Add developer docs

[bentsherman]

• Add the developer docs I wrote with class diagrams
• Add section headers to the docs navbar
• Add the Nextflow green to navbar

TODO:

• Add pages for remaining class diagrams

[netlify]

✅ Deploy Preview for nextflow-docs-staging ready!

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🔍 Latest deploy log	https://app.netlify.com/sites/nextflow-docs-staging/deploys/650737643ef2b30008d2f6d3
😎 Deploy Preview	https://deploy-preview-4065--nextflow-docs-staging.netlify.app
📱 Preview on mobile	Toggle QR Code... Use your smartphone camera to open QR code link.

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[bentsherman]

Look at that beautiful preview! 😄

[bentsherman]

@pditommaso can we merge this one

[marcodelapierre]

I am keen to provide an external review on the dev docs, will be on it next Monday.

[marcodelapierre]

Hi @bentsherman @pditommaso , here some comments/suggestions, from a contents perspective:

Navigation bar

• I LOVE the classification of the sections!
• I suggest moving "Plugins" from "Execution" to "Additional software"

Section Contributing -> Overview

• All links tested OK
• Class Diagrams: I suggest adding a link to the Packages section
• Building and Testing: isn't Gradle also a requirement for building?

Section Contributing -> Packages

• I haven't read everything, mostly flied over the introductory statement and the diagram
• nextflow: Nextflow and Channel still work in progress? any minimal info that can be inserted?
• nextflow.ast: please define/explain concisely "AST"
• nextflow.cache: could these (and any other type of) arrows be introduced in the main Packages page?

Hope this helps to get closer to merge ;)

[bentsherman]

That's weird, I just opened the cache page in the deploy preview and the diagram works 🤷‍♂️

[ewels]

Are we talking about this? In which case yeah, works fine for me too..

[marcodelapierre]

I can see that one fine, too, I mean the Class Diagram section (not page, sorry) inside the Overview page, docs/_build/html/developer/index.html in the built docs.

See screenshot below:

[bentsherman]

I see, well, I don't want to put a whole mermaid diagram there just to show the arrows, but I can put the equivalent code which should give some hint. They are basically the conventions used by Mermaid diagrams: https://mermaid.js.org/syntax/classDiagram.html#defining-relationship

[ewels]

Nice, preview here: https://deploy-preview-4065--nextflow-docs-staging.netlify.app/developer/index.html#class-diagrams

Note

@marcodelapierre note that the deployment preview mentioned in a comment further up continuously updates whenever a new commit is pushed, so you can just look at that rather than needing to build locally...

[marcodelapierre]

I see, well, I don't want to put a whole mermaid diagram there just to show the arrows, but I can put the equivalent code which should give some hint. They are basically the conventions used by Mermaid diagrams: https://mermaid.js.org/syntax/classDiagram.html#defining-relationship

Completely agree, a legend would do in my opinion

[marcodelapierre]

ah damn! Sorry @bentsherman , my finger slipped on the trackpad! reopening now

[marcodelapierre]

Nice, preview here: https://deploy-preview-4065--nextflow-docs-staging.netlify.app/developer/index.html#class-diagrams

Note @marcodelapierre note that the deployment preview mentioned in a comment further up continuously updates whenever a new commit is pushed, so you can just look at that rather than needing to build locally...

thanks Phil, hadn't noticed the preview feature! -- rather than rebuilding myself, I think I would had rather lazily asked Ben for a snapshot 🤣

[ewels]

@marcodelapierre - I discovered website deployment previews on PRs rather recently, and now I can't live without them; adding them to every repository I can 😆

[marcodelapierre]

I tooootally understand, from now on I won't live without them neither!!

[pditommaso]

[ewels]

@pditommaso don't make me 😢 Surely this is negated by me stripping out unnecessary CI checks? 😉

(I was about to argue that I would spend the CPU cycles building locally anyway, but I guess you're right that the web server is running constantly for us to have them).

[marcodelapierre]

ah, good point Paolo!

[pditommaso]

Ok, nice. I made a few changes in the TOC. Nice job!

[mribeirodantas]

🤩 So happy that this PR has been merged! Way to go, guys!

[marcodelapierre]

Love this, love the refreshed docs look! Great initiative @bentsherman! 🤩

[ewels]