Rename index.md to README.md

README.md

@@ -8,7 +8,7 @@
 ## Welcome and Installation Guide
 
 Welcome to the project! This is a Data Science Master's Capstone at Harvard University's Extension School, in collaboration with NOAA.
-Please see here for project setup and installation: [Setup](docs/setup.md).
+Please see here for project setup and installation: [Setup](https://noaa-hes-capstone.github.io/icedyno/setup/).
 
 <p align="center">
   <img src="https://upload.wikimedia.org/wikipedia/en/thumb/8/89/ExtensionFlag.png/170px-ExtensionFlag.png" alt="NOAA Logo", width="200"/>

docs/index.md

@@ -4,41 +4,3 @@
 
 Welcome to the project!
 This is a data science Master's capstone through Harvard University's Extension School, in collaboration with NOAA.
-
-## Documentation
-Mkdocs is the documentation engine that takes hand-written markdown files to a project website.
-Please read more at https://www.mkdocs.org/.
-
-Mkdocstrings is a mkdocs extension that allows autogenerated documentation to be made, by scraping type hints and documentation strings for any python modules within the project.
-
-### Building and serving the documentation commands
-
-* `mkdocs new [dir-name]` - Create a new project.
-* `mkdocs serve` - Start the live-reloading docs server.
-* `mkdocs build` - Build the documentation site.
-* `mkdocs -h` - Print help message and exit.
-
-### Documentation files layout
-
-    mkdocs.yml    # The configuration file.
-    docs/
-        index.md  # The documentation homepage.
-        ...       # Other markdown pages, images and other files.
-
-#### Add a new page or subpage
-To add a new page, in `mkdocs.yml` add the page (or subpage) by:
-```
-site_name: IceDyno Documentation
-
-nav:
-  - Home: index.md
-  - Setup: setup.md
-  - New Page: newpage.md
-    - New SubPage: newsubpage.md
-    - ...
-```
-
-#### Autogenerate documentation for an IceDyno module
-
-Add to a markdown file something like this:
-`::: icedyno.preprocess`

docs/setup.md

@@ -1,7 +1,10 @@
 # Setup
-To get started, clone the repo, checkout this branch, using Linux or Mac install pixi with:  
+To get started, clone the repo, checkout this branch, using Linux install pixi with:  
 ```curl -fsSL https://pixi.sh/install.sh | bash```
 
+For Mac, install via homebrew with
+```homebrew install pixi```
+
 If using windows, install pixi with:  
 ```iwr -useb https://pixi.sh/install.ps1 | iex```
 
@@ -48,3 +51,43 @@ You'll see that the `pixi.toml` and `pixi.lock` files will change after adding y
 
 ## Removing a dependency
 ```pixi remove package_name```
+
+
+# Documentation
+Mkdocs is the documentation engine that takes hand-written markdown files to a project website.
+Please read more at https://www.mkdocs.org/.
+
+Mkdocstrings is a mkdocs extension that allows autogenerated documentation to be made, by scraping type hints and documentation strings for any python modules within the project.
+
+## Building and serving the documentation commands locally
+
+* `mkdocs new [dir-name]` - Create a new project.
+* `mkdocs serve` - Start the live-reloading docs server.
+* `mkdocs build` - Build the documentation site.
+* `mkdocs -h` - Print help message and exit.
+
+## Documentation files layout
+
+    mkdocs.yml    # The configuration file.
+    docs/
+        images/   # Folder for storing local images for documentation, including for the README.md.
+        index.md  # The documentation homepage.
+        ...       # Other markdown pages.
+
+### Add a new page or subpage
+To add a new page, in `mkdocs.yml` add the page (or subpage) by:
+```
+site_name: IceDyno Documentation
+
+nav:
+  - Home: index.md
+  - Setup: setup.md
+  - New Page: newpage.md
+    - New SubPage: newsubpage.md
+    - ...
+```
+
+### Autogenerate documentation for an IceDyno module
+
+Add to a markdown file something like this:
+`::: icedyno.preprocess`