quarto-to-wiki.qmd

# Quarto to wiki introductions and examples
Based on this page: https://quarto.org/docs/publishing/confluence.html

Use this link when asked where to put you page:
https://scilifelab.atlassian.net/wiki/spaces/EBT/pages/2899836938/Quarto+examples

Give the page a name on this format with your name to make it unique: "Quarto_example-Tomas"

## Short introduction on how to render quarto documents directly to the wiki (and how to to it on uppmax)
Per (reviewer Mahesh) 

## Whole projects 

Pixi was used to create the quarto environment.
```{.bash}
pixi init -c conda-forge -c bioconda
pixi add quarto jupyter ipyleaflet plotly pandas statsmodels jupyter-cache
```

Quarto was then used to create a confluence project.

```{.bash}
pixi shell
quarto create project confluence .
```

The quarto project created can be seen at https://github.com/mahesh-panchal/quarto-confluence-project.
The aim was to add a varied selection of quarto markup and interactive elements as well as raw output.

This was then published to Confluence using:

```{.bash}
quarto publish confluence
```

where I was asked to provide the domain `https://scilifelab.atlassian.net`, followed by
my username, an API token (A link to the page was provided to create one), and finally
the url path to where I wanted to publish `https://scilifelab.atlassian.net/wiki/spaces/EBT/pages/2902917121/Quarto+example+-+Mahesh`.
As I was unsure if I would overwrite the work of others I created this page first after 
quarto indicated the folder didn't exist.

I was also instructed by quarto to 
```{.bash}
quarto install chromium
```

At this point Quarto began rendering, but hung at the second page. The issue 
was localised to creating the mermaid diagram. After converting the
mermaid diagram to a code block `{{.mermaid}}` the project sucessfully published 
to confluence.

Several things didn't render although might be achievable in other ways:

- Mermaid diagram rendering failed locally and didn't upload as an image.
- Interactive plotting failed. Perhaps this needs to be embedded as an attachment.
- Interactive map did not produce any kind of map, even a static image.
- References did not work.
- Column layout did not work.

## Quarto document 
Verena (reviewer Jason): `Training-Tech-shorts/quarto-to-wiki/quarto-example-verena/quarto-example-verena.qmd`

## Quarto document 
Cormac (reviewer Guilherme)

## Quarto document  
Jason (reviewer Martin)

## Quarto document  
Guilherme (reviewer Per)

## Quarto document  
Martin (reviewer Verena)