Update PROTEUS documentation

[stuitje]

Feature description

PROTEUS needs a documentation update that:

• Implements Diataxis structure to current docs;
• Implements Zensical (instead of mkdocs);
• Adds some tutorials;
• Adds a code architecture flowchart;
• Adds a detailed API reference;
• Other things (comments welcome).

Related to Issue #421. I have decided to create one issue for this so that it can be tackled in one PR.

Relevant people

@nichollsh @timlichtenberg

[timlichtenberg]

While you're at it; could you please address these (installation instruction) suggestions? :-)
openjournals/joss-reviews#9917 (comment)

[stuitje]

While you're at it; could you please address these (installation instruction) suggestions? :-)
openjournals/joss-reviews#9917 (comment)

Yes, will do 👍

[stuitje]

PROTEUS has been updated with Zensical and a Diataxis structure since PR #654 . A tutorial, API reference and flowchart still needs to be added.

[nichollsh]

@stuitje while working on this issue, would it also be possible for you to update the description of the VULCAN installation steps. At the moment, it's at the bottom of the page, but should now probably sit within the main Install section here (ish): https://proteus-framework.org/PROTEUS/How-to/installation.html#10-install-submodules-as-editable

This is now possible because I have made VULCAN a Python package.

[nichollsh]

I am also working on getting AGNI to work with Julia 1.12 & 1.13, so we might be able to update those sections of the PROTEUS documentation too, soon. Will keep you updated.

[stuitje]

@stuitje while working on this issue, would it also be possible for you to update the description of the VULCAN installation steps. At the moment, it's at the bottom of the page, but should now probably sit within the main Install section here (ish): https://proteus-framework.org/PROTEUS/How-to/installation.html#10-install-submodules-as-editable

This is now possible because I have made VULCAN a Python package.

Sorry for the late reply; yes, I can definitely do this; however perhaps best to wait for Tim's PR?