template-computo-python.qmd

---
title: "Template for contribution to Computo"
subtitle: "Example dedicated to `Python` users"
author:
  - name: Jane Doe
    corresponding: true
    email: janedoe@nowhere.moon
    url: https://janedoe.someplace.themoon.org
    orcid: 0000-0000-0000-0000
    affiliations:
      - name: Name of Affiliation one
        department: Statistics
        url: https://someplace.themoon.org
  - name: John Doe
    email: johndoe@nowhere.moon
    url: https://johndoe.someplace.themoon.org
    orcid: 0000-0000-0000-0000
    affiliations:
      - name: Name of Afficiliation two
        department: Computer Science
        url: https://someplace.themoon.org
date: last-modified
date-modified: last-modified
description: |
  This document provides a template based on the [`quarto`](https://quarto.org/) system for contributions to Computo, using the [`quarto journal extension`](https://github.com/computorg/computo-quarto-extension), the Jupyter kernel (Python user) and `venv+pip` to set-up the dependencies.
abstract: >+
  Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur posuere vestibulum facilisis. Aenean pretium orci augue, quis lobortis libero accumsan eu. Nam mollis lorem sit amet pellentesque ullamcorper. Curabitur lobortis libero eget malesuada vestibulum. Nam nec nibh massa. Pellentesque porttitor cursus tellus. Mauris urna erat, rhoncus sed faucibus sit amet, venenatis eu ipsum.
keywords: [key1, key2, key3]
citation:
  type: article-journal
  container-title: "Computo"
  doi: "xxxx"
  url: https://computo.sfds.asso.fr/template-computo-quarto
  publisher: "Société Française de Statistique"
  issn: "2824-7795"
bibliography: references.bib
github-user: computorg
repo: "template-computo-python"
draft: true # set to false once the build is running
published: false # will be set to true once accepted
format:
  computo-html: default
  computo-pdf: default
jupyter: python3
---

# Introduction

## About this document

This document, accompanied by the [customized GitHub repository](https://github.com/computorg/template-computo-python/), provides a template for writing contributions to **Computo** [@computo]. We show how `Python` code can be included and how the repository can be set up for triggering GitHub actions for rendering the document, with dependencies handled by `venv` and `pip`.

## Setup a GitHub repository for preparing your submission

You can start by clicking on the **"use this template"** button, on the top of the page of the [github repository associated with this document](https://github.com/computorg/template-computo-python/). Of course, you can set your repository private during the preparation of your manuscript.

## Quarto

[Quarto](https://quarto.org/) is a versatile formatting system for authoring documents integrating markdown, LaTeX and code blocks interpreted either via Jupyter or Knitr (thus supporting Python, R and Julia). It relies on the [Pandoc](https://pandoc.org/MANUAL.html) document converter.

## Requirements

You need [quarto](https://quarto.org/docs/get-started/) installed on your system and the [Computo extension](https://github.com/computorg/computo-quarto-extension) to prepare your document. For the latter, once quarto is installed, run the following to install the extension in the current directory (it creates an `_extension` directory which is ignored by git thanks to `.gitignore` by default):

```.bash
quarto add computorg/computo-quarto-extension
```

[`Python`](https://www.python.org/) and [`Jupyter`](https://jupyter.org/install) must be installed on your computer.

## Link with your usual tools

Quarto is expecting a `.qmd` markdown file, but will also works with a standard [Jupyter notebook](https://quarto.org/docs/get-started/hello/jupyter.html) file if you are used to it (it will just require to add the proper YAML metadata^[the same metadata as in the [`template-computo-python.qmd` file](https://github.com/computorg/template-computo-python/blob/main/template-computo-python.qmd) in the first cell, type "Raw", of the notebook]).

**Note**: _More advanced Jupyter-related functionality like Myst/Jupyter book are not supported in this Quarto setup. The markdown syntax inside the Jupyter notebook should follow the Quarto syntax (c.f. [below](#formatting)). If you are more comfortable with using Myst/Jupyter book, we provide a [specific template](https://github.com/computorg/template-computo-myst) but it will requires more formatting work for Computo editorial team, thus highly encourage authors to use the Quarto templates._

# Formatting

This section covers basic formatting guidelines for quarto documents.

