is a template I can use out of the box by just dropping in my content and configurations, rather than designing or building myself
is not feature-poor. I want it to have features like footnotes, jump-to-section links, citations, on-hover pop-ups for citations or footnotes, syntax highlighting for code blocks, etc.
nice to have: ability to draw basic graphs or diagrams (helps in technical explanations)
is not too difficult to customize by editing the code directly, Customizing the looks, structure, or adding functionality if I needed
Programming language doesn't matter much. I can use whatever. I do have a preference for functional languages.
Eleventy seems like a great framework to do this, but as I said I want a template that's ready out of the box not just a framework. The blogging template I found for eleventy does not look as nice as I hope.
Have used Hugo, and I don't really know what you mean by 'not very easy to customize client side code'. Hugo works with 'themes', which you can either download online, or create yourself. Customizing CSS, JS and even the HTML structure can easily be done by modifying/patching said theme.
+1... Started using Zola and built on top of it to learn scss, javascript, and HTML. All that extra building was not required for a running site but was still a great learning experience.
I also enjoyed Zola. Ended up switching off of it, but I think it's a great way to directly jump into writing content. The only reason I switched off was because I wanted more control than it would provide, but for most cases, I think it's completely fine.
I don't know a good template, but whatever you choose make sure it uses Markdown for the post format. Markdown was originally designed for exactly your use case. The Daring Fireball blog has been using Markdown for 20 years now.
There are variants of markdown, and I'd go with Github Flavoured Markdown which has all the features you require and has quite a few improvements over the original spec:
For the few things it can't do, like embedding graphs — Markdown is a superset of HTML, meaning that arbitrary HTML is valid Markdown. You could, for example, use D3.js.
Personally I would also use GitHub as my distribution method. Write your posts in any text editor, push to GitHub, and then a GitHub action triggers an action that re-generates the HTML and publishes your site.
That approach will work well and if it ever stops working well you can easily move part of your system to something else without reinventing the entire thing.
Hugo with a simple theme like book or paper should do it. Alternatively Jekyll or Docusaurus, in principle they're all the same in that they process markdown files and dump out a static site.
Astro for a more feature rich "development" experience.
Framework-wise, I really like Astro. They have some themes you can explore here.
I'm not sure if any themes support charts, graphs, and diagrams out of the box, but they use remark and rehype to convert markdown to html, so you could look for a rehype plugin to do it and add it to your config if you want. For example, you could try using rehype-mermaid to generate diagrams using mermaid.