before submit 20240115

docs/docs/desktop-application.md

@@ -1,8 +1,10 @@
 The SanPy deskop application is an easy to use and powerful GUI designed to satisfy all your analysis needs. You can [download](../download) the desktop appication or [build from source](../install).
 
-## Getting Started
+## Opening a file or folder of raw data
 
-Load a folder of raw data files with the `Load Folder` button, or use the `File - Load Folder ...` menu, or drag and drop a folder from your hard-drive. Once a folder of raw data is loaded, each file in the folder will be shown in a list, one row per raw data file. Selecting a file will display the raw data recording.
+**New!** Open a raw data file with the `File - Open...` menu.
+
+Alternatively, open an entire folder of raw data files with the `File - Open Folder..` menu. Once a folder of raw data is loaded, each file in the folder will be shown in a list, one row per raw data file. Selecting a file will display the raw data recording.
 
 Spike detection is then performed by specifying a threshold in either the derivative of the membrane potential (Detect dV/dt) or the membrane potential (Detect mV).
 

docs/docs/download.md

@@ -1,20 +1,65 @@
-These desktop applications are meant to work out of the box. If there are any issues, please email Robert Cudmore (rhcudmore@ucdavis.edu) and we will fix it.
+# Download and run the deskop applications
+
+The macOS and Windows desktop applications are meant to work out of the box. If there are any issues, please email Robert Cudmore (rhcudmore@ucdavis.edu) and we will fix it.
+
+Downloading and running SanPy is designed to be very simple. You download a file (links below), unzip the download (macOS), and double-click to run. There is no installer, just a downloaded file you can double-click.
 
 ## Mac download
 
-If you have an older Mac with an Intel/x86 chip or if you are unsure then download the `x86` version. If you have a newer Mac with an M1/M2 chip then download the `arm` version.
+If you have an older Mac with an Intel/x86 chip then download the **`x86`** version. If you have a newer Mac with an M1/M2/M3 chip then download the **`arm`** version.
+
+If your not sure which type of Mac you have, then download the **`x86`** version.
+
+[Download macOS x86 zip](https://github.com/cudmore/SanPy/releases/download/v0.2.3/SanPy-macOS-x86.zip){ .md-button .md-button--primary}
+[Download macOS arm zip](https://github.com/cudmore/SanPy/releases/download/v0.2.3/SanPy-macOS-arm.zip){ .md-button .md-button--primary}
+
+### Mac download and run recipe
 
-[Download macOS x86 ](https://github.com/cudmore/SanPy/releases/download/v0.1.25/SanPy-macOS-x86.zip){ .md-button .md-button--primary}
-[Download macOS arm ](https://github.com/cudmore/SanPy/releases/download/v0.1.25/SanPy-macOS-arm.zip){ .md-button .md-button--primary}
+ - Download the `zip` file
+ - Once downloaded, double-click on `SanPy.zip` to uncompress it to `SanPy.app`
+ - **Important:** Move the `SanPy.app` to your `Applications` folder
+ - Double-click on `SanPy.app` (in your Applications folder) to run SanPy
+
+**Troubleshooting:** If you run into security issues, please see [Security on macOS](#security-on-macos).
 
 ## Windows download
 
-We are waiting for our Microsoft Developer Certificate and will provide a direct download as soon as we can. Please check back later. You can always clone the repository and run from source, see [Install](install.md).
+[Download Windows exe](https://github.com/cudmore/SanPy/releases/download/v0.2.3/SanPy.exe
+){ .md-button .md-button--primary}
 
+### Windows download and run recipe
+
+ - Download the `exe` file
+ - Once downloaded, double-click on `SanPy.exe` to run SanPy
+
+**Troubleshooting:** If you run into security issues, please see [Security on Windows](#security-on-windows).
+
+<!--
 ## Current Version
  - Version 0.1.25, Released on May 12, 2023
+-->
 
 ## Current and previous releases (on GitHub)
 
+You can always download all previous versions of SanPy from our GitHub repository.
+
 [Go To Current Release](https://github.com/cudmore/SanPy/releases){ .md-button .md-button--primary }
 
+## Troubleshooting
+
+Here are some common ways to troubleshoot the running of the SanPy GUI on macOS and Windows.
+
+### Security on macOS
+
+If SanPy does not run, the simplest solution is to do the following:
+
+ - Put the `SanPy.app` into your `Applications` folder.
+ - Right click `SanPy.app` and select the `Open` menu. Or, use `command+click` and select the `Open` menu.
+
+ The first time you run SanPy it might take 10-30 seconds to show the GUI. After that, it will open again pretty quick.
+
+### Security on Windows
+
+Same story as on macOS. Work your way through the warnings and it will run on Windows.
+
+On Windows 11, each time you run SanPy, it takes between 10-30 seconds to bring up the GUI. We are working on fixing this.

docs/docs/index.md

@@ -1,4 +1,4 @@
-SanPy is software to perform analysis of whole-cell curent clamp recordings. It is designed to work on a range of excitable cells including cardiac myocytes and neurons. Historically, it was originally designed for spontaneous [cardiac action potentials][cardiac action potential] from [whole-cell current-clamp][patch-clamp] recordings of [cardiac myocytes].
+SanPy is software to perform analysis of whole-cell curent clamp recordings. It is designed to work on a range of excitable cells including cardiac myocytes and neurons. Historically, it was originally designed for spontaneous [cardiac action potentials][cardiac action potential] from [whole-cell current-clamp][patch-clamp] recordings of [cardiac myocytes]. Now, we have extended it to include the analysis of neuronal action potentials.
 
 If you find the code in this repository interesting, please email Robert Cudmore at UC Davis (rhcudmore@ucdavis.edu) and we can get you started. We are looking for users and collaborators.
 

docs/docs/install.md

@@ -1,8 +1,6 @@
-SanPy is designed to run on: macOS, Microsoft Windows, and Linux.
+This page describes how to install SanPy from the command-line.
 
-## Download the SanPy app.
-
-We are building SanPy desktop applications so users can download a single file and get working with just a double-click. This does not require anything special on our users end. **No programming, no installing Python, and no command line**. See our [download](../download) page.
+If you want to download and run SanPy as a pre-built desktop application, please see our easy to follow [download sanpy](../download) page.
 
 ## Install from the command line
 

docs/mkdocs.yml

@@ -63,8 +63,9 @@ nav:
     - Introducing SanPy: index.md
     - Download: download.md
     - Desktop Application: desktop-application.md
+    - Getting Started With The GUI: getting-started-gui.md
     - Plugins: plugins.md
-    - Install: install.md
+    - Install From Command Line: install.md
     - API:
         - Overview: api/overview.md
         - Getting Started: scripting.ipynb