Update headings (#69)

* Improve software section headings

- Fix links to OpenEhys.Onix1 docs

* Fix broken links and formatting

source/Hardware Guide/Headstages/tether-voltage.rst

@@ -20,7 +20,7 @@ host computer will not be able to detect the headstage. A borderline
 voltage can still cause connectivity issues as the headstage occasionally dips
 below the level it needs to function properly.
 
-.. attention:: The :ref:`openephys_onix1ref` Bonsai package automatically sets the
+.. attention:: The :ref:`Bonsai package <openephys_onix1ref>` automatically sets the
    headstage port voltage by default, but allows the user to override the
    voltage setting as well. The documentation linked shows how to use this
    functionality and what valid voltage ranges are for each headstage. This

source/Hardware Guide/Miniscopes/index.rst

@@ -10,7 +10,7 @@ UCLA Miniscope V3
 :Design Repository: https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB
 :Documentation: http://miniscope.org/index.php/Guides_and_Tutorials
 :Compatibility: :ref:`pcie_host`, :ref:`breakout`
-:Software: :ref:`openephys_onix1ref` Bonsai package
+:Software: :ref:`openephys_onix1ref`
 
 .. figure:: /_static/images/miniscopes/ucla-miniscope-v3-render.jpg
     :align: center
@@ -21,7 +21,7 @@ UCLA Miniscope V4
 :Design Repository: https://github.com/Aharoni-Lab/Miniscope-v4
 :Documentation: https://github.com/Aharoni-Lab/Miniscope-v4/wiki
 :Compatibility: :ref:`pcie_host`, :ref:`breakout`
-:Software: :ref:`openephys_onix1ref` Bonsai package
+:Software: :ref:`openephys_onix1ref`
 
 .. figure:: /_static/images/miniscopes/ucla-miniscope-v4-render.png
     :align: center

source/Hardware Guide/PCIe Host/setup-windows.rst

@@ -117,7 +117,5 @@ Install Device Driver
 
 Install Software
 ---------------------------------------
-Have a look at the :ref:`software_guide` page for open-source software options. We
-recommend using :ref:`bonsairef` and the :ref:`openephys_onix1ref` Bonsai package because it provides first class
-support for all ONIX hardware features. 
+Have a look at the :ref:`software_guide` page for software options.
 

source/Software Guide/Open Ephys GUI/index.rst

@@ -1,6 +1,6 @@
 .. _open_ephys_gui:
 
-Open Ephys GUI
+Open Ephys GUI ONIX Plugin
 --------------------------------------------
 
 The `Open Ephys GUI <https://open-ephys.github.io/gui-docs/index.html>`__ is an
@@ -10,8 +10,8 @@ experiments more flexible and enjoyable. It works equally well on macOS, Linux,
 and Windows.
 
 .. note:: An ONIX plugin for the Open Ephys is in development. To access all of
-   ONIX's capabilities right now, have a look at the :ref:`openephys_onix1ref` Bonsai package.
-   **You can still take advantage of the GUI's excellent
+   ONIX's capabilities right now, have a look at the :ref:`openephys_onix1ref`.
+   **In the meantime, you can still take advantage of the GUI's excellent
    ephys visualizaiton tools by streaming data from Bonsai to the GUI using
    the** `Ephys Socket Plugin <https://open-ephys.github.io/gui-docs/User-Manual/Plugins/Ephys-Socket.html>`__.
 

source/Software Guide/OpenEphys.Onix1/index.rst

@@ -1,48 +1,46 @@
-.. _bonsairef:
-
-Bonsai
-========================
-
-`Bonsai <https://bonsai-rx.org/>`__ is a visual programming language (think
-LabView) for `reactive programming
-<https://en.wikipedia.org/wiki/Reactive_programming>`__ with features such as: 
-
-- Real-time compilation of workflows to machine code as they are edited
-  (zero-overhead).
-- A large array of operators for combining and sychronizing asynchronous data
-  streams, which is a major issue in other software.
-- Lots of support for all sorts of hardware outside of ONIX.
-
-Bonsai is ideal for accessing the full power of ONIX hardware and combining it
-with third-party data sources (e.g. machine vision cameras,
-behavioral hardware, etc.), and for real-time processing and manipulation of
-data streams. 
-
 .. _openephys_onix1ref:
 
-OpenEphys.Onix1
-----------------
+Bonsai ONIX Package
+=================================
 
-`OpenEphys.Onix1
-<https://open-ephys.github.io/onix1-bonsai-docs/index.html>`__ is the Bonsai
-package for ONIX hardware. This package contains `Bonsai Operators
+``OpenEphys.Onix1`` is a `Bonsai <https://bonsai-rx.org/>`__ package for ONIX
+hardware. This package contains `Bonsai Operators
 <https://bonsai-rx.org/docs/articles/operators.html>`__ for acquiring and
 sending data to ONIX hardware.
 
