Questions to ask to organize workflow

this is a real cell that i can evaluate.

• How many data scientists are working on one problem?

• Different data sources and problems? Different git repositories.

• Less than 10 data scientists working on the same data but different problems? Same git repository.

• More than 10 data scientists working on the same data but different problems? Different git repositories.

• Where is the data hosted?

  • Local laptop?

  • Consider just doing your own Jupyter Notebook server locally.

  • Server?

  • Can be accessed via SSH? Jupyter server running on server that you SSH tunnel into.
  • Consider JupyterHub.

How to organize the work into two kinds of Notebooks

• Laboratory
• Deliverable

Lab Notebooks

• Keeps a historical record of the analysis explored

• Meant to be a development or scratch place

• Each notebook is controlled by a single Data Scientist

Lab Notebooks

• Split the notebooks when they get too long (turn the page)

• Split the notebooks by topic if it makes sense.

Deliverable Notebooks

• Any Notebook that will be referenced in the future.

• How raw data was transformed into cleaned data.

• The fully polished and final outputs of the analysis.

Deliverable Notebooks

• Peer reviewed via pull requests (other members will review before accepted).

• These notebooks are controlled by the whole Data Science team.

Get organized -- High level directories

• data # Backed up outside of version control
• deliver # Final polished Notebooks for consumption
• develop # Lab Notebooks stored here
• figures #
• src # Scripts/modules stored here

Name the lab-notebooks with the following convention:

• [ISO 8601 date]-[DS-initials]-[2-4 word description].ipynb
• 2015-11-21-JBW-coal-predict-RF-regression.ipynb

Name the lab-notebooks with the following convention:

• [ISO 8601 date]-[DS-initials]-[2-4 word description].ipynb
• 2015-11-21-JBW-coal-predict-RF-regression.ipynb

Name the lab-notebooks with the following convention:

• [ISO 8601 date]-[DS-initials]-[2-4 word description].ipynb
• 2015-11-21-JBW-coal-predict-RF-regression.ipynb

Version Control

How do you peer review code and store analysis in version control?

Further constraints:

• Project manager who wants to see notebooks but doesn't want to install IPython
• Not using Github which renders figure diffs nicely
• Want to review the Python code itself

My Answer

• Each Data Scientist has their own dev branch
• Work is saved and pushed on dev branch daily
• When ready to merge to master, pull request

What to commit?

• .ipynb
• .py
• .html

of all Notebooks (develop and deliver).

• and figures

Benefits

• Record of analysis including dead-ends
• Ability to easily peer review analysis and dead-ends
• Project managers can easily see and read the analysis with GitHub .ipynb or .html without installing ipython

Final organization thoughts

• Organization of workflows in teams is difficult
• Having some standards is better than none
• Sometimes the "wrong thing" exactly solves a problem
• Storing output figures
• Having rendered .html files in commits
• Open to new ideas -- have a better method let me know!

For static slides:

jupyter nbconvert my_r_notebook.ipynb --to slides --post serve

For interactive "live" slides:

https://github.com/damianavila/RISE