@jonny@neuromatch.social
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jonny

@jonny@neuromatch.social

Digital infrastructure 4 a cooperative internet. social/technological systems & systems neuro with some light dynamical systems & crush on topology on the side.

writin bout the surveillance state n makin some p2p

science/work-oriented alt of @jonny

information is political, science is labor

This is a public account, quotes/boosts/links are always ok <3.

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jonny, to random
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I go back on twitter one time and now some economics/MBA bootlicker with cryptocurrencies still in bio in 2024 is telling me how im going to be sued because i in my supervisatory role as a postdoc will be sued by UCLA parents for bewitching undergrads to get arrested while demonstrating. The discourse over there is dire.

jonny,
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Theres so much wrong with literally every part of what hes saying but he is still going, its amazing, like a wounded animal dosed with hallucinogens biting at the enemies they are imagining.

jonny, to random
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jonny,
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Bsky/atproto has a very similar but materially different eventuality as an advertising market, a bit more esoteric, but the same idea of preserving a space between people that can be mined

jonny, to random
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There is a lot of angst about the stand up strike strategy that the #UAW4811 is using. i have mixed but mostly positive feelings, and one of the underrated things about it is exactly the fact that the radical end of every campus is begging to be called up and wildcatting. i'm someone who thinks that the elected leadership and r&f organizing are complementary instead of antagonistic, so like it's both good that it looks like there is the strategic head leading the body and also that the body is unpredictable and wants to push it further. obvi i also think there should be more horizontal r&f in general but there is something that is really working about that dynamic rn.

jonny,
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like i think it would be dope if we called like 4 campuses next week, and it would also be dope if this whole process was working in a way that all the campuses were actually co-organizing it instead of being called by the executive leadership, but that's the longer-term union reorg that this situation motivates and builds energy for

jonny,
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like "deal with us now before you have to deal with us later after you push more radical ppl in here" and it would be good if that was an intentional strategy but hey

NunavutBirder, to random
@NunavutBirder@mas.to avatar

The Victor Bay Point crack has started for the season.

jonny,
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@NunavutBirder do y'all bridge it or is the crack become eventually just the bay having a liquid surface again?

jonny, to python
@jonny@neuromatch.social avatar

Here's an ~ official ~ release announcement for

repo: https://github.com/p2p-ld/numpydantic
docs: https://numpydantic.readthedocs.io

Problems: @pydantic is great for modeling data!! but at the moment it doesn't support array data out of the box. Often array shape and dtype are as important as whether something is an array at all, but there isn't a good way to specify and validate that with the Python type system. Many data formats and standards couple their implementation very tightly with their schema, making them less flexible, less interoperable, and more difficult to maintain than they could be. The existing tools for parameterized array types like nptyping and jaxtyping tie their annotations to a specific array library, rather than allowing array specifications that can be abstract across implementations.

numpydantic is a super small, few-dep, and well-tested package that provides generic array annotations for pydantic models. Specify an array along with its shape and dtype and then use that model with any array library you'd like! Extending support for new array libraries is just subclassing - no PRs or monkeypatching needed. The type has some magic under the hood that uses pydantic validators to give a uniform array interface to things that don't usually behave like arrays - pass a path to a video file, that's an array. pass a path to an HDF5 file and a nested array within it, that's an array. We take advantage of the rest of pydantic's features too, including generating rich JSON schema and smart array dumping.

This is a standalone part of my work with @linkml arrays and rearchitecting neurobio data formats like NWB to be dead simple to use and extend, integrating with the tools you already use and across the experimental process - specify your data in a simple yaml format, and get back high quality data modeling code that is standards-compliant out of the box and can be used with arbitrary backends. One step towards the wild exuberance of FAIR data that is just as comfortable in the scattered scripts of real experimental work as it is in carefully curated archives and high performance computing clusters. Longer term I'm trying to abstract away data store implementations to bring content-addressed p2p data stores right into the python interpreter as simply as if something was born in local memory.

plenty of todos, but hope ya like it.

[Further demonstration of validation and array expression, where a Union of NDArray specifications can specify a more complex data type - eg. an image that can be any shape in x and y, an RGB image, or a specific resolution of a video, each with independently checked dtypes] For example, to specify a very special type of image that can either be a 2D float array where the axes can be any size, or a 3D uint8 array where the third axis must be size 3 a 1080p video from typing import Union from pydantic import BaseModel import numpy as np from numpydantic import NDArray, Shape class Image(BaseModel): array: Union[ NDArray[Shape["* x, * y"], float], NDArray[Shape["* x, * y, 3 rgb"], np.uint8], NDArray[Shape["* t, 1080 y, 1920 x, 3 rgb"], np.uint8] ] And then use that as a transparent interface to your favorite array library! Interfaces Numpy The Coca-Cola of array libraries import numpy as np # works frame_gray = Image(array=np.ones((1280, 720), dtype=float)) frame_rgb = Image(array=np.ones((1280, 720, 3), dtype=np.uint8)) # fails wrong_n_dimensions = Image(array=np.ones((1280,), dtype=float)) wrong_shape = Image(array=np.ones((1280,720,10), dtype=np.uint8)) # shapes and types are checked together, so this also fails wrong_shape_dtype_combo = Image(array=np.ones((1280, 720, 3), dtype=float))
[Demonstration of usage outside of pydantic as just a normal python type - you can validate an array against a specification by checking it the array is an instance of the array specification type] And use the NDArray type annotation like a regular type outside of pydantic – eg. to validate an array anywhere, use isinstance: array_type = NDArray[Shape["1, 2, 3"], int] isinstance(np.zeros((1,2,3), dtype=int), array_type) # True isinstance(zarr.zeros((1,2,3), dtype=int), array_type) # True isinstance(np.zeros((4,5,6), dtype=int), array_type) # False isinstance(np.zeros((1,2,3), dtype=float), array_type) # False
[Demonstration of JSON schema generation using the sort of odd case of an array with a specific dtype but an arbitrary shape. It has to use a recursive JSON schema definition, where the items of a given JSON array can either be the innermost dtype or another instance of that same array. Since JSON Schema doesn't support extended dtypes like 8-bit integers, we encode that information as maximum and minimum constraints on the

