Weave.jl – Scientific Reports Using Julia • Hacker News Board

Weave.jl – Scientific Reports Using Julia

#1

Post by phillc73 » Thu, Feb 04, 2021, 1:49 PM UTC

Weave.jl – Scientific Reports Using Julia
weavejl.mpastell.com

Re: Weave.jl – Scientific Reports Using Julia

#2

Post by mark_l_watson » Thu, Feb 04, 2021, 2:01 PM UTC

Weave looks great! Integrating dev and publishing.

Re: Weave.jl – Scientific Reports Using Julia

#3

Post by likelybear » Thu, Feb 04, 2021, 2:39 PM UTC

I'm a big fan of Weave/knitr/Rmd style notebooks over Jupyter for reproducibility. I've had a great experience with parameterized Weave.jl reports.

My one complaint is that a streamlined dev workflow depends on good caching. knitr nailed that part, checking code hashes and checking dependencies between chunks. Weave.jl caching has been... finicky.

For a completely different style of notebook, folks should check out Pluto.jl https://github.com/fonsp/Pluto.jl

Re: Weave.jl – Scientific Reports Using Julia

#4

Post by junippor » Thu, Feb 04, 2021, 2:47 PM UTC

I use Julia and used to use Python. I've used jupyter lab for both (although for Julia I prefer Atom for IDE)

What is the advantage of Weave.jl over jupyter lab? Is this just a way of integrating something "like jupyter" into Atom?

Re: Weave.jl – Scientific Reports Using Julia

#5

Post by phillc73 » Thu, Feb 04, 2021, 3:15 PM UTC

junippor wrote: post #4

I use Julia and used to use Python. I've used jupyter lab for both (although for Julia I prefer Atom for IDE) What is the advantage of Weave.jl over jupyter lab? Is this just a way of integrating something "like jupyter" into Atom?

It's a way to write scientific reports, or other documents integrating Julia code chunks, from inside your current IDE (Juno, VSCodium etc). There's no need for an external server, like Jupyter. The code execution relies on the IDE's REPL and the locally installed instance of Julia. The reports can be exported to various formats - HTML, PDF etc.

In the R ecosystem it's similar to using RMarkdown.

Re: Weave.jl – Scientific Reports Using Julia

#6

Post by mhh__ » Thu, Feb 04, 2021, 3:34 PM UTC

On the subjects of reports, it would be fun to have a system that parses the LaTeX and forcibly stops you deleting a plot from what generated it.

I sometimes want to scream when watching the practices we get taught for doing "programming" in academia, there's just no standard of trying to do thing right.

Re: Weave.jl – Scientific Reports Using Julia

#7

Post by TobySKT » Thu, Feb 04, 2021, 3:49 PM UTC

Great article!

Re: Weave.jl – Scientific Reports Using Julia

#8

Post by aseerdbnarng » Thu, Feb 04, 2021, 3:53 PM UTC

Genuinely nice. If you do need to mix and match languages in a single document knitr/Rmarkdown has support for the most popular languages including Julia https://bookdown.org/yihui/rmarkdown/language-engines.html and that’s working nicely for me.

Re: Weave.jl – Scientific Reports Using Julia

#9

Post by cbkeller » Thu, Feb 04, 2021, 3:56 PM UTC

I use this to format all the assignment handouts for my intro-to-programming-in-Earth-sciences class. Has worked great so far.

Re: Weave.jl – Scientific Reports Using Julia

#10

Post by arnavs » Thu, Feb 04, 2021, 4:01 PM UTC

I use this stack. One extension I wrote is https://github.com/quantecon/instantiatefromurl.jl, to bind generated notebooks to Julia TOML (i.e. Julia's `requirements.txt`) that lives in a git repo. This means they don't depend on local machine state, so can move and run freely.