[ENH] Update setup instructions: add tree, Copilot setup, configure workspace trust

_includes/copilot-setup.html

@@ -0,0 +1,23 @@
+<div>
+<h4>Setting up GitHub Copilot in VSCode</h4>
+
+<p>
+    In any VSCode window, click the Copilot icon near the bottom left corner of the bottom status bar and select "Use AI Features",
+    then follow the prompts to sign in using GitHub.
+</p>
+<p>
+    <img src="{{ '/assets/images/setup-copilot-status-bar.png' | relative_url }}" alt="Copilot status bar">
+</p>
+
+<p>
+    This will give you access to the [Copilot free plan](https://docs.github.com/en/copilot/concepts/billing/individual-plans) in VSCode.
+</p>
+
+<p>
+    To open the Copilot chat, go to **View > Chat**.
+</p>
+
+<p>
+    Reference: https://code.visualstudio.com/docs/copilot/setup
+</p>
+</div>

_includes/extra-git-setup.html

@@ -3,21 +3,30 @@ <h4>Git configuration</h4>
 
 <p>
     If you have never used Git on your computer, you may have to configure it.
-    The following instructions assume you have already created a GitHub account.
+    The following instructions assume you have already created a GitHub account following the main <a href="{{ 'setup.html' | relative_url }}">Setup</a> page.
 </p>
 
 <p>
-    Type the following commands in a terminal. Make sure to use the email associated with your GitHub account.
-    The <code>user.name</code> can be any name you want to appear as the author of your commits, but we recommend using the name associated with your GitHub profile.
+    Type the following commands in a terminal.
 </p>
+
+
+<p>Notes:</p>
+<ul>
+    <li>For <code>user.email</code>, use the email associated with your GitHub account.</li>
+    <li><code>user.name</code> can be any name you want to use to author your commits, but we recommend using the display name on your GitHub profile.</li>
+</ul>
+
 <p>
 <pre>
-git config --global user.name "Jane Doe"
-git config --global user.email "janedoe@example.com"
-git config --global core.autocrlf true
+git config --global user.name "Jane Doe"  # Set the author name for your commits
+git config --global user.email "janedoe@example.com"  # Set the email linked to your commits
+git config --global core.autocrlf true  # Auto-handle line endings correctly across different OSes
+git config --global init.defaultBranch main  # Make new repos use "main" as the default branch name
+git config --global pull.rebase false  # Make "git pull" combine changes using merge by default
 </pre>
 </p>
 <p>
-    <b>Tip:</b> You can review your configuration at any time with: <code>git config --list</code>
+    <b>Tip:</b> You can check your Git configuration at any time with: <code>git config --list</code>
 </p>
 </div>

_includes/gh-ssh-key-setup.html

@@ -5,13 +5,13 @@
     <li>
       In a terminal, <a href="https://docs.github.com/en/authentication/connecting-to-github-with-ssh/checking-for-existing-ssh-keys">check if you have existing SSH keys in the ~/.ssh directory</a>.
       A public/private key pair typically has the filename format <code>id_ALGORITHM</code> and <code>id_ALGORITHM.pub</code>.
-      If you have existing key files, use a custom name for your SSH key pair in step 2.
+      If you have existing key files, use a different, custom name for your SSH key pair in step 2.
     </li>
     <li>
       <a href="https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent">Generate a new SSH key and add it to the ssh-agent</a>.
       <ul>
-        <li>Ensure to use the default file location for saving the key, unless you already have existing keys - in this case, replace just the <code>id_ALGORITHM</code> (e.g., <code>id_ed25519</code>) part of the file location with an informative keyname like <code>id_ed25519_github</code></li>
-        <li>Choose a passphrase you can remember easily, as you will need to use it for certain Git commands</li>
+        <li>Use the default file location for saving the key, unless you already have existing keys - in this case, replace just the <code>id_ALGORITHM</code> (e.g., <code>id_ed25519</code>) part of the file location with an informative keyname like <code>id_ed25519_github</code></li>
+        <li><strong>Store your passphrase in a secure location</strong>, as you will need to use it for certain Git commands</li>
       </ul>
     </li>
     <li>
@@ -30,7 +30,7 @@
       Locally specify the SSH key to use when connecting to GitHub, so that the right "identity" is always used for local Git operations (useful when you have multiple keys).
       <ol>
         <li>
-          Run the following command (replace <code>id_ed25519</code> with your <strong>private</strong> key's filename if you used a custom key name):
+          Run the following command (if you used a custom key name, replace <code>id_ed25519</code> with your <strong>private</strong> key's filename):
           <pre><code>printf 'Host github.com\n  User git\n  IdentityFile ~/.ssh/id_ed25519\n  IdentitiesOnly yes\n' &gt;&gt; ~/.ssh/config</code></pre>
         </li>
         <li>
@@ -40,8 +40,7 @@
           <pre><code>Host github.com
   User git
   IdentityFile ~/.ssh/id_ed25519
-  IdentitiesOnly yes
-          </code></pre>
+  IdentitiesOnly yes</code></pre>
         </li>
       </ol>
     </li>

