keenwrite VS Zettlr

> like font face, font size, horizontal and vertical element positioning and line spacing, etc.

May I recommend ConTeXt?

For my purposes, KeenType was only meant to provide a real-time "rough draft" of equations rendered inside of KeenWrite[0], my FOSS Markdown editor. That is, I edit in Markdown, then KeenWrite converts the inline TeX-based equations for previewing. When I'm ready to create a "finished" product, KeenWrite exports the Markdown to XHTML then feeds the XHTML, along with a theme, to ConTeXt[1]. The various themes[2] are where font faces sizes, alignment, kerning, etc. are tweaked. In this way content remains completely separated from presentation.

[0]: https://github.com/DaveJarvis/keenwrite

[1]: https://wiki.contextgarden.net/Main_Page

[2]: https://github.com/DaveJarvis/keenwrite-themes

KeenWrite[0], the FOSS Markdown text editor I’ve been working on, includes the ability to render plain text diagrams via Kroki[1]†. See the screenshots[2] for examples. Here’s a sample Markdown document that was typeset[3] using ConTeXt[4] (and an early version of the Solare[5] theme).

One reason I developed KeenWrite was to use variables inside of plain text diagrams. In the genealogy diagram, when any character name (that’s within the diagram) is updated, the diagram regenerates automatically. (The variables are defined in an external YAML file, allowing for integration with build pipelines.)

Version 3.x containerizes the typesetting system, which greatly simplifies the installation instructions that allow typesetting Markdown into PDF files. It also opens the door to moving Kroki into the container so that diagram descriptions aren’t pushed over the Internet to be rendered.

†Kroki, ergo KeenWrite, supports BlockDiag (BlockDiag, SeqDiag, ActDiag, NwDiag, PacketDiag, RackDiag), BPMN, Bytefield, C4 (with PlantUML), Ditaa, Erd, Excalidraw, GraphViz, Nomnoml, Pikchr, PlantUML, Structurizr, SvgBob, UMLet, Vega, Vega-Lite, and WaveDrom.

Note that Mermaid diagrams generate non-conforming SVG[6], so they don’t render outside of web browsers. There is work being done to address[7] this problem.

[0]: https://github.com/DaveJarvis/keenwrite

[1]: https://kroki.io/

[2]: https://github.com/DaveJarvis/keenwrite/blob/main/docs/scree...

[3]: https://pdfhost.io/v/4FeAGGasj_SepiSolar_Highlevel_Software_...

[4]: https://wiki.contextgarden.net/Main_Page

[5]: https://github.com/DaveJarvis/keenwrite-themes/

[6]: https://github.com/mermaid-js/mermaid/issues/2485

[7]: https://github.com/yuzutech/kroki/issues/1410

KeenWrite leverages KeenWrite Themes to change how documents are presented. The Tarmes theme is an example of a very basic theme, meant to act as a base for making new themes. Take a look at Tarmes, which is probably the closest answer to your question. Feel free to add issues against the issue tracker or add questions to the discussion area.

My editor, KeenWrite allows typesetting of TeX, as shown in its screenshots. The reason I developed the editor to be TeX-based is because there are other TeX implementations besides LaTeX. One of them is ConTeXt.

It'll help build cross-platform desktop applications. In theory, it'll mean hooking the build process up to a GitHub action to build platform-specific binaries, such as my FOSS KeenWrite Markdown editor[0], without having to have a copy of every operating system.

To my knowledge, cross-compiling "native" Linux and Windows binaries using Java requires duct tape, chewing gum, and warp-packer.[1]

GraalVM isn't a panacea, though.[2] For example, GraalVM cannot compile Renjin, a pure Java R interpreter, so you have to switch from Renjin to FastR. Switching isn't trivial.

[0]: https://github.com/DaveJarvis/keenwrite

[1]: https://dave.autonoma.ca/blog/2020/06/29/write-once-build-an...

[2]: https://github.com/bedatadriven/renjin/issues/564

> Nevertheless, I would prefer a Markdown-based system

My free, cross-platform desktop Markdown editor, KeenWrite[1], integrates with the ConTeXt typesetting software[2]. I'm working on a branch[3] to make integration containerized[3] because its installation is painful. KeenWrite limits math to plain TeX[4] so that the output can be rendered using any TeX-based typesetter (ConTeXt, LaTeX, MathJax, εχTEX, etc.).

Here's a sample document typeset using ConTeXt (skip to page 40 for the math):

https://pdfhost.io/v/4FeAGGasj_SepiSolar_Highlevel_Software_...

That document theme is called Solare[8].

> that can use CSS and MathML

Adding CSS mixes presentation logic with content, which is something KeenWrite strives to avoid. Instead, KeenWrite implements Pandoc's annotation syntax to keep presentation logic out of the content. I've written about this extensively in my Typesetting Markdown series[5].

You can produce some pretty amazing documents just with annotations, such as the following that I wrote in Markdown and typeset using ConTeXt:

https://impacts.to/downloads/lowres/impacts.pdf

> has a 100% bibtex clone for references.

Markdown fails at references. At some point, I'd like to implement cross-references in KeenWrite. Except there's at least six competing standards for the syntax, which I've also remarked upon[6], making the choice of syntax difficult[7].

[1]: https://github.com/DaveJarvis/keenwrite

[2]: https://wiki.contextgarden.net/Installation

[3]: https://github.com/DaveJarvis/keenwrite/blob/1_typeset_using...

[4]: https://github.com/DaveJarvis/keenwrite/blob/main/docs/scree...

[5]: https://dave.autonoma.ca/blog/2020/04/28/typesetting-markdow...

[6]: https://talk.commonmark.org/t/cross-references-and-citations...

[7]: https://xkcd.com/927/

[8]: https://github.com/DaveJarvis/keenwrite-themes/tree/main/sol...

Both Obsidian and alternatives like Zettlr work well for this. Personally, I use Zettlr. It's not as polished or as feature complete as Obsidian, but it's completely open source which Obsidian is not.

https://www.zettlr.com - will have to take another look at this one.

You can try qownnotes. If you want use the zettelkasten method, I advice you to use zettlr.

If you want to use an application mainly for taking notes and occasionally store code then check out zettlr https://www.zettlr.com/

Markdown editors such as Zettlr are also gaining more useful features.

Ghostwriter, CuteMarkEd, Joplin,or Zettlr? Any of these might be worth looking at.

My other suggestion to OP would be Zettlr, which can work with files outside its workspaces. It’s a little geeky, but no more so than Atom or Obsidian, and it’s a lot more powerful than something like Typora or iA Writer. And like Obsidian and Atom, it’s free.