[HN Gopher] Quarto: A scientific and technical publishing system...
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Quarto: A scientific and technical publishing system built on
Pandoc
Author : nonfamous
Score : 130 points
Date : 2022-01-23 01:44 UTC (21 hours ago)
(HTM) web link (quarto.org)
(TXT) w3m dump (quarto.org)
| [deleted]
| csdvrx wrote:
| Very interesting!
|
| For replicable research, in uni I once built interactive
| visualizations from a R studio source that contained the data +
| the code but that resulted in multiple outputs (html embedding
| the R notebook and markdown files, Microsoft Word, PDF...)
|
| Technically, it was quite simple, but it enabled interesting
| usecases: I could send my homework to my professor in an easily
| readable format, but if he wanted to dig deeper, he could also
| check I did everything right, and he could also alter the data to
| check if it kept working: using the html file, he just had to
| click to the source notebook at the bottom to start tweaking.
|
| It would be wonderful if scientific publishing moved to something
| like that, where the publication would be a subset (ex: Word
| output) of a process that everyone could inspect and alter.
|
| Of course, as datasets are becoming the most valuable ingredient
| in a big soup, I fear this will take a while to happen.
|
| BTW op: your dynamic examples like
| https://htmlpreview.github.io/?https://github.com/quarto-dev...
| are not working in my browser (Edge)
| jjallr wrote:
| Thanks for the heads-up re: Edge! All of those should be
| working now.
| marsa wrote:
| > It would be wonderful if scientific publishing moved to
| something like that, where the publication would be a subset
| (ex: Word output) of a process that everyone could inspect and
| alter.
|
| > Of course, as datasets are becoming the most valuable
| ingredient in a big soup, I fear this will take a while to
| happen.
|
| even though it would be wonderful, having worked in this
| industry i don't see it ever moving to such a system of
| communication (not on any significant level at least).
|
| publishers are a middleman too deeply entrenched to simply cut
| out, and anything resembling a threat to their status will get
| bought out under the guise of 'look we're innovating here' and
| then die a slow silent death.
| csdvrx wrote:
| You don't threaten them, you join them by creating a journal
| like PLoS, fully open access - let's call it "Replicable
| Science".
|
| Require a viral license (like the GPL) for all published
| content, to ensure derivate work using either the data or the
| code must also be made available under similar conditions but
| for both the data and the code, with a clause allowing
| publication to non-open access journals provided that the
| data and the code of the preprint is published on a sister
| journal (let's call it "Replicable Science Reprints") say 1
| month after the publication to the non-open access journal.
|
| If you manage to reach an impact factor high enough to
| incentivize would-be author to submit to this journal, it
| would be quite hard to kill!
|
| Also, the citations would increase the IF over time, by sheer
| virtue of being open access, and encouraging derivative work.
| thangalin wrote:
| Of related interest is my Typesetting Markdown series (skip to
| the later parts to see R and annotations):
|
| https://dave.autonoma.ca/blog/2019/05/22/typesetting-markdow...
|
| I've been working on an editor that can interpolate string
| variables to replace those scripts:
|
| https://github.com/DaveJarvis/keenwrite/blob/master/docs/scr...
|
| Many Markdown publishing systems put YAML headers into Markdown
| documents, which feels like mixing presentation with content.
| With KeenWrite you can do: keenwrite -i
| filename.Rmd -o filename.pdf -v variables.yaml
|
| Meaning, if you wanted to apply a different set of values, you
| can supply a different file, without having to modify the R
| Markdown source. (Of course, you can always write shell scripts
| to concatenate the YAML header prior to processing.)
| civilized wrote:
| Promising idea.
|
| It's worth noting that, in RStudio + RMarkdown, you can already
| mix different languages in chunks.
|
| But for those who would rather not work in RStudio, maybe this
| will be appealing.
| jjallr wrote:
| Hi there, member of Quarto team here. Quarto is actually being
| created by the same core group that created R Markdown. It's
| essentially the same idea but implemented in a cross-language
| fashion. I should also note that it is designed to be highly
| compatible w/ existing formats (you can render nearly all R
| Markdown documents as well as Jupyter Notebooks unmodified w/
| Quarto).
| salamandersauce wrote:
| So is the main difference instead of using the R markdown
| package to compile a PDF or whatever you use a standalone
| tool? I'm not quite sure what cross-language means here I
| guess. Does Quarto also offer more beyond what R markdown
| does in functionality? A quick glance at your site didn't
| show anything but I didn't look too hard TBH.
| jjallr wrote:
| The idea is that we've separated running computations into
| pluggable "engines" (whereas in R Markdown everything was
| hard-coded to use R/Knitr). In Quarto we can use Knitr, or
| Jupyter, or Observable JS (and can add additional engines
| in the future). R Markdown was a tool created exclusively
| for R users whereas Quarto is for users of any language
| that want to create reproducible documents with
| Pandoc/markdown.
| civilized wrote:
| This is all great. It's high time we supplemented Jupyter
| with a plain text language-agnostic format. Jupyter is a nice
| notebook but falls short of an effective format for
| shareable, reproducible, collaborative research.
| sterlinm wrote:
| This looks amazing. I've already got a number of projects in mind
| for this.
|
| It seems like since this is a standalone executable it should
| play nicely with different environments as long as those
| environments have the components needed for that engine. I'm
| thinking about how this would integrate with multiple different
| Conda environments.
| jtbayly wrote:
| Does anybody know if there is any relationship between this
| project and Rbookdown?
| jjallr wrote:
| Yes, it's being created by the same group that created R
| Markdown / Bookdown. Similar concept but implemented in a
| cross-language fashion rather than being tied to R.
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