Add docs clarifications and updates (#140)

* Update dev packages, lint files

* Remove some pre-commit checks

* Add some docs clarifications

docs/beginner_guide/execution.md

@@ -1,4 +1,4 @@
-# Running the Segmentation Tool
+# Processing Images with Kelp-O-Matic
 
 Each time you want to run a classification on new imagery follow these steps.
 
@@ -109,6 +109,26 @@ Once you have constructed your command, execute it by pressing ++enter++.
 Wait for the progress bar to reach 100%, then open the results in an image processing or spatial analysis software such as QGIS or ArcGIS.
 Review the results for errors and edit as needed.
 
+??? tip "Checking GPU Usage"
+
+    If you have a GPU, you should be able to run `nvidia-smi` to check its status.
+    You can see here what processes are using the GPU, and how much memory they are using.
+
+    If Kelp-O-Matic is running, you'll have to run this in a new Poweshell window or tab.
+    If Kelp-O-Matic is actively using the GPU, you should see it listed here.
+
+#### Aborting Processing
+
+If you need to stop the processing of an image, you can press ++ctrl+c++ in the terminal to send a signal to the process
+that it should stop. This will stop the processing and return you to the command prompt.
+
+This is useful, for example, if you realize that you entered the wrong path and need to correct it but don't want to
+wait for `kom` for finish running.
+
+This command is standard in the terminal. It is used to send a signal to the running process that it should stop.
+
+---
+
 **Part 3 Kelp Segmentation is now complete!**
 
 Continue to [Part 4](./post_processing.md) to learn how to post-process the results.

docs/beginner_guide/install_env_setup.md

@@ -1,30 +1,40 @@
-# Virtual Environment Setup and Installation
+# Environment Setup and Installation
 
 It is recommended to install Kelp-O-Matic in a virtual environment to avoid conflicts
 with other Python packages present on your system. `uv` is our recommended environment manager, so we'll use it in this
 guide.
 
-??? question "Why UV"
+??? question "Why UV?"
 
     `uv` is a Python environment manager that is easy to use and works on Windows, MacOS, and Linux.
     It is a good choice for beginners and experienced users alike. It's extremely fast and lightweight, and provides a
     simple way to manage Python environments and install packages.
 
 ## UV Virtual Environment Setup
 
-1. Install `uv` using their [installation instructions](https://docs.astral.sh/uv/getting-started/installation/).
-    1. This will make a new command available in your terminal called `uv`.
-    2. Check the official instructions for installation, but generally, you're going to copy and paste the installation
-       command they provide (e.g. `curl ...`) into your terminal and press ++enter++. Read and follow the instructions
-       and prompts that are printed.
+1. Install `uv` using their [Standalone installer instructions](https://docs.astral.sh/uv/getting-started/installation/).
+    1. At the time of writing these docs, the command to run is:
 
-2. Once UV is installed, create a new "virtual environment" in your preferred location with the following commands:
+        === "Windows"
+            ```powershell
+            powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"
+            ```
+        === "MacOS/Linux"
+            ```bash
+            curl -LsSf https://astral.sh/uv/install.sh | sh
+            ```
+
+    2. Once you copy and paste the command into your terminal, press ++enter++. Read and follow the instructions
+       and prompts.
+    3. Once installation is finished, you will have a new terminal command: `uv`.
+
+2. Use to create a new "virtual environment" in your preferred file system location with the following commands:
     ```bash
     cd path/to/your/preferred/location
     uv venv my_env_name  # my_env_name is the name of your virtual environment. You can choose any name you like.
     ```
 
-    ??? question "What's a Virtual Environment"
+    ??? question "What's a Virtual Environment?"
 
         A virtual environment is a self-contained directory that contains a Python installation for a particular version
         of Python, plus a number of additional packages. It allows you to work on a specific project without affecting
@@ -33,9 +43,23 @@ guide.
         It's a good practice to create a new virtual environment for each project you work on. This way, you can install the
         specific versions of the packages you need for that project without affecting other projects.
 
+
 3. Activate the virtual environment
 
     === "Windows"
+        !!! warning "Windows Permissions"
+            The first time you run the command below, you will likely need to change your PowerShell execution policy
+            to allow running scripts. You can do this by running the following command in PowerShell:
+
+            ```powershell
+            Set-ExecutionPolicy -ExecutionPolicy RemoteSigned -Scope CurrentUser
+            ```
+
+            You should only need to do this once. After that, you can activate the virtual environment as written above.
+
+            If you skip this, you will see an error message saying something like *`kelpTest\Scripts\activate.ps1 cannot
+            be loaded because running scripts is disabled on this system.`*
+
         ```powershell
         .\my_env_name\Scripts\activate
         ```
@@ -62,9 +86,21 @@ Now that you have your virtual environment set up, you can install Kelp-O-Matic
 `uv`.
 
 1. Install Kelp-O-Matic using the following command:
-    ```bash
-    uv pip install kelp-o-matic
-    ```
+
+    === "Windows"
+        If you have a NVIDIA GPU:
+        ```powershell
+        uv pip install kelp-o-matic --index-url https://download.pytorch.org/whl/cu124
+        ```
+        Otherwise:
+        ```powershell
+        uv pip install kelp-o-matic
+        ```
+
+    === "MacOS/Linux"
+        ```bash
+        uv pip install kelp-o-matic
+        ```
 
 !!! important
 

docs/beginner_guide/terminal_crash_course.md

@@ -1,4 +1,4 @@
-# Terminal Crash Course
+# Crash Course on the Terminal
 
 The terminal is a text-based interface to your computer. It allows you to run
 commands to interact with your computer. The terminal is where you will run the
@@ -13,8 +13,7 @@ depending on your operating system, so choose the tab below based on which is re
     On Windows, there are two default terminal options: Command Prompt and PowerShell.
     You can use either of these to run the Kelp-O-Matic tool. We recommend using PowerShell.
 
-    To open PowerShell, search for "PowerShell" in the search bar and click on the
-    application that appears.
+    To open PowerShell, search for "PowerShell" in the search bar and click on "Windows PowerShell".
 
 === "MacOS/Linux"
     On MacOS and Linux, the default terminal is called Terminal. To open Terminal, search for "Terminal" in the search bar

mkdocs.yml

@@ -7,9 +7,9 @@ nav:
   - Home: index.md
   - Beginner Guide:
       - beginner_guide/index.md
-      - Terminal Crash Course: beginner_guide/terminal_crash_course.md
-      - Installation and Virtual Environment Setup: beginner_guide/install_env_setup.md
-      - Running the Segmentation Tool: beginner_guide/execution.md
+      - Crash Course on the Terminal: beginner_guide/terminal_crash_course.md
+      - Environment Setup and Installation: beginner_guide/install_env_setup.md
+      - Processing Images: beginner_guide/execution.md
       - Post-Processing: beginner_guide/post_processing.md
   - Installation: installation.md
   - Data Requirements: expectations.md