This thesis is written using quarto, documentation here.

The dependencies are managed with uv (installation). If uv is installed, the commands defined in the Makefile can be used:

• make show will render the HTML version of the thesis in a browser window, updated in real time as the underlying files change;
• make html will render the HTML version of the thesis as a static website;
• make pdf will render the PDF version of the thesis.
• make showp will render the revealjs version of the defense presentation.

A figure based on code can be made like:

#| label: fig-my-figure
#| fig-cap: "Caption"

# Matplotlib calls

Code execution can be controlled with the freeze argument.

Figures can be rendered optionally only when making html, see here.

Examples with figures on the side.

Alternatively, importing an existing figure can be simply achieved with the pandoc syntax:

![Caption](figure-filename.png){#fig-my-figure}

See the example here. Arbitrary-width columns and divs.

# Import dependencies
import plotly
import plotly.graph_objs as go

# Configure Plotly to be rendered inline in the notebook.
plotly.offline.init_notebook_mode()

# Configure the trace.
trace = go.Scatter3d(
    x=[1, 2, 3],  # <-- Put your data instead
    y=[4, 5, 6],  # <-- Put your data instead
    z=[7, 8, 9],  # <-- Put your data instead
    mode='markers',
    marker={
        'size': 10,
        'opacity': 0.8,
    }
)

# Configure the layout.
layout = go.Layout(
    margin={'l': 0, 'r': 0, 'b': 0, 't': 0}
)

data = [trace]

plot_figure = go.Figure(data=data, layout=layout)

# Render the plot.
plotly.offline.iplot(plot_figure)

See here. To vary the citation style see here.

• Section title: ## Title {#sec-title}
• Equation: {#eq-title} after the final $$

Example:

$$ 
e^{i \pi} + 1 = 0
$$ {#eq-euler-identity}

Example with multiple lines. Do not use the align environment!

$$ 
\begin{aligned}
e^{i \pi} + 1 &= 0 \\ 
e^{i \pi} &= -1
\end{aligned}
$$ {#eq-euler-identity}

Reference as @eq-title or [Equation @eq-title]

Generally, @citekey, [@citekey], [@citekey, some page]

To get aligned multiple lines, use the aligned environment instead of align.

All mathjax symbols: see here.

Using Unicode characters such as ☾ in equations works for HTML output, but they do not render correctly to LaTeX.

Snippet:

::: {#nte-title .callout-note collapse="true"}
##### Title

Text
:::

where note can be substituted by warning, important, tip or caution, see the docs.

Info here.

See the tables documentation.

Simple example:

import astropy.units as u
from IPython.display import Markdown

x = 10 * u.m

Markdown(f'The value of $x$ is {x.to_string(precision=2, format="latex_inline")}')

• even when activating the link-citations: true option in the document yaml, the citations do not appear as links in the pdf output (but they do in the html output)

• Tips and tricks
• Code execution and caching options
• HTML customization

uv run quarto render path/to/file.qmd

• press g to jump to a slide number
• press o to go into "overview mode"
• press s to get the speaker view
• navigate without pauses with Alt+arrow
• press r for scroll view
• Ctrl+click to zoom
• c to get the canvas:
  • x to cycle colors
  • backspace to erase the drawing