Merge pull request #147 from brown-ccv/doc-ver-3

refactor: update dependencies and change syntax details to support do…

docs/quick_start.mdx

@@ -5,7 +5,6 @@ title: Quick Start
 description: Quick start guide for Honeycomb
 ---
 
-import CodeBlock from "@theme/CodeBlock";
 import TabItem from "@theme/TabItem";
 import Tabs from "@theme/Tabs";
 
@@ -174,10 +173,9 @@ NVM (Node Version Manager) is a tool for installing and using multiple versions
         </em>
       </TabItem>
       <TabItem value="mac" label="macOS">
-        <CodeBlock language="sh">
-          curl -o-
-          https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.4/install.sh | bash
-        </CodeBlock>
+        ```shell 
+        curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.4/install.sh | bash
+        ```
       </TabItem>
     </Tabs>
 

package.json

@@ -11,14 +11,14 @@
     "clear": "docusaurus clear"
   },
   "dependencies": {
-    "@docusaurus/core": "^2.4.0",
-    "@docusaurus/preset-classic": "^2.4.0",
-    "@docusaurus/theme-mermaid": "^2.4.1",
-    "@mdx-js/react": "^1.6.21",
-    "clsx": "^1.2.1",
-    "docusaurus-lunr-search": "^3.3.2",
-    "react": "^17.0.0",
-    "react-dom": "^17.0.0"
+    "@docusaurus/core": "^3.4.0",
+    "@docusaurus/preset-classic": "^3.4.0",
+    "@docusaurus/theme-mermaid": "^3.4.0",
+    "@mdx-js/react": "^3.0.1",
+    "clsx": "^2.1.1",
+    "docusaurus-lunr-search": "^3.4.0",
+    "react": "^18.3.1",
+    "react-dom": "^18.3.1"
   },
   "browserslist": {
     "production": [

versioned_docs/version-3.0.0/configuration.md

@@ -5,16 +5,16 @@ title: Configuration
 
 ## Environment Variables
 
-Honeycomb uses environment variables during **build** and **run** time to control the different configurations. Below we list the environment variables used by the app and indicate their properties via badges and text. Optional variables are labeled with the ![optional](https://img.shields.io/badge/-optional-yellow) badge and mandatory variables are labeled with the ![default <default-value>](https://img.shields.io/badge/default-<defaultvalue>-yellow) badge with their default value specified. The ![buildtime](https://img.shields.io/badge/-buildtime-blue) badge indicates the variable is used during the build/compilation phase (`npm build`) while the ![runtime](https://img.shields.io/badge/-runtime-purple) badge indicates the variable is used during the executable run (`npm run dev`).
+Honeycomb uses environment variables during **build** and **run** time to control the different configurations. Below we list the environment variables used by the app and indicate their properties via badges and text. Optional variables are labeled with the ![optional](https://img.shields.io/badge/-optional-yellow) badge and mandatory variables are labeled with the ![default `<default-value>`](https://img.shields.io/badge/default-<defaultvalue>-yellow) badge with their default value specified. The ![buildtime](https://img.shields.io/badge/-buildtime-blue) badge indicates the variable is used during the build/compilation phase (`npm build`) while the ![runtime](https://img.shields.io/badge/-runtime-purple) badge indicates the variable is used during the executable run (`npm run dev`).
 
 ### Dev Mode Only
 
 - `ELECTRON_START_URL` ![string](https://img.shields.io/badge/-string-grey)![optional](https://img.shields.io/badge/-optional-yellow): URL (e.g. `http://localhost:3000`) where the front end of the app is being hosted - also used in `electron.js` to indicate the app is running in dev mode.
 
