iiinova — where your digital self keeps evolving

Dr Frames Catherine White @oxinabox.net · 23/09/2026

It seems there is actually no great way to do open telemetry over GitHub actions. Solutions seem to be: Kinda broken: eg setup-opentelemetry Completely nuts: eg thoth Not opentelemetry: gha_buildevents Or only run in post, so can't be traceparent of stuff running in steps. Everything else.

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Dr Frames Catherine White @oxinabox.net · 07/09/2026

I do not like been given 2+ page long reports generated by claude They violate the expectation that anything i am being asked to read took at least 2x as long to write as it will for me to read it. And documents that I can't trust not to be lying to me with a great deal of confidence hurt my brain

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Dr Frames Catherine White @oxinabox.net · 29/08/2026

Slides from my pycon-au lightning talk. "There is only one operation for which humans care about enough to implement quintuple dispatch" It's either pro-or-anti multiple dispatch I guess. (For screen reader accessible see on canva: canva.link/jg27bz1t3q5n... It's almost all text)

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Dr Frames Catherine White @oxinabox.net · 29/08/2026

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Dr Frames Catherine White @oxinabox.net · 12/08/2026

it's quiet amusing to me that LayeredLayouts.jl has 11 direct dependants (and 2 more indirect). Laying out DAGs is useful. Its why many languages implement smart heuristic algorithms for them. I did not implement a smart heuristic algorithms. I implemented the NP-Hard always optimal algorithm.

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Dr Frames Catherine White @oxinabox.net · 15/05/2026

On the maintaince of academic software there are two things I will always remember: (1/3)

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Catherine Frames @oxinabox.bsky.social · 15/05/2026

Then: "why doesn't your kinetic model have any parameters" Me: "😭they are all state😭 why does everything effect everything?😭" Them: "how's your solver doing?" My solver: 😭

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Dr Frames Catherine White @oxinabox.net · 15/05/2026

added to my startup.jl `ENV["JULIA_PKG_PRESERVE_TIERED_INSTALLED"] = "true"` so hopefully i can stop precompiling things constantly when making minor changes to dependencies a package that indirectly depends on hundreds of packages. Somethings always getting updated at that scale

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Dr Frames Catherine White @oxinabox.net · 13/03/2026

It is starting to feel like I am going to have to learn all the theory behind Hit-and-run samplers, and other MCMC / probabilistic programming stuff.

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Dr Frames Catherine White @oxinabox.net · 30/01/2026

Something I have been thinking about on and off is about the annotation of function primatives with properties, like nilpotent, associative, commutative, etc, then using (type) inference to infer this about functions built in them. Then using that for automatic parallelism and other optimisations.

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Catherine Frames @oxinabox.bsky.social · 29/01/2026

I accidentally turned on AI completion in VS-Code yesterday. And I though "_fine_, I will finally try this thing" and I am really not liking having my tab completion lie to me? I just have to check it when it doesn't work, then look up the right way. When I could have just immediately looked it up

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Dr Frames Catherine White @oxinabox.net · 19/11/2025

the amount of hatred i have for good tests that were marked "skip" because they are too slow that have bit rotted, is only exceeded by my hatred for good tests that were marked "skip" that are still good and would have caught bugs had they not been set to skip

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GomahuAzarashi @gomahuazarashi.bsky.social · 17/12/2025

I've just created a #JuliaLang package BlueskyClient.jl github.com/AtelierArith... . You can post text, images with ALT text, GIFs, and MP4 videos from the package. Give it a try!

github.com

GitHub - AtelierArith/BlueskyClient.jl: Client application for Bluesky based on AT Protocol

Client application for Bluesky based on AT Protocol - AtelierArith/BlueskyClient.jl

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Dr Frames Catherine White @oxinabox.net · 14/01/2026

this is a really cool page on all the tricks you can use to express different ideas in terms of (Mixed Integer) linear programming. Cos the whole thing is very tricky. Like the trick of splitting variables so you can have L1 regularisation which is nonlinear in naive implementation

docs.mosek.com

9 Mixed integer optimization — MOSEK Modeling Cookbook 3.4.0

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Dr Frames Catherine White @oxinabox.net · 02/12/2025

I have spent far too much time dealing with flakey tests and nondeterministic failures today

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Dr Frames Catherine White @oxinabox.net · 19/11/2025

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Dr Frames Catherine White @oxinabox.net · 11/11/2025

yes, I find i often in python I have modules that are really just one function (at least in their public API). Because it makes sense for all that to be in one file. Combined with explict imports and it makes quiet a complexity of import headers.

