Fix: Docs (#551)

* fix: prioritized the use of subordinate metadata when choosing between feature level and subordinate level

* fix: revisions to SmartPeak GUI section

* feat: added a starting point for the server section

* wip: revising and expanding features

* fix: updated version for installation instructions

* wip: revising and expanding features

* fix/feat: update faqs

* fix: removed paramters now that it is redundant with the faqs

* feat: updated FAQ section

* fix: small changes to start and server pages

* feat: added images and descriptions to missing FAQ sections

* feat: added images and descriptions to missing FAQ sections

* fix: revised select features from best dilution section of features

* fix/feat: updated audit trail in features; fixed a couple of bugs found when building the docs

* fix: other bugs found after building the docs

* feat: updates to features audit trail section

* feat: updates to features audit trail section

* fix: edited HPLC tutorial page

* wip: adding LC-MS/MS-SRM tutorial

* feat, wip: added DDA and DIA tutorials

* fix: revisions to FIAMS tutorial

* fix: table reformatting

* wip: fixing tables in tutorials...

* wip: fixing tables in tutorials...

* fix: removed instrument specifics in tutorial names

* fix: broken tables in the tutorials

* feat: updated all tutorial acquisition schematics

* feat: added additional sections for features

* fix: bug in server usage section

* fix: updated documentation for the server to include dockerhub images

* fix: updated features to include a section on workflow steps

* wip: updating optimize calibration curve usage and example

* feat: added new screenshots for features

* fix: bugs in features

* feat: optimize calibration curves feature section

* wip: added screenshots for lcms-srm tutorial

* feat: body for lcms-srm tutorial

* wip: adding dda methods

* wip: workflows for DDA workflows

* feat: added dda tutorial body

* feat: dda tutorial screenshots

* fix: bugs in lcms dda tutorial

* fix: bugs in tables in dda tutorial

* fix, feat: preparing for PR and small bug fixes

Author: dmccloskey

docs/about/parameters.rst

@@ -3,7 +3,7 @@
 Using SmartPeak GUI
 ----------------------------------------------------------------------------------------------------------
 
-After successful installation of SmartPeak, on Windows open menu start and browse for relevant icon, you can also find the shortcut on desktop.
+This page describes the graphical user interface (GUI) for working with SmartPeak. SmartPeak GUI provides functionality to facilitate users to get up and running as quickly as possible.  SmartPeak GUI also provides various graphical views and plots to enable faster debugging and configuration of workflows and algorithms.  After installation of SmartPeak on Windows, MacOS, and/or Linux, a shortcut should be available for quickly launching the application.
 
 .. _logs:
 

docs/faq.rst

@@ -9,17 +9,17 @@ Example on Ubuntu
 
 .. code-block:: bash
 
-    wget https://github.com/AutoFlowResearch/SmartPeak/releases/download/v1.2.0/SmartPeak-1.2.0-Linux.deb
-    sudo dpkg -i SmartPeak-1.2.0-Linux.deb
+    wget https://github.com/AutoFlowResearch/SmartPeak/releases/download/v1.26.0/SmartPeak-1.26.0-Linux.deb
+    sudo dpkg -i SmartPeak-1.26.0-Linux.deb
     sudo apt-get install -f
 
-User can also use GUI by double clicking on SmartPeak-1.2.0-Linux.deb icon and requesting installation through Ubuntu Software.
+User can also use GUI by double clicking on SmartPeak-1.26.0-Linux.deb icon and requesting installation through Ubuntu Software.
 
 
 Example on Windows
 ------------------
 
-Download latest release for windows, e.g. ``SmartPeak-1.2.0-win64.exe`` and double click on the icon.
+Download latest release for windows, e.g. ``SmartPeak-1.26.0-win64.exe`` and double click on the icon.
 The wizard will guide you through the installation process.
 
 A warning from Windows Defender SmartScreen may appear.

docs/guide/guistart.rst renamed to docs/guide/gui.rst

@@ -0,0 +1,23 @@
+.. begin_smartpeak_server_usage
+
+Using SmartPeak Server
+----------------------------------------------------------------------------------------------------------
+
+This page describes the remote server for scaling SmartPeak to large and computationally demanding workflows using high performance computing (HPC) resources. 
+The SmartPeak Server utilizes containerization and gRPC to enable users to connect, control, and view a remote session using the SmartPeak GUI.  
+An IT administrator would most likely be required to set-up the remote server on the HPC resources and ensure file transfer and security are in place.
+The SmartPeak team maintains containerized versions of the SmartPeak `CLI <https://hub.docker.com/r/autoflowresearch/smartpeak-cli>`_ and `Server <https://hub.docker.com/r/autoflowresearch/smartpeak-server>`_ on DockerHub that are required for setting up the workers and server, respectively.
+
+.. todo::
+    Describe the functionality of the SmartPeak Server.
+
+.. todo::
+    Describe how to set-up the SmartPeak Server as an IT administrator.
+
+.. todo::
+    Describe how to connect to the SmartPeak Server as a user.
+
+.. warning::
+    SmartPeak Server is currently experimental!
+
+.. end_smartpeak_server_usage

docs/guide/install.rst

@@ -1,13 +1,20 @@
 Tutorials & Demos
 =============================================================================
 
-This section covers a breadth of walkthroughs using different datasets and analytical techniques.
+This section covers a breadth of walkthroughs using different datasets and analytical techniques.  
+All of the datasets used in the tutorials can be found on `GitHub <https://github.com/AutoFlowResearch/SmartPeak/tree/develop/src/examples/data>`_.  
+The datasets and input files can be used as templates for getting started with a new and similar workflow in SmartPeak.
 
+* :doc:`tutorials/Targeted_quantitation_with_LC-MSMS_5500_QTRAP_RapidRIP`.
 
 * :doc:`tutorials/Targeted_quantitation_with_HPLC_data`.
 
 * :doc:`tutorials/Non-targeted_FIA-MS_analysis_with_Thermo_Orbitrap`.
 
+* :doc:`tutorials/Non-targeted_LC-MSMS_DDA_analysis_with_Thermo_Orbitrap`.
+
+* :doc:`tutorials/Non-targeted_LC-MSMS_DIA_analysis`.
+
 * :doc:`tutorials/Targeted_flux_analysis_with_LC-MSMS_Agilent_Lipidomics`.
 
 * :doc:`tutorials/Targeted_flux_analysis_with_GC-MS_SIM_Agilent`.