Contribution Instructions

Contribution Instructions#

Step 0: Formatting Check#

Follow these tips to make sure your project notebook looks great:

  • The top of the notebook should be a Markdown cell with # Informative title here. The title you choose will appear on the class website table on contents. Choose a title that is concise and exciting.

  • Under the title, write **Prepared by:** Your name (xyz@nd.edu, 2023) you may optionally make your name a hyperlink to your GitHub profile (recommended). If you edited an existing notebook, write **Prepared by:** Prof. Alexander Dowling, Your name (xyz@nd.edu, 2023).

  • Review the tutorial on creating publication quality plots.

  • Follow the guidelines on code formatting.

  • Organize your notebook with sections ## and subsections ###. Unless really neccessary, do not have subsubsections ####, as this looks ugly on the website.

  • Read your notebook carefully for grammar and spelling. Optionally, you can try this experimental spell checker.

  • If you are creating class excerises, put the solutions (in a code cell) between the comments ### BEGIN SOLUTION and ### END SOLUTION. When I publish the notebooks to the website, a script will automatically remove the answer and replace it with # Your solution here.

Step 1: Create a GitHub Account#

Keep the username professional and do not include personal identifying information such as your birthday or birthyear.

Step 2: Create a Fork in GitHub#

On GitHub for the class repository, find the bottom to create a fork:

Then create a fork under your username. It is best to keep the default settings:

Step 3: Create a Branch in GitHub#

On GitHub, find the drop down box containing “Branch:”.

To create a branch, type a meaningful name such as your project description or your last names. Do not include spaces.

Step 4: Upload your .ipynb File#

First, rename your .ipynb file to contain a few descriptive words. You may use - instead of spaces. For example, Systems-Bio-Regression.ipynb.

Select your new branch from the dropdown menu. Then navigate to the /notebooks/contrib-dev folder and choose the Upload files button.

Step 5: Upload any Image Files#

First, rename any of your image files (recommended formats: .png, .jpeg, .jpg) to contain a few descriptive words. You may use - or _ instead of spaces. For example, constraint_set_visualization.png.

Select your new branch from the dropdown menu. Then navigate to the /media/contrib folder and choose the Upload files button.

Step 6: Create a Pull Request#

On the main class repository, create a pull request to merge your branch on your fork into the contributed-notebooks branch on the main class repository. After uploading the new notebook file to your branch, you should see an orange/yellow box with your branch name.

Choose Compare & pull request.

This should take you to a screen with the title Open a pull request:

Make sure you see contributed_notebooks in the base repository <– your branch name in your fork repository. Then add a descriptive comment (what did you change) and click Create pull request.

Tag @adowling2 in the comments of your pull request.

Step 7: Run JypyterBook to Publish to the Class Website#

Prof. Dowling will take care of this step.