When the code bot says "I see the issue now" I cannot emphasise enough how much it has not and will not see the issue now or at any point in the future, in any future, in any universe, across all space and time

@ericsfraga I think the Sinclair scientific also used RPN

So you joined PSF (Python Software Foundation) as a supporting member because they gave up money for the sake of inclusion. Great! Donated? That's great too!

I'd also encourage you to look at The Carpentries and give them some money. They did the same thing. And they do good work!

https://www.carpentries.org

@lamdba Thank god I don't have to boycott python

@johncarlosbaez I check a month or two ago before the settlement and I noticed several of my scientific papers are in the list of things they used too. Will check into this further.

This spring, we had a wonderful time at the CERN shaping the future of the Snakemake Workflow Management System during the Snakemake Hackathon. Next spring we will meet in Munich!

If you want to take part in the Snakemake development, you can still register here: https://indico.cern.ch/e/snakemake-meeting-2026

#Snakemake #HPC #Bioinformatics #physics #dataanalysis #ReproducibleComputing #OpenScience

@khinsen I have no axe to grind. I tend to habitually try new tech to see if I can extract some value from it, but life is too short to mess with every shiny thing.

@michaelc thanks so much for the clear advice

@michaelc I'm a bit late to this particular party being a Mac user but there are family members on windows 10. Am I going to have to do something to help support them?

@CindyWeinstein

Wait...! Oh shit, I just thought of something.

Not to be conspiratorial or anything, but have #JohnMastodon and #JohnAntifa ever been seen in the same place at the same time?

🤔

@khinsen If you've never tried this yet, all I can suggest is give it a go, I think you would be surprised. It surprised me how good Claude 4.5 is for instance at both doing code review for snakemake pipelines, and describing and comparing FASTA files with no other information than sequence and headers. We all love to hate on AI here for various reasons but when you get your heands on the state of the art tools, they are quite something.

@khinsen one thing I hadn't considered in this context but if you fed the code review tool the draft of the paper describing the tool as well as the code itself, it should have no difficulty inferring the intent of the code providing the paper is well written. This should address the concern about not being able to formalise correctness for purpose - the text of the paper should clearly articulate the purpose.

@khinsen code review tools are pretty good these days. They will spot a wide range of errors in syntax and logic, and be quite capable of inferring intent from the code and summarising it, and identifying where the code does not match the intent. Peer-review of code augmented by automated coding tools can be quick and easy, at least first pass, and should be done routinely.

Incidentally, if you are writing research code, and not using automated tools to review before running it, you should be.

@crozilla Can't they say they destroyed it but give the codes to Europe to look after?

@LeeDugatkin also applies to writers of scientific papers

Book writer friends, PLEASE read this:
Many of you have likely heard that Anthropic pirated bits from hundreds of thousands, maybe millions, of books.
They are paying out a total of 1.5 billion dollars after losing in court. $3000 per qualifying book.
My literary agent has been deeply involved in this lawsuit. She wrote to her her authors "If you had a book published before August 2022, it’s likely a pirated copy of your book ended up in that training set, and you may be eligible to join the class action and share in any monetary damages."
No later than October 2, there will be a searchable database where you can see if one or more of your books is part of the settlement.
Even before that I suggest you go here to find out much more here as there are actions you can take now:
https://authorsguild.org/advocacy/artificial-intelligence/what-authors-need-to-know-about-the-anthropic-settlement/

For #UK and #Ireland folks, a house martin conservation group urgently needs details of still present colonies so that rehabbed birds can be released into them or at least to migration hotspots where HMs are. This is so they have the best chance to successfully migrate south. Mobile number and email address on their website.

https://housemartinconservation.com/rehabilitation

#Birds

@adamhsparks @adamsteer remember when common wisdom was that you should never use your real name on the internet and anyone who demanded it was up to no good?

If you feel like you haven't had enough exercise today, put this on, and I guarantee that within a minute you'll be up and dancing around. And the sax in the last few minutes is just 😍

Goat - Ouroboros

https://www.youtube.com/watch?v=rH1HnlwNFec

@naturepoker interesting