[HN Gopher] Weave.jl - Scientific Reports Using Julia
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Weave.jl - Scientific Reports Using Julia
Author : phillc73
Score : 115 points
Date : 2021-02-04 13:49 UTC (9 hours ago)
(HTM) web link (weavejl.mpastell.com)
(TXT) w3m dump (weavejl.mpastell.com)
| arnavs wrote:
| 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.
| TobySKT wrote:
| Great article!
| mark_l_watson wrote:
| Weave looks great! Integrating dev and publishing.
| aseerdbnarng wrote:
| 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.
| snicker7 wrote:
| Org-mode can also do the trick.
| likelybear wrote:
| 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
| sp33der89 wrote:
| Why would one chose Pluto over say Weave or the other way
| around?
| tfehring wrote:
| Genuinely curious, what makes Weave and Pluto "completely
| different" styles of notebook? Is there some reason that Pluto
| features like interactivity and reactivity couldn't be
| incorporated in Weave, at least in theory? I get that they
| focus on different problems, but based on how R Markdown is
| often used in practice, it seems like there's a lot of overlap
| between the two problem spaces.
| mhh__ wrote:
| 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.
| 3JPLW wrote:
| Lots of the sciml.ai packages and documentation use Weave -- you
| can look there for some examples. Here's one:
|
| https://diffeq.sciml.ai/stable/tutorials/sde_example/
| cbkeller wrote:
| I use this to format all the assignment handouts for my intro-to-
| programming-in-Earth-sciences class. Has worked great so far.
| junippor wrote:
| 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?
| phillc73 wrote:
| 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.
| fn-mote wrote:
| Generic advantages:
|
| - no binaries in your source code make git diff more useful
|
| - continue to use your favorite editor especially if you don't
| like the notebook interface and keybindings
|
| - batch mode can be good or bad, people might not like it as
| much for exploratory analysis but prefer it when they have a
| lot of writing to do and want to polish "later"
| junippor wrote:
| > no binaries in your source code make git diff more useful
|
| Oh damn that's a good one. Thanks for pointing it out.
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