 ### Desktop Only
 
-- `EVENT_MARKER_PRODUCT_ID`![string](https://img.shields.io/badge/-string-grey)![optional](https://img.shields.io/badge/-optional-yellow)![runtime](https://img.shields.io/badge/-runtime-purple): The product ID of the event marker (e.g. `0487`).  If not set, it will use the `productID` set in `public/config/trigger.js` if available, or attempt to connect using the com name.
-- `EVENT_MARKER_COM_NAME` ![string](https://img.shields.io/badge/-string-grey)![optional](https://img.shields.io/badge/-optional-yellow)![runtime](https://img.shields.io/badge/-runtime-purple): The com name of the event marker (e.g. `COM3`). If not set, it will use the `comName` set in `public/config/trigger.js`.  If the `productID` is set (not an empty string), this field will be ignored.
+- `EVENT_MARKER_PRODUCT_ID`![string](https://img.shields.io/badge/-string-grey)![optional](https://img.shields.io/badge/-optional-yellow)![runtime](https://img.shields.io/badge/-runtime-purple): The product ID of the event marker (e.g. `0487`). If not set, it will use the `productID` set in `public/config/trigger.js` if available, or attempt to connect using the com name.
+- `EVENT_MARKER_COM_NAME` ![string](https://img.shields.io/badge/-string-grey)![optional](https://img.shields.io/badge/-optional-yellow)![runtime](https://img.shields.io/badge/-runtime-purple): The com name of the event marker (e.g. `COM3`). If not set, it will use the `comName` set in `public/config/trigger.js`. If the `productID` is set (not an empty string), this field will be ignored.
 - `REACT_APP_VIDEO`![boolean](https://img.shields.io/badge/-boolean-lightgrey)![default false](https://img.shields.io/badge/default-false-yellow)![buildtime](https://img.shields.io/badge/-buildtime-blue): whether the participant is being video recorded. This can be used when the task is running as a desktop app (electron).
 - `REACT_APP_USE_EEG`![boolean](https://img.shields.io/badge/-boolean-lightgrey)![default false](https://img.shields.io/badge/default-false-yellow)![buildtime](https://img.shields.io/badge/-buildtime-blue): whether the event marker/EEG is available. This can be used when the task is running as a desktop app (electron).
 - `REACT_APP_USE_PHOTODIODE`![boolean](https://img.shields.io/badge/-boolean-lightgrey)![default false](https://img.shields.io/badge/default-false-yellow)![buildtime](https://img.shields.io/badge/-buildtime-blue): whether the photodiode is in use. This can be used when the task is running as a desktop app (electron).
@@ -31,30 +31,30 @@ Honeycomb uses environment variables during **build** and **run** time to contro
 
 - ![build time](https://img.shields.io/badge/-buildtime-blue): Build-time environment variable are configured before the application is built and cannot be changed at run-time. They are configured via `.env` files before building. Instead of using a single `.env` file, we prefer to defined separate files under the `env/` directory, and use a package called `dotenv-cli` before building`.
 
-The `dotenv-cli` comes with the `dotenv` command that can be used to properly load the needed variables. This command does not run directly from the command line (terminal). Instead, to set build-time environment variables, we need to add a  script to `package.json` with the following format:
+The `dotenv-cli` comes with the `dotenv` command that can be used to properly load the needed variables. This command does not run directly from the command line (terminal). Instead, to set build-time environment variables, we need to add a script to `package.json` with the following format:
 
 ```json
 "[build|dev]:<script name>": "dotenv -e env/<your env file> npm run [build|dev]"
 ```
 
 Honeycomb includes so scripts for common scenarios. For instance, you can run:
 
-``` console
+```console
 npm run dev:home
 ```
 
-``` console
+```console
 npm run dev:home:video
 ```
 
-``` console
+```console
 npm run dev:clinic
 ```
 
-``` console
+```console
 npm run dev:clinic:video
 ```
 
