[Feature] Mermaid and graphviz diagrams

[sneakers-the-rat]

Fix: openjournals/joss#1281
Builds on:

• Add missing dependencies #45
• Update default template for pandoc>=3.1.7 #46

Add support for graphviz and mermaid diagrams using https://github.com/pandoc-ext/diagram

• Vendored lua plugin bc no clean way to include it otherwise and i hate using submodules
• symlinked to filters directory
• added to default filters
• configured to enable/diable diagram engines consistent with security recs in source repo
• added deps to dockerfile
• wrote examples in example/paper.md

Works in the tex, html, and jats formats

eg. PDF:

Also added an example of how to include a highlighted code block because i thought it was weird we didn't have one

(Again sorry for non-modular PR, couldn't get the code to run otherwise)

[tarleb]

Thank you! I'm not sure yet about #45, but the other PRs look good. I'm holding off a little longer, as we should also update the pandoc version in the docker container, which is proving a bit more difficult than expected.

[sneakers-the-rat]

Thoughts on this? I rebased and the test is now failing for a reason that is totally mysterious to me.

Looks like it's not this PR: https://github.com/openjournals/inara/actions/runs/9450955436/job/26030778792

[tarleb]

Looking good. I still have some reservations, mostly because of the tremendous size of the mermaid-cli tool: it requires a full browser to be installed in the docker image, making the image more difficult to use for people with bad/limited internet connections.

CC @arfon, I'd be interested to hear your take on this.

As for the test failures: yes, that's just a problem with the test workflow: the login and push actions should only run on the main branch. Otherwise they'll fail due to insufficient permissions.

[sneakers-the-rat]

the tremendous size of the mermaid-cli tool:

oops, ya you're right. there's gotta be a smaller tool than that, mermaid.js is like 3MB. i'll take a look

the login and push actions should only run on the main branch.

I guess that's the next fix then :) but there also seems to be a failure in the pdf build that looks unrelated? like a latex error? and it started happening in other PRs too recently

[tarleb]

I've opened #70 to keep track of the PR issue.

[arfon]

Definitely would be cool so support this so thanks for the contribution here @sneakers-the-rat! Did you manage to find a smaller Docker image to support this?

[sneakers-the-rat]

now that i'm thinking about this again, i think we'll also want version pinning, especially re: mermaid. maybe we can do both things at once - i wonder if there is a way to peek at the yaml frontmatter when making the docker image? and if we did that we could see if a given doc uses a particular dependency. I think we'll want to do this generally if we want to do flexible document formatting (which i think would be a lovely goal), so let me take a look at that, unless y'all know of a way already :)