jonny,
@jonny@neuromatch.social avatar

and with that, i'm on strike.

jonny,
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@al_merose
It tries to be a passthrough to existing array libraries as much as possible. So if they do, then yes, and in the spots where im making new interfaces I try and abide by it. Havent made a formal commitment yet but its just v1 so not opposed just havent implemented formally yet!

wgahnagl, to random

if you noticed all the pictures coming back online all at once that's because I plugged the ethernet cables that go to the server back into the router

jonny,
@jonny@neuromatch.social avatar

@wgahnagl keeping the internet on the ground where it belongs

jonny, to random
@jonny@neuromatch.social avatar

Prepping for strike and deciding what is struck labor and what isnt is forcing me to draw hard lines where none exist lmao. Like everything I do is in some way "my job." Maintaining this instance is "my job," so is like teaching ppl stuff informally and chatting with people in different orgs and doing idle PRs to FOSS projects and etc.

Using the standard of "stuff that in any way benefits my employer" is helpful but there are still some edge cases where im like "ok life is just labor and there is no good answer here."

jonny, to random
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lana, to random
@lana@mstdn.science avatar

Oh dang! I hate writing citations and I've always used Scholar to write them for me (even for citing my own papers, and it never got that wrong). Nothing to do with wether I've read the papers...
Also despite many attempts over the years I've never managed to make zotero generate latex citations....
https://dair-community.social/@alex/112497411007577712

jonny,
@jonny@neuromatch.social avatar

@lana
Ive always done better bibtex extension -> auto updating .bib file for a project folder and its worked pretty well :)
https://jon-e.net/blog/2022/04/16/a-halfway-decent-latex-setup/

tdverstynen, to random
@tdverstynen@neuromatch.social avatar

How to set the stage for a coup if you fail to win an election.

I am becoming more and more convinced that we will see broader civil unrest with this election than we saw on Jan. 6th, 2021.

https://www.nytimes.com/interactive/2024/05/24/us/politics/trump-election-results-doubt.html?unlocked_article_code=1.uU0.j3tj.4D6vxTM1eJZg&smid=nytcore-ios-share&referringSource=articleShare&sgrp=c-cb

jonny,
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@tdverstynen
Ya either result will mean go time for the fascist paramilitaries

jonny,
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@tdverstynen
Just building systems of resilience and resistance bc fascism is a periodic disease of the state. We havent been idle either even if we are further behind on stuff like weapons and fighting and etc. We make up for it in being able to actually do solidarity and care and self correct. We got unions and affinity groups and mutual aid orgs and so we arent starting from nowhere. But yeah it will be a mess

Alexlee, to academicchatter
@Alexlee@sciences.social avatar

Nobody told me about the snakes! @academicchatter

jonny,
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@RossGayler
Weird how despite all the incorrect answers google absolutely nails the subtleties of this complex and time honored tradition

iris, to random
@iris@neuromatch.social avatar

Rory brought home a mouse again :ratstand:​

jonny,
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@iris my cat fears the outside and also mice even though she pretends to kill them all day long to look tough. but i did live in a place that had a sort of unpatchable complex of holes in the eaves and an attic/insulation thing that made it so rodents continually nested above the place where i put my head when i slept

jonny,
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@iris there is the bucket/divingboard/hole kind like this overkill example (but you get the idea of "tall space that's easy to fall into but hard to jump out of") https://www.youtube.com/watch?v=X7KPqSnQG5U

but i think you'd have to be watching bc cat can probably go in and fish them out. so ig if you make the hole narrow enough then it would be fine. peanut butter has never failed me tho, a tiny little drop and they come from hundreds of meters

jonny,
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@iris dang that was literally the first video that came up with "bucket mouse trap" but i am like why do they have so many mice

jonny,
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@iris like almost immediately they aren't even attracted by the food they are just diving in bc everyone else is in there

jonny,
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@iris the rodents are just a fact of life yno? sometimes they land in your place because another beloved creature was showing off, other times they just need to get warm and have some babies, just gotta scoot em out of their olfactory navigation range away from the place and back into the scrubby fields where they wanted to be anyway

breakfastgolem, to random
@breakfastgolem@goblin.camp avatar

Reading is my passione

jonny,
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jonny,
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