To render a document, run `quarto render`. By default, both PDF and HTML documents are generated:

```.bash
quarto render template-computo-python.qmd # renders both HTML and PDF
```

::: {.callout-tip}
## Note

To check the syntax of the formatting below, you can use the `</> source` button at the top right of this document.
:::

## Basic markdown formatting

**Bold text** or _italic_

- This is a list
- With more elements
- It isn't numbered.

But we can also do a numbered list

1. This is my first item
2. This is my second item
3. This is my third item

## Mathematics

### Mathematical formulae

[LaTeX](https://www.latex-project.org/) code is natively supported[^lualatex], which makes it possible to use mathematical formulae:

[^lualatex]: We use [lualatex](https://lualatex.org/) for this purpose.

$$
f(x_1, \dots, x_n; \mu, \sigma^2) =
\frac{1}{\sigma \sqrt{2\pi}} \exp{\left(- \frac{1}{2\sigma^2}\sum_{i=1}^n(x_i - \mu)^2\right)}
$$

It is also posible to cross-reference an equation, see @eq-mylabel:

$$
\begin{aligned}
D_{x_N} & = \frac12
\left[\begin{array}{cc}
x_L^\top & x_N^\top \end{array}\right] \,
\left[\begin{array}{cc}  L_L & B \\ B^\top & L_N \end{array}\right] \,
\left[\begin{array}{c}
x_L \\ x_N \end{array}\right] \\
& = \frac12 (x_L^\top L_L x_L + 2 x_N^\top B^\top x_L + x_N^\top L_N x_N),
\end{aligned}
$$ {#eq-mylabel}

### Theorems and other amsthem-like environments

Quarto includes a nice support for theorems, with predefined prefix labels for theorems, lemmas, proposition, etc. see [this page](https://quarto.org/docs/authoring/cross-references.html#theorems-and-proofs). Here is a simple example:

::: {#thm-slln}
## Strong law of large numbers

The sample average converges almost surely to the expected value:

$$\overline{X}_n\ \xrightarrow{\text{a.s.}}\ \mu \qquad\textrm{when}\ n \to \infty.$$
:::

See @thm-slln.

## Python Code

Quarto uses either Jupyter or knitr to render code chunks. This can be triggered in the yaml header. In this tutorial, we use `Jupyter`  (`Python` and `Jupyter` must be installed on your computer).

``` yaml
---
title: "My Document"
author "Jane Doe"
jupyter: python3
---
```

`python` code chunks may be embedded as follows:

```{python python-code}
import numpy as np
x = np.random.normal(0, 1, 10)
x
```

## Figures

Plots can be generated as follows:

```{python stem-plot}
#| label: fig-stem-plot
#| fig-cap: "A basic Stem plot"

import matplotlib.pyplot as plt
import numpy as np

x = np.linspace(0.1, 2 * np.pi, 41)
y = np.exp(np.sin(x))

plt.stem(x, y)
plt.show()
```

It is also possible to create figures from static images:

:::{#fig-logo}

![](https://computo.sfds.asso.fr/assets/img/logo_text_vertical.png){height=200}

Computo logo (label)
:::


## Tables

Tables (with label: `@tbl-mylabel` renders @tbl-mylabel) can be generated with markdown as follows

| Tables   |      Are      |  Cool |
|----------|:-------------:|------:|
| col 1 is |  left-aligned | $1600 |
| col 2 is |    centered   |   $12 |
| col 3 is | right-aligned |    $1 |
: my table caption {#tbl-mylabel}

## Handling references {#sec-references}

### Bibliographic references

References are displayed as footnotes using
[BibTeX](http://www.bibtex.org/), e.g. `[@computo]` will be displayed
as [@computo], where `computo` is the bibtex key for this specific
entry. The bibliographic information is automatically retrieved from
the `.bib` file specified in the header of this document (here:
`references.bib`).

### Other cross-references

As already (partially) seen, Quarto includes a mechanism similar to the
bibliographic references for sections, equations, theorems, figures,
lists, etc. Have a look at [this
page](https://quarto.org/docs/authoring/cross-references.html).