_includes/setup-python-package.html

@@ -2,9 +2,9 @@
 
 <p>
 <pre>
-conda config --append channels conda-forge
-conda config --set channel_priority strict
-conda create -n qlsc612 -y python=3.12 flake8 jupyterlab jupyter nilearn matplotlib seaborn bokeh statsmodels plotly wordcloud
+conda config --append channels conda-forge  # add conda-forge as a source for packages (channel)
+conda config --set channel_priority strict  # prioritize packages based on channel order
+conda create -n qlsc612 -y python=3.12 flake8 jupyter nilearn matplotlib seaborn bokeh statsmodels plotly wordcloud
 conda activate qlsc612
 </pre>
 </p>
@@ -16,3 +16,8 @@
 The last line, <code>conda activate qlsc612</code>,
 will activate this Python environment (the default environment is <code>base</code>).
 </p>
+
+<p>
+Once the commands have finished running, you should see `(qlsc612)` at the beginning of your terminal prompt
+to indicate that the new environment is active.
+</p>

_includes/vs-code-workspace-trust-popup.html

@@ -0,0 +1,12 @@
+<blockquote>
+  <p>
+    <strong>NOTE:</strong>
+    The first time you run <code>code .</code> in a folder,
+    you may see a popup asking "Do you trust the authors of the files in that folder?"
+  </p>
+  <p>
+    Select "Yes, I trust the authors", and if available, also check the box that says
+    "Trust the authors of all files in the parent folder".
+    This will enable full features and extensions in your VSCode workspace.
+  </p>
+</blockquote>

setup/linux.md

@@ -6,7 +6,7 @@ description: Instructions for setting up on Linux
 
 ### Bash shell
 
-You already have it! Depending on which version of Linux you’re running you may
+You already have it! Depending on which version of Linux you're running you may
 need to type `bash` inside the terminal to access it. To check whether this is
 necessary, follow these steps:
 
@@ -25,28 +25,34 @@ If you are prompted to install it follow the instructions on-screen to do so.
 
 {% include extra-git-setup.html %}
 
-#### Creating an SSH key for GitHub
+#### Create an SSH key for GitHub
 
-When following the GitHub docs below, make sure to select the **Linux** instructions.
+When following the GitHub docs in the steps below, make sure to select the **Linux** instructions at the top of the page.
 