-``` console
+```console
 npm run dev:firebase
 ```

versioned_docs/version-3.0.0/setup_details.md

@@ -18,7 +18,7 @@ In addition, Honeycomb relies on Electron to package the cross-platform desktop
 
 ### Brew
 
-All of the required dependencies for honeycomb on MacOS can be installed via the brewfile. See the [quick start](quick_start.md/#installing-prerequisites-with-homebrew-for-macos) for more information.
+All of the required dependencies for honeycomb on MacOS can be installed via the brewfile. See the [quick start](quick_start.md#installing-prerequisites-with-homebrew-for-macos) for more information.
 
 ### Manual Installation (MacOS)
 
@@ -59,7 +59,7 @@ Running `choco install chocolatey.config` is the equivalent of calling `choco in
 
 ### Python on Windows (pyenv)
 
-Installing and managing Python on Windows is a notoriously difficult task even for advanced developers. It is best practice to have exactly 1 tool for managing python on your system, which is a rule for most things in software development (this is what [npm](quick_start.md/#3-install-npm-packages) does for node packages). **We highly recommend uninstalling Python and using pyenv even if you never anticipate using python again.** We promise the extra setup today will pay great dividends in the future!
+Installing and managing Python on Windows is a notoriously difficult task even for advanced developers. It is best practice to have exactly 1 tool for managing python on your system, which is a rule for most things in software development (this is what [npm](quick_start.md#3-install-npm-packages) does for node packages). **We highly recommend uninstalling Python and using pyenv even if you never anticipate using python again.** We promise the extra setup today will pay great dividends in the future!
 
 First and foremost, turn off both Python App Installers in the "App Execution Aliases" settings. **Please complete this step even if you already have a Python manager**
 

versioned_docs/version-3.1.x/environment_variables.mdx

@@ -5,7 +5,7 @@ title: Environment Variables
 description: Overview of environment variables used by Honeycomb
 ---
 
-Honeycomb uses environment variables during **build** and **run** time to control the different configurations. Below we list the environment variables used by the app and indicate their properties via badges and text. Optional variables are labeled with the ![optional](https://img.shields.io/badge/-optional-yellow) badge and mandatory variables are labeled with the ![default <default-value>](https://img.shields.io/badge/default-<defaultvalue>-yellow) badge with their default value specified. The ![buildtime](https://img.shields.io/badge/-buildtime-blue) badge indicates the variable is used during the build/compilation phase (`npm build`) while the ![runtime](https://img.shields.io/badge/-runtime-purple) badge indicates the variable is used during the executable run (`npm run dev`).
+Honeycomb uses environment variables during **build** and **run** time to control the different configurations. Below we list the environment variables used by the app and indicate their properties via badges and text. Optional variables are labeled with the ![optional](https://img.shields.io/badge/-optional-yellow) badge and mandatory variables are labeled with the ![default `<default-value>`](https://img.shields.io/badge/default-<defaultvalue>-yellow) badge with their default value specified. The ![buildtime](https://img.shields.io/badge/-buildtime-blue) badge indicates the variable is used during the build/compilation phase (`npm build`) while the ![runtime](https://img.shields.io/badge/-runtime-purple) badge indicates the variable is used during the executable run (`npm run dev`).
 
 ### Dev Mode Only
 
@@ -27,12 +27,10 @@ Honeycomb uses environment variables during **build** and **run** time to contro
 
 ## Understanding Build-Time and Run-Time Variables
 
-
 - ![runtime](https://img.shields.io/badge/-runtime-purple): Run-time environment variables allow for quick changes before running the task. They are convenient since they don't require building a whole different executable. For a Desktop Application, these are set at the system level and must be available at the time where the task runs. See [this tutorial for OS specific instructions.](https://www.imatest.com/docs/editing-system-environment-variables/#Windows). For a Firebase Application, these must be stored in the Firestore.
 
 - ![build time](https://img.shields.io/badge/-buildtime-blue): Build-time environment variables are configured before the application is built and cannot be changed at run-time. They are configured via `.env` files before building. Instead of using a single `.env` file, we prefer to define separate files under the `env/` directory, and use a package called `dotenv-cli` before building`.
 
-
 The `dotenv-cli` comes with the `dotenv` command that can be used to properly load the needed variables. We write our npm scripts with the following format:
 
 ```json title="package.json"

versioned_docs/version-3.1.x/quick_start.mdx

@@ -7,7 +7,6 @@ description: Quick start guide for Honeycomb
 
 import Tabs from "@theme/Tabs";
 import TabItem from "@theme/TabItem";
-import CodeBlock from "@theme/CodeBlock";
 import cloneCodeButton from "./assets/clone-code-button.webp";
 import nvmrc from "./assets/nvmrc.png";
 import workflowPermissions from "./assets/workflow-permissions.png";
@@ -170,9 +169,9 @@ NVM (Node Version Manager) is a tool for installing and using multiple versions
         value="mac"
         label="macOS"
       >
-        <CodeBlock language="sh">
-          curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.4/install.sh | bash
-        </CodeBlock>
+        ```shell 
+        curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.4/install.sh | bash
+        ```
       </TabItem>
     </Tabs>
 

versioned_docs/version-3.2.x/quick_start.mdx

@@ -7,7 +7,6 @@ description: Quick start guide for Honeycomb
 
 import Tabs from "@theme/Tabs";
 import TabItem from "@theme/TabItem";
-import CodeBlock from "@theme/CodeBlock";
 import cloneCodeButton from "./assets/clone-code-button.webp";
 import nvmrc from "./assets/nvmrc.png";
 import workflowPermissions from "./assets/workflow-permissions.png";
@@ -170,9 +169,9 @@ NVM (Node Version Manager) is a tool for installing and using multiple versions
         value="mac"
         label="macOS"
       >
-        <CodeBlock language="sh">
-          curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.4/install.sh | bash
-        </CodeBlock>
+        ```shell 
+        curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.4/install.sh | bash
+        ```
       </TabItem>
     </Tabs>
 

versioned_docs/version-3.3.x/quick_start.mdx

@@ -5,7 +5,6 @@ title: Quick Start
 description: Quick start guide for Honeycomb
 ---
 