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Dr Frames Catherine White @oxinabox.net · 14/11/2025

does python 3 have an abstract base class for strings? I feel like it should. because for data-structures like a rope you want the string API, but you definately do not want to store it like a string, so inheriting from str is no good. en.wikipedia.org/wiki/Rope_(d...

en.wikipedia.org

Rope (data structure) - Wikipedia

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Dr Frames Catherine White @oxinabox.net · 11/11/2025

I wanted to see if I was part of the Anthropic settlement class: ✅ Book on LibGen before 2021 ✅ Book has ISBN ❎ were registered with the United States Copyright Office Alas, I am not. While my rights have obviously been violated, it is not in a way that is covered by this court case.

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Dr Frames Catherine White @oxinabox.net · 30/09/2025

So we had a model incorporating thermodynamic constrains called a ThermoModel. And another model with enzyme constraints called a GeckoModel. (Gecko = Genome-scale model Enzyme Constraints, using Kinetics and Omics.) And we were making a model to combine them. Some kind of ThermoGecko.

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Dr Frames Catherine White @oxinabox.net · 23/09/2025

I need to set julia to always run with bounds checks enabled. I have done this before. The big virtue is no more redoing precompilation between running normally and running tests. Since julia makes seperate compliation caches for the 3 different settings for bounds checks. +tests always have them on

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Dr Frames Catherine White @oxinabox.net · 13/09/2025

I made an OpenSCAD library for engraving emoji into 3D prints. github.com/oxinabox/ope...

tiles with 💂🏿,💃,🏔️,👁️, or 🖼️ engraved into them. They are shown in color. You can see the color gives different depths

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Dr Frames Catherine White @oxinabox.net · 24/08/2025

Pretty happy with this for something I designed and printed all in one day, while doing other things. It snugly fits the brace on the back of mirrors. Which has a funny bumpy shape. No more bracelets scattered over my dressing table.

A 3D printed lattice with hooks inserted.
The top fits into a brace in back of the mirror

The unadorned back of the mirror. Showing the weird bumpy brace

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Guillaume Dalle @gdalle.bsky.social · 22/08/2025

🚨 Breaking news 🚨 Two epic tutorials announced for #JuliaCon Local Paris 2025: one about Pluto notebooks and one about using JuMP for optimization. Be sure to get your tickets this week, otherwise the early bird pricing will be gone 🦜 @juliacon.bsky.social @julialang.org @pydataparis.bsky.social

A flashcard for a tutorial at JuliaCon Local Paris 2025. The speakers are Fons Van Der Plas (educational technology officer at TU Eindhoven) and Boshra Ariguib (master's student in CS at the University of Stuttgart). The title is "How to tell an interactive story with Pluto: lectures and dashboards".
The conference takes place on October 2nd and 3rd, see the website at https://juliacon.org/local/paris2025/

A flashcard for a tutorial at JuliaCon Local Paris 2025. The speaker is Benoît Legat (assistant professor at UCLouvain). The title is "Optimization with JuMP".
The conference takes place on October 2nd and 3rd, see the website at https://juliacon.org/local/paris2025/

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Dr Frames Catherine White @oxinabox.net · 03/08/2025

I ordered a 3D printer. I haven't had access to one since I left uni in 2018. And that one was ancient and temperamental.

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Dr Frames Catherine White @oxinabox.net · 03/08/2025

I should implement the same design o want to 3D print in OpenSCAD, Descartes.jl, ConstructiveGeometry.jl, ImplicitCAD and a few other programatic CADs. Then compare and contrast

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Dr Frames Catherine White @oxinabox.net · 03/08/2025

One julia thing I am coming around to after using python for a bit is explicit imports. I used to be moderately hard against it. Working out where something is from is a tooling problem that is kinda solved. But when jumping into a codebase where you are unfamiliar with the whole ecosystem...

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Dr Frames Catherine White @oxinabox.net · 03/08/2025

The 1 module per file pattern is not idiomatic Julia. I am dubious of its success in python where it is built in and required. You end up with a hell of avoiding circular dependencies. And trying to match API organisation (external) to development organisation (internal) is just messy. Long files.

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Dr Frames Catherine White @oxinabox.net · 03/08/2025

Sometimes it's fun to pick up random open source repos and contribute to them. Yesterday I picked up ConstructiveGeometry.jl Which is a Julia based OpenSCAD alternative. It's a 1 person effort not touched in 4 years, and I got it working with latest releases of its dependencies etc. and made a PR

github.com

GitHub - plut/ConstructiveGeometry.jl: Algorithms and syntax for building CSG objects within Julia.

