Olivier Leroy

I am a geographer interested in all things spatial and open science!

he/him/homard

Blog: https://branchtwigleaf.com/about.html

Public Key

npub108cgmgnzu9jcued6fncevdn08c69njeam85675ehs39hhnx43tmsaj2gse

NIP-05 Address

defuneste_at_fosstodon.org@momostr.pink

Profile Code

nprofile1qqs8nuyd5f3wzevwvkayeuvkxehnudzeev7an6d02vmcgjmmen2c4acpz3mhxue69uhhyetvv9ujuerpd46hxtnfduqs6amnwvaz7tmwdaejumr0dsfacgrg

Publishing to

relay.damus.io

nos.lol

Author Public Key

npub108cgmgnzu9jcued6fncevdn08c69njeam85675ehs39hhnx43tmsaj2gse

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Last Notes

2026-10-29 23:43:48 UTC

speaking of TIL: @npub1e8h…7zjt I discover today that --search-paths[=kind] can take "exact" (default) , "prefix", or "suffix" where it build PATH depending on it. Very useful for folk using guix in foreign distro.
It is not documented everywhere so not sure if it will works with every commands but that is still pretty handy1
(https://guix.gnu.org/manual/1.5.0/en/html_node/Invoking-guix-package.html#index-search-paths-1)

2026-09-11 16:05:31 UTC

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100% outlook is so bad that it make teams look good ... WSL and plain notepad are my best MS products

2026-09-10 12:59:14 UTC

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true that it is exhausting and we are also playing in that "attention economy" ... we definitely need to be more on "build my stuff and not paying to your shit show.." bit that is hard...

2026-08-14 15:48:17 UTC

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I think you (sadly) underestimate the number of user that also use the same python that the one within their OS ...
@npub1e8h…7zjt

2026-08-05 12:48:55 UTC

RE: https://mastodon.social/@AltTextHealthCheck/117017130190251455
#fosstodon we can do better!
#note1k85…rdr7

2026-08-04 19:57:24 UTC

#rstats I inherited a script with 25 call to gc(). Is that still needed? Where should I read about it outside the doc?

2026-08-03 17:12:22 UTC

Happy Bday Pandoc!
https://pandoc.org/twenty-years-of-pandoc.html
Very interesting blog to read:
> I decided to use Haskell, and then decided to write a document converter in it.
> Thus, a project that started out as nothing more than the product of procrastination was nurtured by the joy of writing in Haskell and by its increasing usefulness for my own academic work.

2026-07-28 00:38:01 UTC

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I have plenty of similar questions!
https://fosstodon.org/@defuneste/116975251735106302
#note125y…dgtt

2026-07-27 17:02:47 UTC

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cool glad you also knew someone!

2026-07-24 13:44:51 UTC

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I am quite curious ir (lol)!
I think the tool is useful and my guts was telling me we need (#rstats) some kind of similar tool that is not "slap a package on it".
It seems the tool lives in the "shell layer" at that point when should you consider going straight to nix/guix ?

2026-07-24 12:55:44 UTC

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I feel the same ... (also libraraies)

2026-07-22 14:30:01 UTC

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I will stole that expression!

2026-07-22 14:26:42 UTC

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what is "more participatory" ? Should it equate to an empowering tool?

2026-07-21 15:47:27 UTC

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This was for @npub1ju9…m3zj tutorial and i mostly wanted to quickly track stuff so not a real project and more for dev. purposes (side note I should get some PID and PPID when trying to grok concurrent R stuff :blobthinkingeyes: ).
"fixing" environment while following a tutorial was a bit challenging since also at first I was one version behind with an R package.
As I said I am mostly a guix toddler playing with wooden toys in a relatively safe play mat :)

2026-07-21 15:21:00 UTC

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on that case I wanted htop (definitely in guix), realized it was on my "user" profile but not in the project profile.
I can add it to the project profile but at that time I realized for a lot of projects I rely on generic tools like htop and that I should "organize" that. Still procrastinate on improving my workflow (and writing about it ..).

2026-07-21 15:11:56 UTC

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I think it is a good workflow if you want to just have the project dependencies but I usually want some stuff like the usual shell tools.
I think you do not need that since those tools for you will be managed by Arch.

2026-07-21 12:55:01 UTC

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yeah i tend to do terminal + emacs (one day we will have quarto build in guix ...).
I am still a guix toddler (cute but not efficient), I failed using your workflow and considering "layering guix profiles" instead (like described in futurile blog post).

2026-07-21 12:36:40 UTC

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Resist :)

2026-07-16 13:00:09 UTC

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oh I am
jealous!! can you take some pictures of "dancing trees"?

2026-07-07 21:28:30 UTC

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yes I also "manage" emacs&co with guix which was a pain while switching between profiles. I am considering "merging" /combining manifest now 🤷‍♂️

2026-07-07 20:56:01 UTC

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20 GB with guix gc -c ... I also need to improve here (but i try to use less and less apt).