## Advanced formatting

Advanced formatting features are possible and documented (including interactive plots, pseudo-code, (Tikz) diagrams, Lua filters, mixing R + Python in the same document), but are beyond the scope of this simple introduction. We point several entries in this direction.

::: {.callout-warning}
## More information

- [The Quarto web site](https://quarto.org) for comprehensive documentation, including:
  + [Tutorial](https://quarto.org/docs/get-started/)
  + [User guide](https://quarto.org/docs/guide/)
  + [Options reference](https://quarto.org/docs/reference/)

- [The template distributed with the Computo Quarto extension](https://computo.sfds.asso.fr/computo-quarto-extension/), which uses such advanced features.

- [Our mock version of the t-SNE paper](https://computo.sfds.asso.fr/published-paper-tsne/), a full and advanced example using Python and the Jupyter kernel.

- [The previously published papers in Computo](https://computo.sfds.asso.fr/publications/) can be used as references.

:::

# Finalize your submission

## Handle `Python` dependencies with `venv`

To make your work reproducible, you need to fix the packages and environment used to run your analysis. For `Python`, `venv` is one of the possible reliable method, supported by the community. You basically need a couple of commands to setup your environment on your local machine. First, to create a new virtual environment in the directory `my_env`

``` .bash
python3 -m venv my_env
```

and activate it

``` .bash
source my_env/bin/activate
```

Then installed the packages required to perform your analysis. Here,

``` .bash
python3 -m pip install jupyter matplotlib numpy
```

Once you are all set up, you need to save your working environment into a file so that anyone can reproduce your analysis on their side:

``` .bash
python3 -m pip freeze > requirements.txt
```

The corresponding `requirements.txt` file [found in this repository](https://github.com/computorg/template-computo-python/blob/main/requirements.txt) is then

```{.bash filename="requirements.txt"}
jupyter
matplotlib
numpy
```

::: {.callout-important}
`requirements.txt` is the only file that needs to be versioned by git.
:::

More details for using `venv` and `pip` can be found on the [quarto page dedicated to environments](https://quarto.org/docs/projects/virtual-environments.html#using-venv).

### What about `conda`?

For `conda` users, it is also possible to follow the same path with your favorite version of `conda`. There is a [quarto page dedicated to the conda environments](https://quarto.org/docs/projects/virtual-environments.html#using-conda).

## Continuous integration

The repository associated with this template is pre-configured to trigger an action on push that performs the following:

1. Check out the repository on an `ubuntu-latest` machine
2. Install quarto and dependencies, including the Computo extension
3. Install Python (3.10) and dependencies with `venv`, using your `requirements.txt` file
4. Render your .qmd file and Publish the results on a gh-page (both HTML and PDF)

The file [.github/workflows/build_n_publish.yml](https://github.com/computorg/template-computo-python/blob/main/.github/workflows/build_n_publish.yml) is largely inspired from [this file](https://quarto.org/docs/publishing/github-pages.html#example-jupyter-with-venv).

Once this is successful, you are ready to submit your manuscript to the [Computo submission platform](https://computo.scholasticahq.com/).

::: {.callout-warning}
The first time, you possibly need to create the branch for the action to work. This can be done by running the following command from your computer, in your git repository:

```.bash
quarto publish gh-pages
```

Then, set the branch `gh-page` as the source of your github page, and trigger the action to check that everything works fine.
:::

### What about CI and `conda`?

[The build and deploy process of our Computo quarto extension](https://github.com/computorg/computo-quarto-extension/blob/main/.github/workflows/build.yml) shows how `miniconda` can be set used in place of `venv`. The main striking difference is the use of a `environment.yml` file in place of `requirements.txt`.

## Data and large files

If your submission materials contain files larger than 50MB, **especially data files**, they won’t fit on a git repository as is. For this reason, we encourage you to put your data or any materials you deem necessary on an external “open data” centered repository hub such a [Zenodo](https://zenodo.org/) or [OSF](https://osf.io/).

# References {.unnumbered}

::: {#refs}
:::