Algorithms and syntax for building CSG objects within Julia. - plut/ConstructiveGeometry.jl

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Dr Frames Catherine White @oxinabox.net · 01/08/2025

DataStructures.jl v0.19 has been released.. Our first breaking release in 5 years. It shouldn't be too breaking if you kept up with removing deprecated calls. (For reference 0.18 has 22 patch releases which was an annoying amount of backporting to do. Might be a record for backporting) #julialang

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Dr Frames Catherine White @oxinabox.net · 12/07/2025

Biology be like: So 1 gene encodes for 1 protein right? It's 1-1. Well no, some genes are no coding. Ok so it's 1-0/1 Well no, each AA can come from multiple different codons so two different genes can technically make the same protein. Ok so many-0/1. (It gets worse though)

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Dr Frames Catherine White @oxinabox.net · 29/07/2025

I actually quite like SQL. Nice language to express things in. Though how different versions of the same query will perform is mysterious

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Dr Frames Catherine White @oxinabox.net · 12/07/2025

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Dr Frames Catherine White @oxinabox.net · 02/07/2025

Something i just said seriously at work: "How different is a human from yeast anyway? Probably not that different."

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Dr Frames Catherine White @oxinabox.net · 27/06/2025

What database normalisation rule is broken by having redundant information For example have a column for middle name and another column for middle initial. It clearly breaks some rule as they could be updated separately and end up inconsistent.

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Dr Frames Catherine White @oxinabox.net · 25/06/2025

I was away for one week and someone added a `utils` file to the code base. `utils` files are an antipattern because it's a meaningless name, an unclear grouping. (A utils folder is ok if the files have good names). And it tends to be where evil code lives. often without tests. Cos "its just utils".

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Dr Frames Catherine White @oxinabox.net · 13/06/2025

I wish github had a thing that would let me right click an item in a check-list and open a subissue with it's text as the title. And edit the original post's checklist to be a link to that subissue. That would make breaking stuff down for project management purposes much better.

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Dr Frames Catherine White @oxinabox.net · 12/06/2025

I thought Dask was supposed to be this really reliable thing, especially when using it with Coiled so I can't screw up my infrastructure. But I have been fighting it all day, of it seemingly getting to a point where it stops talking back to client...

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Dr Frames Catherine White @oxinabox.net · 12/06/2025

NetworkX allowing anything to be the nodes in graphs is solidly nicer than Graphs.jl Look how nice it is to go from a CobraPy model (a reaction network) to a (bipartite) Graph:

Screenshot of code
```
G = nx.Graph()
G.add_nodes_from(model.reactions, bipartite=0)
G.add_nodes_from(model.metabolites, bipartite=1)
for rxn in model.reactions:
for met in rxn.metabolites.keys():
G.add_edge(rxn, met)
```

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Dr Frames Catherine White @oxinabox.net · 06/06/2025

Python is a 1 based language. It's just that indexing is written as `x[-i]`. The hyphen is important! Also lists are printed backwards.

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Dr Frames Catherine White @oxinabox.net · 04/06/2025

Classic bio-data hell 🥰🥰🥰 I realised our tests depend on 5 subtly different GEMs for the ecoli core metabolism. And they can't be substituted for each other without some rework. Plus 2 for yeast, and 1 for salmonella.

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Dr Frames Catherine White @oxinabox.net · 04/06/2025

for any axis L of a convex polyhedron H a function taking a point in P and returning the cross sectional area of a slice of H is convex. similar for any direction D perpendicular to L, a function f_D(p in L) that returns the width of H in that direction D at point p, is convex. So a question:

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Dr Frames Catherine White @oxinabox.net · 30/05/2025

Inheritance was a mistake. Multiple inheritance, multiply so.

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Mehmet Hakan Satman @jbytecode.bsky.social · 28/05/2025

JOSS has now published more than 3,000 articles, and I've personally edited 60 of them (still editing +5). Being a part of JOSS has been one of the most fulfilling experiences of my life. @joss-openjournals.bsky.social #JOSS

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Dr Frames Catherine White @oxinabox.net · 29/05/2025

Anyone else with Github Teams suddenly see all Github Actions failing because if billing reasons? Today we started see that all of a sudden and i was confused cos out billing looks good. Then i noticed we had a new(?) budget tab. Which said 100% used ($0/$0). Changing that got things working again

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