project-template

A template for Jupyter Notebook based research projects. I try to describe the project goals, organization, and data here.

Notebooks: the project narrative

• *.ipynb | The core of your project narrative and analyses. TODO create template notebook Template.ipynb.

• presentation.mplstyle | My custom matplotlib stylesheet for default plot properties How to use in notebooks:

  import matplotlib.pyplot as plt
  >>> plt.style.use('presentation.mplstyle.py')
  

• environment.yml | The project virtual environment generated with conda env export --no-builds > environment.yml. I strongly recommend documenting the packages you use for analyses for the sake of reproducibility. conda is a cross-platform package manager that allows you to do so easily.

Stay organized with a couple folders

• data | Store data here. Provide instructions to access data if it's too big, sensitive, etc. and is stored somewhere else.

• plots | Save generated figures here; this way, figures can be viewed without rendering notebooks.

• scripts | I usually store bash scripts and utility functions/classes here.

References

Inspiration taken from googling many blog posts (and dealing with clutter over the years).

https://github.com/outlierbio/ob-project-template