Install Python. Quarto Render All the Things

PyData NYC 2022

Daniel Chen

Hello 👋

Munsee Lenape

Daniel Chen

@chendaniely

• Postdoctoral Research and Teaching Fellow, UBC, MDS-Vancouver

• Data Science Educator, Posit, PBC (Posit Academy)

• The Carpentries

• Author, Pandas for Everyone

Quarto

What is Quarto?

Who Would Use Quarto?

• Data Scientist
  • Jupyter Notebooks
    • Analysis
    • Reports + Documentation
• Academic
  • Papers

• Technical Writer
  • Blog
  • Website
  • Presentation
  • Book

• Quarto Gallery: https://quarto.org/docs/gallery/
• Quarto Guide: https://quarto.org/docs/guide/
• Quarto Reference: https://quarto.org/docs/reference/

Doesn’t Jupyter do that?

Julia + Python + R

Let’s talk about Jupyter Notebooks…

Joel Grus JupyterCon 2018

Jeremy Howard “I like notebooks”

What I do like about Notebooks

Daniel’s List

• Technical Writing
  • ✅ Literate programming
  • ❌ Editing JSON
• Data Science
  • More an output format than a source document
  • ✅ Great for posting code+output (e.g. a workshop)
  • ❌ Not great for source control collaborative document
• Teaching
  • ✅ nbgrader for course assignment creation + grading
  • ✅ Restart Kernel > Run All

Quarto vs Jupyter

Quarto ➡️ Jupyter

Let’s do an analysis

Load - EDA - Plot - Model

from palmerpenguins import load_penguins

penguins = load_penguins()
penguins.head()

	species	island	bill_length_mm	bill_depth_mm	flipper_length_mm	body_mass_g	sex	year
0	Adelie	Torgersen	39.1	18.7	181.0	3750.0	male	2007
1	Adelie	Torgersen	39.5	17.4	186.0	3800.0	female	2007
2	Adelie	Torgersen	40.3	18.0	195.0	3250.0	female	2007
3	Adelie	Torgersen	NaN	NaN	NaN	NaN	NaN	2007
4	Adelie	Torgersen	36.7	19.3	193.0	3450.0	female	2007

Load - EDA - Plot - Model

import pandas as pd

penguins.describe()

	bill_length_mm	bill_depth_mm	flipper_length_mm	body_mass_g	year
count	342.000000	342.000000	342.000000	342.000000	344.000000
mean	43.921930	17.151170	200.915205	4201.754386	2008.029070
std	5.459584	1.974793	14.061714	801.954536	0.818356
min	32.100000	13.100000	172.000000	2700.000000	2007.000000
25%	39.225000	15.600000	190.000000	3550.000000	2007.000000
50%	44.450000	17.300000	197.000000	4050.000000	2008.000000
75%	48.500000	18.700000	213.000000	4750.000000	2009.000000
max	59.600000	21.500000	231.000000	6300.000000	2009.000000

Load - EDA - Plot - Model

from plotnine import ggplot, aes, geom_boxplot, theme_xkcd

(
  ggplot(
    data=penguins,
    mapping=aes(x="sex", y="body_mass_g", color="species")
  )
  + geom_boxplot()
  + theme_xkcd()
)

<ggplot: (377115112)>

Load - EDA - Plot - Model

import statsmodels.formula.api as smf

penguins["sex_01"] = penguins.sex.replace({"male": 1, "female":0})
pen_no_na = penguins.dropna()

log_reg = smf.logit("sex_01 ~ body_mass_g", data=pen_no_na).fit()
log_reg.params

Optimization terminated successfully.
         Current function value: 0.595563
         Iterations 5

Intercept     -5.162542
body_mass_g    0.001240
dtype: float64

Model Ops

Isabel Zimmerman
Holistic MLOps for
Better Science

Let’s go make things

Create .qmd or .ipynb

The YAML header

---
format: html
---

---
format: html
title: Quarto Document
subtitle: Data Science!
author: Daniel Chen
toc: true
toc-deph: 3
code-overflow: scroll
code-line-numbers: true
execute: 
  echo: true
keep-md: true
keep-ipynb: true
jupyter: python3
---

• HTML Reference: https://quarto.org/docs/reference/formats/html.html

The .qmd code chunk

```{python}
#| echo: true
#| eval: true

from palmerpenguins import load_penguins

penguins = load_penguins()
penguins.head()
```

• Markdown
• Engine: {python}, {r}, etc
  • Knitr for {r}
  • Jupyter for any other block {python}, {julia}, etc
• Chunk options: #|
• Code

Make the document!

