File Format section below). This sequence can be paused, modified or added to, and resumed during an experiment, although changes on the current or previous lines will not take effect!
+
+Note: Unlike the original Rxn Queue plugin, this version includes a timing element. The queue will proceed to the next set of reaction conditions after a specified delay, which can be set by the user. This allows for more controlled timing between reactions.
+
+
+Acquisition
+-----------
+
+Download and install the plugin from the official GitHub release page listed below.
+
+**Downloads**
+
+- **Plugin (.vip file):**  
+  `Rxn Q 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_rxn_q_timing>`_