-:Code: https://github.com/open-ephys/onix-bonsai-onix1 
-:Compatibility: ONIX Hardware, UCLA miniscopes & variants
-:Documentation: https://open-ephys.github.io/onix1-bonsai-docs/index.html
+:Code: https://github.com/open-ephys/bonsai-onix1
+:Compatibility: All ONIX hardware, Neuropixels, UCLA miniscopes & variants
+:Documentation: https://open-ephys.github.io/bonsai-onix1-docs/index.html
 
 .. raw:: html
 
-        <a href="https://open-ephys.github.io/onix1-bonsai-docs/index.html"><span class="std std-ref custom-card">
+        <a href="https://open-ephys.github.io/bonsai-onix1-docs/index.html"><span class="std std-ref custom-card">
         <div class="card text-center page-card">
 
-            <header> 
+            <header>
                 <h1>Go to the OpenEphys.Onix1 Docs <i class="fas fa-external-link"></i></h1>
             </header>
             <img src="../../_static/images/bonsai-lettering.svg"
             class="page-card-img-marg hover-zoom" alt="OpenEphys.Onix1 bonsai
             package documentation">
 
         </div>
+
+What is Bonsai?
+------------------------------
+`Bonsai <https://bonsai-rx.org/>`__ is a visual programming language (think
+LabView) for `reactive programming
+<https://en.wikipedia.org/wiki/Reactive_programming>`__ with features such as:
+
+- Real-time compilation of workflows to machine code as they are edited
+  (zero-overhead).
+- A large array of operators for combining and sychronizing asynchronous data
+  streams, which is a major issue in other software.
+- Lots of support for all sorts of hardware outside of ONIX.
+
+Bonsai is A good choice for accessing the full power of ONIX hardware and
+combining it with third-party data sources (e.g. machine vision cameras,
+behavioral hardware, etc.), and for real-time processing and manipulation of
+data streams. The documentation linked above contains detailed instructions on
+how to use Bonsai with ONIX hardware along with fully useable example workflows,
+data loading scripts, etc.

source/Software Guide/index.rst

@@ -14,17 +14,19 @@
     oni-repl/index
     Bonsai.ONIX (DEPRECATED) <Bonsai.ONIX/index>
 
-:ref:`Bonsai <bonsairef>`
-    :ref:`openephys_onix1ref` is a :ref:`bonsairef` package for acquiring data from ONIX
-    hardware for real-time experiments. Bonsai is very good at processing the
+:ref:`Bonsai ONIX Package <openephys_onix1ref>`
+    :ref:`OpenEphys.Onix1 <openephys_onix1ref>` is a `Bonsai
+    <https://bonsai-rx.org/>`__ package for acquiring data from ONIX hardware
+    for real-time experiments. Bonsai is very good at processing the
     heterogeneous data streams produced by ONIX hardware.
 
-:ref:`Open Ephys GUI <open_ephys_gui>`
-    The Open Ephys GUI can be used for ONIX data visualization.
+:ref:`Open Ephys GUI ONIX Plugin <open_ephys_gui>`
+    The `Open Ephys GUI <https://open-ephys.github.io/gui-docs/>` excels at
+    electrophysiology data visualization and recording.
 
-:ref:`oni-repl <oni_repl>`
-    A simple command-line application that can be used for debugging and basic
-    streaming IO with ONIX hardware.
+:ref:`Command line application <oni_repl>`
+    `oni-repl` is a simple command-line application that can be used for
+    debugging and basic streaming IO with ONIX hardware.
 
 .. tip:: ONIX uses an `ONI-compliant API
    <https://open-ephys.github.io/ONI/api/index.html>`__ that is software
@@ -35,5 +37,5 @@ Deprecated Software
 ___________________________________
 
 - The :ref:`bonsai_onixref` pages provide information about the original Bonsai
-  package, which has been superseded by :ref:`openephys_onix1ref`
+  package, which has been superseded by :ref:`OpenEphys.Onix1 <openephys_onix1ref>`.
 

source/Software Guide/oni-repl/index.rst

@@ -1,9 +1,10 @@
 .. _oni_repl:
 
-oni-repl
+Command Line Application
 ===================================
 
 .. toctree::
+    :hidden:
     :maxdepth: 1
 
     usage
@@ -33,11 +34,11 @@ hardware to perform the following:
 - Bulk initialize device register state
 
 .. note:: ``oni-repl`` was created for hardware debugging and as a test program
-    for `liboni <https://open-ephys.github.io/ONI/api/liboni/index.html>`__. 
-    However, its simplicity and lack of abstraction compared to
-    :ref:`bonsai_onixref` make it useful as an example of how to use 
-    `liboni <https://open-ephys.github.io/ONI/api/liboni/index.html>`__ and
-    for quickly examining hardware state and hub firmware versions.
+   for `liboni <https://open-ephys.github.io/ONI/api/liboni/index.html>`__.
+   However, its simplicity and lack of abstraction compared to
+   :ref:`bonsai_onixref` make it useful as an example of how to use `liboni
+   <https://open-ephys.github.io/ONI/api/liboni/index.html>`__ and for quickly
+   examining hardware state and hub firmware versions.
 