% quarto render examples/01-quarto.qmd

Executing '01-quarto.ipynb'
  Cell 1/4...Done
  Cell 2/4...Done
  Cell 3/4...Done
  Cell 4/4...Done

pandoc 
  to: html
  output-file: 01-quarto.html
  standalone: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  toc: true
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  title: Quarto Document
  subtitle: Data Science!
  author: Daniel Chen
  toc-deph: 3
  jupyter: python3
  
Output created: 01-quarto.html

Works on your existing Jupyter notebook

% quarto render examples/02-jupyter.ipynb --execute

Starting python3 kernel...Done

Executing '02-jupyter.ipynb'
  Cell 1/5...Done
  Cell 2/5...Done
  Cell 3/5...Done
  Cell 4/5...Done
  Cell 5/5...Done

pandoc 
  to: html
  output-file: 02-jupyter.html
  standalone: true
  section-divs: true
  html-math-method: mathjax
  wrap: none
  default-image-extension: png
  
metadata
  document-css: false
  link-citations: true
  date-format: long
  lang: en
  
Output created: 02-jupyter.html

Profit!

Profit more!

Shiny for Python: Interactive apps and dashboards made easy-ish

Joe Cheng

Winston Chang

Python…

Common error

$ quarto preview talk.qmd 

Starting python3 kernel...Traceback (most recent call last):
  File "/opt/quarto/share/jupyter/jupyter.py", line 21, in <module>
    from notebook import notebook_execute, RestartKernel
  File "/opt/quarto/share/jupyter/notebook.py", line 16, in <module>
    import nbformat
ModuleNotFoundError: No module named 'nbformat'
Python 3 installation:
  Version: 3.10.8
  Path: /usr/bin/python3
  Jupyter: (None)

Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter

(shivers) Happy Halloween, everybody🖤🧡🕷️🕸️ pic.twitter.com/jSYW5l7QJw

— Allison Horst (@allison_horst) October 31, 2022

Python Setup

Pyenv

Calvin Hendryx-Parker - Bootstrapping Your Local Python Environment

Anaconda

Virtual Environments

• Built-in Python 3.5+ venv
• pyenv-virtualenv plugin
• pipenv
• conda

Posit Academy

• Pyenv + pipenv

• Posit/Rstudio Minimum viable python: https://solutions.rstudio.com/python/minimum-viable-python/

UBC-MDS

• Anaconda based installation guide

Finding the binaries

• Make sure you are in the correct environment
  • which python
  • pyenv versions
• Check your Jupyter settings in Quarto
  • quarto check
• In VSCode
  • Python: Select Interpreter

The Jupyter kernel

• In your YAML:

jupyter: python3

• You do not need to “register” the kernel in your env

python -m ipykernel install --user --name myenv --display-name "Python (myenv)"

Other formats

What can you do: Gallery

https://quarto.org/docs/gallery/

How can you do: Get Started + Guide

• https://quarto.org/docs/get-started/
• https://quarto.org/docs/guide/

Share: Github

Share: Quartopub

• https://quartopub.com/

Learn more

• Tom Mock: Getting Started with Quarto workshop
• Allison Hill: The Happiest Notebooks on Earth
• Gordon Shotwell: An overview of Quarto, and Jupyter
• Mine Çetinkaya-Rundel & Julia Stewart Lowndes: Hello Quarto: Share, Collaborate, Teach, Reimagine

Try Quarto!

1. https://quarto.org/
2. Get Started (aka install)
3. Guides (Pick a project)
4. Website: quarto create-project mysite --type website
5. quarto preview mysite
6. Profit?