2026-06-15 19:06:34 UTC

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the first one took me the weekend to digest:)
I have no opinion or any skills related to how a project workflow should be implemented (also R has no module 😅 so we simplified some of it, or not) and was fine with the "hack" for projects = profile
but yes I was "seduced" by the idea of having something more integrated at the project lvl

2026-06-15 18:10:58 UTC

@npub1e8h…7zjt have you see the post comparing nix and guix? (before it get removed by the author) I did not know about flakes but it seems your workflow is close to it and for "dumb" users like me could use something similar at the project level (by similar single entry points not relying on some direnv/shell tricks, not that those tricks are bad)

2026-06-10 19:43:01 UTC

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dput() is quite nice for sharing small reprex

2026-05-02 14:30:26 UTC

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I have also not tried a project that need some services also, I might do that soone.

2026-05-02 14:29:11 UTC

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no big problem, I have emacs and git on "my" profile. I loaded it in the project. Instead I should consider either having git from the package manager of the OS.
I usually also use .envrc for credentials so I might source another file from it.
None of that is "big issue", I feel guix has a lot of different way of doing similar idea and we night need to find a "good" opinionated way.

2026-05-01 23:31:14 UTC

RE: https://fosstodon.org/@defuneste/116501764536500708
so far it it surprisingly easy, I went with @npub1e8h…7zjt direnv "path" instead of the approach from the cookbook.
Opening a beer.
#note13df…7f66

2026-05-01 22:50:50 UTC

Ok, it is Friday, I have some beers, kids are fed (but not in bed). I am setting a up a specific project with guix. The project will need tons of crap: duckdb, uv and snake and maybe something too look like an object storage!

2026-04-16 16:05:31 UTC

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coffee is for you! (hope you can repair the framework!!)

2026-04-16 12:58:31 UTC

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oh I may need that!

2026-04-08 01:06:38 UTC

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No ambiguity I am just sloowww (and like to understand) !

2026-04-08 00:59:22 UTC

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I am slowly reaching the level to understand your blog :)

2026-04-08 00:34:11 UTC

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guix is a functional package manager, you can use it in gha since most of your action probably run in linux (it will prob be slower than getting binary but I could be wrong). I hope it gave us some unified way of managing environment.

2026-04-07 13:39:33 UTC

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I am still unclear if i want to go the guix path for that (and do not if It will be correct) but always good to have other options!

2026-03-04 22:49:39 UTC

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yes this is def one of the issues were people start going "R6"

2026-03-04 20:53:40 UTC

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I am on the fence with that, I think it is easier to let a user than generate the list and them maybe convert to yaml (but I could be wrong).

2026-03-04 20:10:44 UTC

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the type issue that think Norway (NO) is false.
But yeah, I do not get why "persistent" data should be some yaml, json is not that bad (and in my use case a list in .R totally fine)

2026-03-04 20:03:11 UTC

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let me have a Norway problem and over engineering it!

2026-03-04 19:31:03 UTC

I am that close to use a config file as an argument instead of a simple list! #rstats send coffee!

2026-02-25 17:01:19 UTC

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it was my fault for not being clear! at least I got some good other grep use cases :)

2026-02-25 15:26:58 UTC

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My bad, my question was why not having line number a default. I am adding -n all the time

2026-02-25 15:08:44 UTC

what are the case when you are using grep and do not want lines number?

2026-02-18 14:36:03 UTC

RE: https://mstdn.social/@fpianz/116090511117501606
bookmarking!
#note1yuc…hyun

2026-02-17 02:23:35 UTC

Ok important question: How the f. do you pronounce SSH'ing ?

2026-01-12 21:23:00 UTC

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oh! you can change the list while operating on it!

2026-01-12 21:11:26 UTC

#Rstats teach me something: why do we need foreach() when we have lapply()? What do I miss?

2026-01-04 00:21:36 UTC

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I am still a total beginner here but I like that you can have multiple "channels"

2026-01-04 00:19:10 UTC

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I will nerd snipe you on that :) I can write the more beginner stuff blog post 😉 I was just about documenting my totally noob test on guix (hence why I needed quarto). I feel guix can simplify a lot of overhead.
In some way I am "discovering" that quarto has a lot of dependencies (which obv. has perks and downsides).

2026-01-04 00:13:56 UTC

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this is really helpful -> https://packages.guix.gnu.org/search/ but it can "convert" package name: R packages use dot and not -
https://packages.guix.gnu.org/packages/r-spatstat-geom/3.6-1/ is in R "spatstat.geom"

2026-01-04 00:07:27 UTC

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yup worked, it need other packages so I am going to use guix this time to install them and see

2026-01-04 00:06:46 UTC

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yup no issue here, R can get knitr it seems something from quarto cli, I run `quarto check` and it seems fine now, still unclear if it is because I installed some package in a "classic" R ubuntu path or if that an effect of quarto check

2026-01-03 23:57:00 UTC

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in my "user" profile

2026-01-03 23:37:06 UTC

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quarto do not find knitr (and more). R libpath seems correct.

2026-01-03 22:47:15 UTC

I have started a fight to install some basic #Rstats libraries in #guix in the core place that is the "store" so far I am loosing the match!
(already surrender for quarto and used the binary lol)
So far it seems more on the quarto side.