-import CodeBlock from "@theme/CodeBlock";
 import TabItem from "@theme/TabItem";
 import Tabs from "@theme/Tabs";
 
@@ -188,9 +187,9 @@ NVM (Node Version Manager) is a tool for installing and using multiple versions
         value="mac"
         label="macOS"
       >
-        <CodeBlock language="sh">
-          curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.4/install.sh | bash
-        </CodeBlock>
+        ```shell 
+        curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.4/install.sh | bash
+        ```
       </TabItem>
     </Tabs>
 

versioned_sidebars/version-1.1.0-sidebars.json

@@ -1,59 +1,58 @@
 {
-    "version-1.1.0/someSidebar": [
-      {
-        "collapsed": true,
-        "type": "category",
-        "label": "Overview",
-        "items": [
-          {
-            "type": "doc",
-            "id": "version-1.1.0/intro"
-          },
-          {
-            "type": "doc",
-            "id": "version-1.1.0/folders"
-          }
-        ]
-      },
-      {
-        "collapsed": true,
-        "type": "category",
-        "label": "HowTo",
-        "items": [
-          {
-            "type": "doc",
-            "id": "version-1.1.0/quick_start"
-          },
-          {
-            "type": "doc",
-            "id": "version-1.1.0/version_control"
-          },
-          {
-            "type": "doc",
-            "id": "version-1.1.0/ci"
-          },
-          {
-            "type": "doc",
-            "id": "version-1.1.0/configuration"
-          },
-          {
-            "type": "doc",
-            "id": "version-1.1.0/event_triggers"
-          },
-          {
-            "type": "doc",
-            "id": "version-1.1.0/online_integration"
-          },
-          {
-            "type": "doc",
-            "id": "version-1.1.0/troubleshooting"
-          },
-          {
-            "type": "doc",
-            "id": "version-1.1.0/npm_scripts"
-          }
-        ]
-      }
-    ]
-  }
-
+  "someSidebar": [
+    {
+      "collapsed": true,
+      "type": "category",
+      "label": "Overview",
+      "items": [
+        {
+          "type": "doc",
+          "id": "intro"
+        },
+        {
+          "type": "doc",
+          "id": "folders"
+        }
+      ]
+    },
+    {
+      "collapsed": true,
+      "type": "category",
+      "label": "HowTo",
+      "items": [
+        {
+          "type": "doc",
+          "id": "quick_start"
+        },
+        {
+          "type": "doc",
+          "id": "version_control"
+        },
+        {
+          "type": "doc",
+          "id": "ci"
+        },
+        {
+          "type": "doc",
+          "id": "configuration"
+        },
+        {
+          "type": "doc",
+          "id": "event_triggers"
+        },
+        {
+          "type": "doc",
+          "id": "online_integration"
+        },
+        {
+          "type": "doc",
+          "id": "troubleshooting"
+        },
+        {
+          "type": "doc",
+          "id": "npm_scripts"
+        }
+      ]
+    }
+  ]
+}

versioned_sidebars/version-2.x-sidebars.json

@@ -1,17 +1,17 @@
 {
-  "version-2.x/someSidebar": [
+  "someSidebar": [
     {
       "collapsed": true,
       "type": "category",
       "label": "Overview",
       "items": [
         {
           "type": "doc",
-          "id": "version-2.x/intro"
+          "id": "intro"
         },
         {
           "type": "doc",
-          "id": "version-2.x/folders"
+          "id": "folders"
         }
       ]
     },
@@ -22,39 +22,39 @@
       "items": [
         {
           "type": "doc",
-          "id": "version-2.x/quick_start"
+          "id": "quick_start"
         },
         {
           "type": "doc",
-          "id": "version-2.x/version_control"
+          "id": "version_control"
         },
         {
           "type": "doc",
-          "id": "version-2.x/firebase"
+          "id": "firebase"
         },
         {
           "type": "doc",
-          "id": "version-2.x/ci"
+          "id": "ci"
         },
         {
           "type": "doc",
-          "id": "version-2.x/configuration"
+          "id": "configuration"
         },
         {
           "type": "doc",
-          "id": "version-2.x/event_triggers"
+          "id": "event_triggers"
         },
         {
           "type": "doc",
-          "id": "version-2.x/online_integration"
+          "id": "online_integration"
         },
         {
           "type": "doc",
-          "id": "version-2.x/troubleshooting"
+          "id": "troubleshooting"
         },
         {
           "type": "doc",
-          "id": "version-2.x/npm_scripts"
+          "id": "npm_scripts"
         }
       ]
     }