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Posts by John Marshall

Resolved some Python type checking issues by adding type overloads to clarify the different return types (which are selected by a bool parameter) today, but damned if I can figure out how to make that cooperate with monkey-patching the function in question… 😵‍💫

6 hours ago 0 0 0 0

If that's directed at me, perhaps you should consider a few seconds of checking my timeline… 🤣

1 day ago 0 0 0 0

Where in the post does it say it's about the United States of America?

1 day ago 0 0 2 0

I've always had to look up the arguments for `git bisect start` every time but maybe this time this mnemonic will stick: they're in ALPHABETICAL ORDER!

git bisect start BAD GOOD
git bisect start NEW OLD

5 days ago 0 0 0 0
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Apple update turns Czech mate for locked-out iPhone user • The Register : Lock-screen keyboard no longer accepts háček in student's alphanumeric passcode

Apple user being advised data is unrecoverable after iOS update removes the ability to enter certain Czech accented characters, which are in his password (a háček), from the lock screen keyboard. www.theregister.com/2026/04/12/i...

1 week ago 23 10 1 2

Look, I don't think much of Luxon either, but that's a bit unfair.

1 week ago 2 0 0 0
Windcave 3DS process from their Secure FAQ.

Windcave 3DS process from their Secure FAQ.

Windcave is now asking for an email address as part of 3DS verification data. That's a nope. Anything works in that field, for now - I've tested.

1 week ago 1 2 1 0
Missed type narrowing in `assert len(r) == …` which should imply `r` is not None · Issue #11365 · microsoft/pyright In the following code, after the first assert it would seem that the type of r could be narrowed to list[int], which would prevent the pyright diagnostic on the second assert: def foo() -> list[int...

Thanks for the reply, but what I'm hearing is don't bother submitting issues to pyright…

1 week ago 0 0 0 0
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rewrites.bio - A manifesto for bioinformatics Principles for responsible AI-assisted rewriting of bioinformatics tools.

I'm both excited and a little terrified. It feels like a wave of AI-assisted tool rewrites is coming to bioinformatics whether we like it or not.

We figured that the best we can do is to try to get ahead of it, so we wrote down some principles for doing it responsibly: rewrites.bio

2 weeks ago 26 12 4 6
Release with CVE fixes? · Issue #1402 · pysam-developers/pysam Would you mind releasing a version with 4c50e83 ?

Dear open-source maintainer,

I'm not going to lift a finger to help, but I do feel the need to put some more pressure on you.

3 weeks ago 0 0 0 0
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My term on InternetNZ board is ending soon after nine long years.

In my seat please prioritise those with a broad lived experience & real technical knowledge. We have values driven people, we need DNS/Domain name knowledge. I had real-world expertise with internet scams, phishing, abuse etc.

3 weeks ago 71 34 3 2
Kraken2 NCBI RefSeq Complete V205 database on AWS - Registry of Open Data on AWS

If not the core_nt entry near the bottom of that list, how about the S3 bucket listed at registry.opendata.aws/kraken2-ncbi... ?

Otherwise what is the NCBI path in the source code? As @kiwibrew.bsky.social guessed, like most of us I have some experience of refinding stuff there after site reorgs…

3 weeks ago 2 0 0 0
Mac has deprecated openssl in favor of Common Crypto · Issue #2649 · irods/irods https://developer.apple.com/library/mac/documentation/Darwin/Reference/ManPages/man3/CC_crypto.3cc.html

2014: “OSX is an important platform for the community so think it should be a high priority” say maintainers.
2015: This issue opened after discussion on my related issue.
2016: openssl/*.h is now gone.
… 🦗 🦗 …
2026: We do not currently support building iRODS on MacOS. Closed.

#ThisIsBioinformatics

4 weeks ago 1 0 0 0
An email (not the first!) from “noreply github team @ providence.org” entitled “Action Required: 1 Repositories Missing APM” complaining that “The following repositories associated with your account are missing a valid APM (Application Portfolio Management) value: […] PSJH/Strategic-Technology-Enablement.htslib”.

I have nothing whatsoever to do with Providence or their Strategic Technology Enablement, do not have an account with them and cannot take any action related to them. And I have not been a core htslib maintainer for almost a decade.

