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spestana authored Jan 26, 2024
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## Course Website

The course website ([https://mountain-hydrology-research-group.github.io/data-analysis/](https://mountain-hydrology-research-group.github.io/data-analysis/)) is hosted on [GitHub Pages](https://pages.github.com/) as a repository under the Mountain-Hydrology-Research-Group github organization, [here](https://github.com/Mountain-Hydrology-Research-Group/data-analysis). It is organized and formatted with the [jekyll-rtd-theme](https://jekyll-rtd-theme.rundocs.io/) built on top of the [rundocs.io](https://rundocs.io/) framework. See the [jekyll-rtd-theme](https://jekyll-rtd-theme.rundocs.io/) documentation for information on formatting and webpage layout.

Each webpage is created from a markdown (.md) file, which is a plain text file where formatting is specified in the [markdown](https://guides.github.com/features/mastering-markdown/) syntax. Page organization is controlled by nesting directories containing special README.md files that contain some formatting information, and by creating special headers within a document such as `## My Document Subsection Name`.
The course website ([https://mountain-hydrology-research-group.github.io/data-analysis/](https://mountain-hydrology-research-group.github.io/data-analysis/)) is hosted on [GitHub Pages](https://pages.github.com/) as a repository under the Mountain-Hydrology-Research-Group github organization, [here](https://github.com/Mountain-Hydrology-Research-Group/data-analysis). It is organized and formatted as a [Jupyter Book](https://jupyterbook.org/en/stable/intro.html).

### Getting started

1. **Log into your github account**, or create an account at https://github.com/ (Note: your account will need to be connected to the Mountain-Hydrology-Research-Group github organization)
1. **Log into your github account**, or create an account on [github](https://github.com/) (Note: your account will need to be connected to the Mountain-Hydrology-Research-Group github organization)
2. **Go to the course website repository** at https://github.com/Mountain-Hydrology-Research-Group/data-analysis
3. **Create your own [fork](https://www.earthdatascience.org/workshops/intro-version-control-git/about-forks/) of the repository**. (It is good practice to work on a separate fork, your own personal copy, of the repository while you update the website.)
4. **[Clone](https://www.earthdatascience.org/workshops/intro-version-control-git/basic-git-commands/) the repository** onto the class JupyterHub or to your personal computer. (The advantage of having a clone of the respository on the JupyterHub is to test out the jupyter notebooks for labs in the same environment students will be using.)
5. Repeat steps 2-4 with the [repository containing homework solutions](https://github.com/Mountain-Hydrology-Research-Group/data-analysis-solutions). (This is a private repository accessible only to approved users. It is not connected to the class website.)
6. **When you are ready to publish the website**, click on *Settings* (with the gear icon) in the menu at the top of the repository page. On the left side of the Settings menu, click on *Pages*. Now you need to tell GitHub to enable "Pages" and which branch you would like to publish. For the dropdown menu under *Source* make sure that "Deploy from a branch" is selected. Then used the dropdown menu under *Branch* to select the branch you want to publish (most likely this is the "main" branch), then from the new dropdown menu that appears with the folder icon, make sure that "/ (root)" is selected. This is telling GitHub where the files for your website are located. Then click "Save" and the website should be up in a few minutes.
6. **Add and Commit changes to your own fork** as you work on updating content.
7. When your own fork is now up to date with your changes, **open a [pull request](https://www.earthdatascience.org/workshops/intro-version-control-git/pull-request/)** to merge the changes from your fork into the repository under the Mountain-Hydrology-Research-Group github organization.

The website is currently published through github pages, so the following step only needs to be taken if the site was ever un-published. I am just including it here for reference. When you are ready to publish the website, click on *Settings* (with the gear icon) in the menu at the top of the repository page (the Mountain-Hydrology-Research-Group repository, not your own fork). On the left side of the Settings menu, click on *Pages*. Now you need to tell GitHub to enable "Pages" and which branch you would like to publish. For the dropdown menu under *Source* make sure that "Deploy from a branch" is selected. Then used the dropdown menu under *Branch* to select the branch you want to publish (currently this is the "gh-pages" branch), then from the new dropdown menu that appears with the folder icon, make sure that "/ (root)" is selected. This is telling GitHub where the files for your website are located. Then click "Save" and the website should be up in a few minutes.

### File organization

In your cloned respository, in the top level `data-analysis/` directory, you can find a `README.md` file (the home page of the website), and several subdirectories. Each subdirectory below here that is used for website organization needs to have a special README file with formatting information (these are already present for the existing subdirectories).
* `data-analysis/overview`, contains syllabus and project pages ("a" and "b" in the filenames are used here to sort the pages alphabetically)
* `data-analysis/modules`, each module/lab corresponds roughly to one week of the quarter. The `module#.md` files create the main page for each module with the lab and homework assignment text, while the `lab#/` folder corresponding to that modules contains the jupyter notebook files. The `data/` folder contains any data files for labs or homeworks.
* `data-analysis/resources`, jupyter and python documentation and links to other websites of interest to students learning hydrology, statistics, and programming
* `data-analysis/images` folder containing any images to embed on the website
In your cloned respository, in the top level `data-analysis/` directory, you can find a subdirectory called `book` which contains the website. Under `book` course content is organized into:
* `overview` folder, contains syllabus and project pages
* `modules` folder, each module/lab corresponds roughly to one week of the quarter. The `module#.md` files create the main page for each module with the lab and homework assignment text, while the `lab#/` folder corresponding to that modules contains the jupyter notebook files. The `data/` folder contains any data files for labs or homeworks.
* `resources` folder, jupyter and python documentation and links to other websites of interest to students learning hydrology, statistics, and programming
* `images` folder containing any images to embed on the website
* the file `_toc.yml` controls the table of contents displayed on the left side of the website

### Updating the website and Jupyter Notebooks

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