Python (and C++ and R) project management. Built on the conda dev environment, and is primarily aimed at ML, data science, scientific python.
Comes highly recommended by others.

A fairly exciting Zotero notes plugin which makes you able to create long-form notes (with an outliner), connect individual notes through links (akin to connecting knowledge fragments in a Zettelkasten), and auto-export notes as e.g. markdown files (keeping in sync with Obsidian notes or other markdown systems).

Seems like a very nice step up from the default note management!

Specifically intended to read and annotate scientific papers PDFs, with note functionality, snapshotting, LaTeX (SyncTeX, BibDesk, PDFSync) integration, export, highlight&annotation view and more.

I don't think it will replace the more keyboard-driven sioyek for me but it is a nice alternative.

Very useful spatio-temporal analysis tools within the python / jupyter ecosystem.

Can do all sorts of spatial analysis and visualization, but also more specific things like spatial inequality computation (using e.g. Theil index, Gini, ...).

Perhaps the best free and opensource audio transcription (and editing) software I have found.
Comes with a huge variety of language models and punctuation additions.

Works offline.

Free.

Good!

Open source transcription software. Does have a SaaS model but can apparently be self-hosted.

Seems really neat - auto-transcribe most of it then put it into different speaker roles and highlight low-confidence words so you can fix them.

Allows creating pandoc filters in python instead of lua.

An exhaustive guide on researching user needs (intended for products but equally applicable to other consumption-facing processes).

Very neat and condensed collection of thoughts about interview- and observation-style research.

Make awesome display tables using Python.

A really nice, simple table package and can do impressive outcomes.
Not sure if it also works for docx/pdf or just html?

A commandline tool to undertake literature reviews.

Seems a little too 'magic' for my liking to fully indulge but something similar could prove extremely powerful to future literature reviews.

Seems to be the upcoming search engine functioning similarly to Microsoft Academic.

Built to be completely open, fully available as open data, built on open technologies. Very nice.

Semantic Scholar uses groundbreaking AI and engineering to understand the semantics of scientific literature to help Scholars discover relevant research.

Semantic search, tries to imitate Microsoft Academic somewhat. Not completely open but still can be a good resource for academic queries.

Presenting a whole new perspective on research discovery services. Intelligent data and quick access to state-of-the-art insights.

Bringing mainly 'insights' but can still be useful as a scholarly query engine.

A 'simplified' bibliography reference format like bibtex or biblatex.

Uses yaml under the hood and is super simple to understand:

Doan2020:
    type: Article
    title: Kinetics and luminescence of the excitations of a nonequilibrium polariton condensate
    author: ["Doan, T. D.", "Tran Thoai, D. B.", "Haug, Hartmut"]
    doi: "10.1103/PhysRevB.102.165126"
    page-range: 165126-165139
    date: 2020-10-14
    parent:
        type: Periodical
        title: Physical Review B
        volume: 102
        issue: 16
        publisher: American Physical Society

One interesting fact is that it uses one (or multiple) 'parent' keys to signify where something is from which in turn use the same simple keys (type, title, ...) as the original document to describe themselves.
So, instead of a million individual keys to describe an entry we use a more recursive format with each having the same couple keys.
This could be really interesting for a closer papis integration with its standard yaml format for example.

Format readme here.

I am not sure how 'mature' the format is, however.
It has been created for the typst typesetting language afaik, and that is still pretty new/fluctuating as of now as well.

Alternative to mermaid, plantuml, graphviz. Can be used in quarto.

Is a single golang cli binary at the core which I much (much) prefer to the javascript-dependent client-side nature of mermaid.

Otherwise, the DSL looks competent and fairly descriptive.
Supports displaying markdown, code, images, icons, or latex formulas in the diagrams.
Could be a good choice for quick diagrams!

A new markup-based typesetting system that is powerful and easy to learn.

This is very exciting. It actually allows some fairly advanced constructs and environments but keeps its (basic) syntax at a similarly simple level such as markdown.

It even has a 'code mode' in which you can call arbitrary expressions and pass arguments just doing #myfunc(myargument:true, another: 12). And those are then programmed in typst language (which I have not looked into yet). And even most basic markup is done in those so they are definitely powerful!

Basically wants to be LaTeX 2.0-ish. Does not yet have the same advanced page-orphan algorithms etc however. Can be used in quarto from 1.4 as markup language!

An academic publishing workflow with automatic doi -> citation processing and (I think?) writing in markdown then publishing as pdf/docx/html documents.

Similar to quarto in other words, but taking a bit of a different approach. Also has a sister-repository with an AI assistant for the publishing process which seems like a neat tool to try.

Another terminal-based slide presentation tool. This one seems nice in that it simply uses markdown and every horizontal rule marks a new slide. Simple, efficient, nice.

Also has a simple guide on how to export slides to pdf on the page.

Very simple, basic functionality slide software. Has a couple of ..interesting features like

Slides with exuberant amount of lines or characters produce rendering glitches intentionally to prevent you from holding bad presentations.

but in general seems quite nice

Zotero plugin that links your Markdown database to Zotero. Jump directly from Zotero Items to connected Markdown files. Automatically tags Zotero Items so you can easily see which papers you've made notes for