2025-12-03 14:40:19 UTC

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yes similar to nix (I am following because some french researchers are using/developing it). @npub1e8h…7zjt did a nice introduction about it with direnv.

2025-12-03 14:25:50 UTC

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Understands!
Then I might bother you are about GUIX package manager? Did you look into it?

2025-12-03 14:04:11 UTC

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do you have a post on why not r2u?
(thanks for clarifying for fedora, I should distro hoppes into it to learn it more!)

2025-12-03 13:25:11 UTC

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I do not have any idea of Posit client OS distribution. Would fedora users more likely to use cran2copr or simply prefer building from source? (I am on Ubuntu and either build from source or use r2u).

2025-11-23 14:02:49 UTC

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to much stuff but good luck!

2025-11-13 03:31:12 UTC

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I was under some rocks to not know about direnv!

2025-11-12 13:39:42 UTC

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Perfect! thanks!

2025-11-12 13:34:14 UTC

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a bit too afraid of switching from ubuntu "confy" and my laptop is too old to run some VM and test (yes 4GB of ram is a lot for me). Hopefully soon I will be able to get a "new" one and then I will gic into Guix!
Thanks for documenting your experience! (will save me a lot if troubles)

2025-11-07 12:54:06 UTC

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Pretty sure you have a good finish!

2025-11-05 23:01:28 UTC

#RStats we are in Changelog last podcast as the weird one that do not pin their versions of package 🥳
https://changelog.com/podcast/665

2025-08-06 19:03:22 UTC

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ouch ...

2025-08-04 21:16:44 UTC

Hi everyone, by any chance do I know someone at NOAA fisheries? #FediHire

2025-08-01 13:49:04 UTC

spotted @npub1080…cr2f in the wild:
(footer of https://simplecss.org/demo)
https://cdn.fosstodon.org/media_attachments/files/114/953/817/606/375/883/original/af6edeb39416e3a7.png

2025-07-25 12:36:33 UTC

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we should def go back to ESS/emacs (or neovim). Sadly I do not have any time to spare on that.
I know some started resources: https://ess-intro.github.io/ while it is good I think they are far from perfect (I think a more opinionated config is a must first)

2025-05-25 12:01:36 UTC

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amazed by the colors you can get!

2025-05-19 12:34:46 UTC

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gRuix ? :P

2025-05-01 12:20:03 UTC

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my mom is on Ubuntu and yes! Disabling the notifiers help, since she did not like it at all.

2025-04-04 12:24:42 UTC

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I have not get this one but I stile watch too much YouTube. I think it plays the role of "TV I am tired" and it is bad.

2025-03-12 12:18:47 UTC

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😭 ... every thing need to be reached by car ...

2025-02-17 13:07:27 UTC

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two weeks ago I went to an R govy talks (about https://contributor.r-project.org/cran-cookbook/ ) and I learned a "poor" TA (thank you Beni Altmann!) had to review half of CRAN submissions. Given that (no money) I think CRAN is doing very well. Obv. it does not mean that it should not be improved :p

2025-02-04 01:14:31 UTC

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do you need the arrows pointing to each distributions?
if not Rmarkdown R for the distribution and LateX for annotations should works.

2025-01-14 12:52:27 UTC

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same points of view here! The goal is to build enough bridges so people realize slowly they do not need to feed billionaires and predatory practices.

2024-12-19 20:06:01 UTC

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can we have the "pedantic_coin" package (just one function):
coin <- function() {
if (rbinom(1 ,1, .5) == 0) "head" else "tails"
}

2024-11-19 17:34:53 UTC

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yup or rowsum's family

2024-11-19 16:34:19 UTC

#Rstats kind of sad (but I get why) that `+`(1, 2, 3) is not working like LISP (+ 1 2 3).
pedantic day2

2024-09-13 20:30:48 UTC

#Rstats I was in the dark, doing Regex (SQL) on a bunch of CSV that have important but messy "metadata" in their filename. Then a coworker told me, "hey why don't you rename all of those filename in R before your ingestion".
The light came in form of file.rename (and some quick and easy functions)!
syntax is file.rename(from, to)
(yes vectorized but from and to need obv to be same length)

2024-08-06 21:20:32 UTC

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it could work differently on other task view but @npub1rhf…9ku4 is pretty open and happy to get contribution for the spatial one.

2024-08-06 20:26:19 UTC

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I do not know about all the CTV but for the spatial you just post an issue or just do a PR here -> https://github.com/cran-task-views/Spatial/

2024-08-02 12:27:10 UTC

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both great read thanks! I work with csv (and tsv) daily and one point that should be added is that they work well with basic linux shell tooling, like head, cut etc..
Love also SQLite but I am not sure analysts will use it and duckDB/parquet is a real combo killer but suffer the same "curse" that SQLite maybe. Second link mentioned Python but #RStats also has good interface to both of them.

2024-08-01 15:44:15 UTC

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some are also quite "not best practices" but def "working solution"

2024-08-01 15:22:50 UTC

#Rstats an other day where I commit before saving the file (yeah I should check the diff ...) thanks: https://ohshitgit.com/#change-last-commit
editing to mention: https://maelle.github.io/saperlipopette/ for practices!