DSCI 522 Lecture 6

Reproducible reports

Sky Sheng

📜 Recap from non-interactive scripts

Recap: What is __main__?

__name__ is a special built-in variable in Python. The value of __name__ depends on how the Python file is being executed:

  • When you run the script directly: _name__ == “main”
  • When you import the script as a module: __name__ == the module’s name (filename without .py)

Try it out yourself! 👩‍💻

Let’s use the same repostiory as we have been using in the past 2 lectures:

  1. Clone the repository if you have not yet done so:
git clone https://github.com/skysheng7/DSCI522_data_validation_demo.git
  • If you already cloned this repository last time, please git pull to get the latest updates.

  1. You can open this folder with any IDE or your choice. You do not neccessarily need to do docker compose up to launch the container.

  2. Go to the scripts directory, and run the main_test.py script.

  3. Run the import_main_test.py script.

  4. Observe the outputs.

Run the scripts and observe how __name__ changes depending on how the script is being executed.

main_test.py script

print(f"__name__ is: {__name__}")

def my_function():
    print("Hello from my_function!")

if __name__ == "__main__":
    print("Running as main script")
    my_function()

import_main_test.py script

import main_test

Today’s topic: Reproducible reports

What You See Is What You Get (WYSIWYG) editors

Do you have any complains with Microsoft Word documents? 😅

Reproducible reports powered by code

  • You are very familiar with R Markdown & Jupyter already.

  • You might have used LaTeX in the past.

  • Today we will talk about Quarto! All of the slides, website you have seeen in this course are built with Quarto!

    • Why we use Quarto over LaTeX? 🤔

Converting Jupyter Notebooks to Quarto

  1. Install quarto in your conda environment if you have not yet done so.
conda install quarto
  • Note: Please remember to redo conda lock of your enviornment, rebuild docker image after instaling quarto.
  • If you are running things locally, you may need to manually convert your conda enviornment to jupyter kernel:
python -m ipykernel install --user --name <conda_env_name> --display-name "Python (<conda_env_name>)"
  1. Convert your Jupyter Notebook to Quarto.
quarto convert notebook.ipynb

👩‍💻 Quarto demo

We will use this repository to demo Quarto today: https://github.com/UBC-MDS/dsci-522-individual-assignment-quarto-python

  • Quarto in RStudio
  • Quarto in VSCode

Tips for M3

Scripts:

  • At least 4 scripts, living in a folder with reasonable name (e.g., scripts).
  • README should document exactly how to run each in command line (in sequence).
  • All scripts should run, no error, no warning.
  • All output (e.g., plots, tables, artifacts) should be saved by code in the script.
  • Well organized, broken down into smaller scripts. Well documented, consistent namiing and documentation style.

Tips for M3

Reports:

  • No value should be hard-coded in the report.
  • All plots should be rendered properly, with proper size, font size, etc.
  • No code should be visible in the final rendered report.

Reproducibility:

  • Anyone with no knowledge of docker should be able to reproduce your results based on instructions in your README file.

🎯 Milestone grading policy update

  • In week 4, you will get the chance to make changes based on TA’s feedback. You will be able to get 50% of the points back for each question you lost marks for through M1-M3.

⭐️ Good luck with M3!