 {% include gh-ssh-key-setup.html %}
 
 ### VSCode
 
 1. Go to [this page](https://code.visualstudio.com/) and click the download
    button for either the `.deb` (Ubuntu, Debian) or the `.rpm` (Fedora, CentOS) file.
-1. Double-click the downloaded file to install VSCode
+2. Double-click the downloaded file to install VSCode
    (you may be prompted to type your administrator password during the install).
+3. To confirm that everything worked, open a terminal and type `code .` (include the period).
+   This should open the current directory in a VSCode window.
+
+{% include vs-code-workspace-trust-popup.html %}
 
 #### VSCode extensions
 
 1. Open the Visual Studio Code application.
-1. Open the Extension side panel by pressing `Ctrl+Shift+X`.
+2. Open the Extension side panel by pressing `Ctrl+Shift+X`.
    In the search bar at the top of this panel
    search for each of the following extensions and press `Install` for the first entry that appears.
 
 {% include vs-code-extensions.html %}
 
+{% include copilot-setup.html %}
+
 ### Python
 
 1. Open a new terminal and type the following lines (separately) into the
@@ -57,23 +63,23 @@ When following the GitHub docs below, make sure to select the **Linux** instruct
    bash Miniconda3-latest-Linux-x86_64.sh
    ```
 
-1. A license agreement will be displayed and the bottom of the terminal will read `--More--`.
+2. A license agreement will be displayed and the bottom of the terminal will read `--More--`.
    Press `Enter` or the space bar until you are prompted with
-   "Do you accept the license terms? [yes|no]."
-   Type `yes` and then press `Enter`
-1. The installation script will inform you that it is going to install into a default directory (e.g., `/home/$USER/miniconda3`).
+   `Do you accept the license terms? [yes|no]`.
+   Type `yes` and then press `Enter`.
+3. The installation script will inform you that it is going to install into a default directory (e.g., `/home/$USER/miniconda3`).
    Leave this default and press `Enter`.
-1. When you are asked
-   "Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no],"
+4. When you are asked
+   `Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no]`,
    type `yes` and press `Enter`.
    Exit the terminal once the installation has finished.
-1. Re-open a new terminal.
-   Type `which python` into the terminal and it should return a path (e.g., `/home/$USER/miniconda3/bin/python`).
-   - If you do not see a path like this then please try typing `conda init`,
+5. Re-open a new terminal.
+   Type `which python` into the terminal and check that it returns a path like `/home/$USER/miniconda3/bin/python`.
+   - If you do not see a path like this, try typing `conda init`,
      closing your terminal, and repeating this step.
      If your issue is still not resolved skip the following step
      and contact an instructor on the `#help-installation` channel of the Slack workspace.
-1. Type the following to remove the installation script that was downloaded:
+6. Type the following to remove the installation script that was downloaded:
 
    ```bash
    rm ./Miniconda3-latest-Linux-x86_64.sh
@@ -90,13 +96,24 @@ When following the GitHub docs below, make sure to select the **Linux** instruct
    [Debian](https://docs.docker.com/engine/install/debian/),
    [Fedora](https://docs.docker.com/engine/install/fedora/),
    [CentOS](https://docs.docker.com/engine/install/centos/)). Make sure to
-   follow the “Install using the repository” method!
-1. Once you’ve installed Docker make sure to follow the
+   follow the "Install using the repository" method!
+2. Once you've installed Docker make sure to follow the
    [post-install instructions](https://docs.docker.com/engine/install/linux-postinstall/)
-   as well. You only need to do the “Manage Docker as a non-root user” and
-   “Configure Docker to start on boot” steps.
-1. Open a new terminal and type `docker run hello-world`. A brief introductory
-   message should be printed to the screen.
+   as well. You only need to do the "Manage Docker as a non-root user" and
+   "Configure Docker to start on boot" steps.
+3. Open a new terminal and type `docker run hello-world`.
+   If the installation worked, a brief introductory message should be printed to the screen.
+
+### Install the `tree` command
+
+`tree` is a helpful command for viewing directory structures, and is strongly recommended.
+
+1. Open a terminal, and check if you have `tree` already installed by running `tree --version`.
+   - If you see a version number, you're all set!
+   - If you see a message like `tree: command not found`, install it by running:
+      ```bash
+      sudo apt-get update && sudo apt-get install -y tree
+      ```
 
 ---