An email (not the first!) from “noreply github team @ providence.org” entitled “Action Required: 1 Repositories Missing APM” complaining that “The following repositories associated with your account are missing a valid APM (Application Portfolio Management) value: […] PSJH/Strategic-Technology-Enablement.htslib”. I have nothing whatsoever to do with Providence or their Strategic Technology Enablement, do not have an account with them and cannot take any action related to them. And I have not been a core htslib maintainer for almost a decade.

Perhaps Providence St. Joseph Health should consider not spamming open source maintainers who have nothing whatsoever to do with their application portfolio governance. 🧬🖥️

1 month ago 2 0 0 1

The NZ NACTFirst govt that replaced the Ardern govt, which oversaw one of the most successful covid responses in the world, have rejected the WHO pandemic rules which were agreed during negotiations co-chaired by the Ardern govt's Director General of Health.

Pathetic, vindictive, ghouls.

1 month ago 63 21 1 0

Okay, that is indeed pretty cool!

1 month ago 1 1 0 0
Samtools Samtools

Release 1.23.1 of HTSlib, SAMtools, and BCFtools is now available from GitHub. This fixes crashes that could occur when reading malformed CRAM or GZI files. See htslib.org/download/ for links to tarballs and release notes.
🧪🧬🖥️
#samtools #bioinformatics #genomics

1 month ago 3 1 0 0
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…other than that as proposed they'll apply to way more people. However as a layman I would have guessed that “breaching your visa conditions” would pretty much automatically make you “liable for deportation”…

Looked for answers in the Regulatory Impact Statement, but the link in the bill is 404?! 🤷

1 month ago 0 0 0 0

I don't disagree with your characterisation of the changes in general.

But the existing §280/§309 largely already provide the same powers. Proposed changes look to just reword and add “breaching/ed their visa” alongside “liable for deportation/turnaround”, but otherwise the powers appear unchanged.

1 month ago 0 1 1 0

I guess they live in sensible countries that don't have mandatory helmet laws for when you're just popping down to the shops.

1 month ago 2 0 1 0

It took the editor four days to copy'n'paste the set reply for this to my complaint. I look forward to forwarding the complaint to the media council, but perhaps I shouldn't have bothered replying back to the editor first…

1 month ago 1 1 0 0
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Glassworm Returns: Invisible Unicode Malware Found in 150+ GitHub Repositories The Glassworm supply chain attack is back. Researchers uncovered malware hidden in invisible Unicode characters across 150+ GitHub repositories, plus npm packages and VS Code extensions.

Are you still hiding if no one is looking?

People aren't reading the code at all—they'd see the weird decoder+eval—and machines can see that and also the private use code points.

Also, it's been public since May 2025 and GitHub/NPM/Microsoft have done nothing.

www.aikido.dev/blog/glasswo...

1 month ago 39 14 1 1

This article doesn’t ask the question that is crucial for RNZ’s primary audience: is the New Zealand government helping Vanuatu to get the resolution passed, or is it helping the USA to block it?

1 month ago 12 9 0 0

One NZ is celebrating the dark sky pollution of Starlink in its advertising. Not just the service, but the actual sodding lights.
Send for the Hera Lindsay Bird post yet again.

1 month ago 7 3 0 0

"Sloppelganger" is one for the ages

1 month ago 1150 279 4 5

Pretty awful. I used to walk past this building a couple of times a week, essentially every time I went to the city centre.

1 month ago 0 0 0 0

And maybe don't expect the term “British Isles” to get a great reception in every part of that diagram.

1 month ago 4 0 0 0
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Muhammad Ali: Poetic Peom
Muhammad Ali: Poetic Peom YouTube video by Makellow

If you’ve never watched it, I recommend it. It’s only a couple minutes: m.youtube.com/watch?v=0K5b...

1 month ago 98 20 0 0

Correlation between “people who say ‘[project] has been a consistent issue in our dependency chain’ blah blah” and “people who have never reported any of these supposed issues to [project]” remains 100%.

1 month ago 1 0 0 0

New Zealand should be coordinating with the EU and other like-minded countries to collectively negotiate proper safeguards, not quietly capitulating.

1 month ago 116 22 1 0