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For scientific notes I'm really liking Jupyter notebooks using the MyST save option. All the pluses of Jupyter as a simple text markdown format, I can commit, d

by saboot 4y ago

For scientific notes I'm really liking Jupyter notebooks using the MyST save option. All the pluses of Jupyter as a simple text markdown format, I can commit, diff, easily switch to another editor if I like

nerdponx 4y ago
It's a real shame that the "R Markdown" format never caught on, basically just Markdown with fenced code blocks that also act as runnable cells. I think RStudio really dropped the ball on marketing it outside of the R community, starting with its name (implying that it only works for R) and tying the reference implementation to R (the Knitr package). I haven't looked at MyST before, but it looks very much inspired by R Markdown (and of course without so much as a nod thereto anywhere on its website). I also wonder if it is a distinct Markdown dialect from CommonMark, or if it is a superset of CommonMark? It would be pretty cool to use MyST inside my code editor (Vim? Emacs? VS Code?) to run code blocks, essentially what R Markdown is/was. Or does that already exist? I would love to start using that instead of or in addition to notebooks. I really hate to see so much fragmentation in this space. It's just a markup language, I don't see why everyone needs to have their own special snowflake variant. It feels like everyone wants to be the one to strike it big and achieve fame and glory, and they'd rather not collaborate too much with others lest they risk losing their chance to be the big winner. Edit: I stand corrected! Yes, they directly reference R Markdown as a source of inspiration in the specification, which also states that MyST is indeed a superset of CommonMark: https://www.myst.tools/docs/spec/commonmark https://www.myst.tools/docs/spec/commonmark. I'll definitely want to try this out then, thanks for the recommendation!
- tvb12 4y ago
  I think Rstudio made a decent attempt to address that marketing problem. They introduced Quarto as a language-agnostic R Markdown. https://quarto.org/docs/faq/rmarkdown.html#quarto-sounds-similar-to-r-markdown.-what-is-the-difference-and-why-create-a-new-project https://quarto.org/docs/faq/rmarkdown.html#quarto-sounds-sim...
  - i_am_proteus 4y ago
    Quarto is great. Basically ipynb markdown plus pandoc, and so far my experiences with it have been that it Just Works.
    - nerdponx 4y ago
      How well does it work with Python or Julia as well as R? Does it support Jupyter kernels, or does it use its own system?
      - tvb12 4y ago
        It works with all three. Jupyter is supported as an "engine". Although I haven't tried, it sounds like any Jupyter kernel will work. https://quarto.org/docs/faq/#what-programming-languages-are-supported-in-quarto https://quarto.org/docs/faq/#what-programming-languages-are-...
- saboot 4y ago
  You are welcome, I only learned of it a few weeks ago and it solves a lot of problems. It's still relatively new, so while jupyter notebooks / lab support, using it inside other editors with runnable code blocks is still a work in progress. VS Code looks to have an extension for previewing the markdown, but I dont think it can run python code blocks in it (for now). I agree with you, RStudio's R Markdown feature was my favorite part about it, easily wrote my assignments for a statistics class with it. For more about MyST check out the talk I recently was introduced to it https://www.youtube.com/watch?v=A-UCO1F09M4 https://www.youtube.com/watch?v=A-UCO1F09M4
paro_nej 4y ago
FWIW, texmacs files are encoded like any other markup language. This makes it the texmacs files very easy for any git-fu.

by saboot 4y ago

nerdponx 4y ago

It's a real shame that the "R Markdown" format never caught on, basically just Markdown with fenced code blocks that also act as runnable cells. I think RStudio really dropped the ball on marketing it outside of the R community, starting with its name (implying that it only works for R) and tying the reference implementation to R (the Knitr package). I haven't looked at MyST before, but it looks very much inspired by R Markdown (and of course without so much as a nod thereto anywhere on its website). I also wonder if it is a distinct Markdown dialect from CommonMark, or if it is a superset of CommonMark? It would be pretty cool to use MyST inside my code editor (Vim? Emacs? VS Code?) to run code blocks, essentially what R Markdown is/was. Or does that already exist? I would love to start using that instead of or in addition to notebooks. I really hate to see so much fragmentation in this space. It's just a markup language, I don't see why everyone needs to have their own special snowflake variant. It feels like everyone wants to be the one to strike it big and achieve fame and glory, and they'd rather not collaborate too much with others lest they risk losing their chance to be the big winner. Edit: I stand corrected! Yes, they directly reference R Markdown as a source of inspiration in the specification, which also states that MyST is indeed a superset of CommonMark: https://www.myst.tools/docs/spec/commonmark https://www.myst.tools/docs/spec/commonmark. I'll definitely want to try this out then, thanks for the recommendation!

tvb12 4y ago
I think Rstudio made a decent attempt to address that marketing problem. They introduced Quarto as a language-agnostic R Markdown. https://quarto.org/docs/faq/rmarkdown.html#quarto-sounds-similar-to-r-markdown.-what-is-the-difference-and-why-create-a-new-project https://quarto.org/docs/faq/rmarkdown.html#quarto-sounds-sim...
- i_am_proteus 4y ago
  Quarto is great. Basically ipynb markdown plus pandoc, and so far my experiences with it have been that it Just Works.
  - nerdponx 4y ago
    How well does it work with Python or Julia as well as R? Does it support Jupyter kernels, or does it use its own system?
    - tvb12 4y ago
      It works with all three. Jupyter is supported as an "engine". Although I haven't tried, it sounds like any Jupyter kernel will work. https://quarto.org/docs/faq/#what-programming-languages-are-supported-in-quarto https://quarto.org/docs/faq/#what-programming-languages-are-...
saboot 4y ago
You are welcome, I only learned of it a few weeks ago and it solves a lot of problems. It's still relatively new, so while jupyter notebooks / lab support, using it inside other editors with runnable code blocks is still a work in progress. VS Code looks to have an extension for previewing the markdown, but I dont think it can run python code blocks in it (for now). I agree with you, RStudio's R Markdown feature was my favorite part about it, easily wrote my assignments for a statistics class with it. For more about MyST check out the talk I recently was introduced to it https://www.youtube.com/watch?v=A-UCO1F09M4 https://www.youtube.com/watch?v=A-UCO1F09M4

paro_nej 4y ago

FWIW, texmacs files are encoded like any other markup language. This makes it the texmacs files very easy for any git-fu.