 .. code-block:: none
 

source/Software Guide/oni-repl/usage.rst

@@ -1,19 +1,19 @@
 .. _oni_repl_usage:
 
-Usage
+``oni-repl`` Usage
 ====================================
 
 .. code-block:: console
 
-    oni-repl <driver> [slot] [-d] [-D <value>] [-n <value>] [-i <device index>] 
-    [--rbytes=<bytes>] [--wbytes=<bytes>] [--dumppath=<path>] [-h,--help] [-v,--version] 
+    oni-repl <driver> [slot] [-d] [-D <value>] [-n <value>] [-i <device index>]
+    [--rbytes=<bytes>] [--wbytes=<bytes>] [--dumppath=<path>] [-h,--help] [-v,--version]
 
 Required Arguments
 -----------------------------------
-<driver>        
+<driver>
     Hardware driver to dynamically link (e.g. **riffa**,
     **ft600**, **test_driver**, etc.)
-[slot]           
+[slot]
     Index specifying the physical slot occupied by hardware being controlled.
     If none is provided, the driver-defined default will be used.
 
@@ -58,33 +58,33 @@ index 0) and a single headstage (starting at device index 256).
 
 .. code-block:: console
 
-   $ ./liboni-test riffa 0 
+   $ ./liboni-test riffa 0
 
-       Jon Newman @ MIT                     **                
-       Jie Zhang @ MIT                     ////               
-       Aarón Cuevas López @ UPV             ///.              
-       Josh Seigle @ Allen                  ///,.             
-       Jakob Voigts @ MIT                   *///,             
-                         *.                  ///,,            
-                       ,####/                ///,,,           
-                     ,,,,/####//             *///,,.          
-                   ,,,,,   //##////           ///,,,          
-                 ,,,,,      ,///#/////        ///.,,,         
-               ,,,,,          //// //////     *///,,,,        
-             ,,,,,             ,////  /////,   /// ,,,,       
-            ,,,,                 ////   ,/////.///  ,,,       
-         .,,,,                    .////    ,///##//  ,,,      
-       .,,,,                        ////      */###/ .,,,     
-      ,///***,,..........,,,...      ,////      /##(///,,,    
-         .,,,,,,**,,..................,((((,..../(((((((((.   
-              .,......,                .*(((/...,(((,,,(###   
-                   .........              ////   ///.  ///,   
-                        ........,          ,///* */// ////    
-       Open Ephys Org.       .,......,       //// ///.///     
-                                  ........,   *///(/////      
-       Supporting open science         .,......,//((((//      
-       since 2010.                          ....,/(##(/       
-                                                 .,###.       
+       Jon Newman @ MIT                     **
+       Jie Zhang @ MIT                     ////
+       Aarón Cuevas López @ UPV             ///.
+       Josh Seigle @ Allen                  ///,.
+       Jakob Voigts @ MIT                   *///,
+                         *.                  ///,,
+                       ,####/                ///,,,
+                     ,,,,/####//             *///,,.
+                   ,,,,,   //##////           ///,,,
+                 ,,,,,      ,///#/////        ///.,,,
+               ,,,,,          //// //////     *///,,,,
+             ,,,,,             ,////  /////,   /// ,,,,
+            ,,,,                 ////   ,/////.///  ,,,
+         .,,,,                    .////    ,///##//  ,,,
+       .,,,,                        ////      */###/ .,,,
+      ,///***,,..........,,,...      ,////      /##(///,,,
+         .,,,,,,**,,..................,((((,..../(((((((((.
+              .,......,                .*(((/...,(((,,,(###
+                   .........              ////   ///.  ///,
+                        ........,          ,///* */// ////
+       Open Ephys Org.       .,......,       //// ///.///
+                                  ........,   *///(/////
+       Supporting open science         .,......,//((((//
+       since 2010.                          ....,/(##(/
+                                                 .,###.
 
           +--------------------+-------+-------+-------+-------+---------------------
           |                    |       |Firm.  |Read   |Wrt.   |
@@ -150,4 +150,4 @@ index 0) and a single headstage (starting at device index 256).
                a - reset the acquisition clock counter
                x - issue a hardware reset
                q - quit
-       >>> 
+       >>>