John Marshall

New releases for HTSlib (github.com/samtools/hts...), SAMtools (github.com/samtools/sam...) and BCFtools (github.com/samtools/bcf...) Some of these are security fixes, so do please update.

Don’t let ANYONE tell you you can’t vote! Cast a special vote NO MATTER WHAT. It will then be counted as a disallowed vote and we will be able to see how much this evil government cheated. #nzpol

HTSJDK 6.0.0 is released! Major updates include: - Full support for VCF 4.0-4.5 (finally) - Full support for BCF 2.2 (including bgzf) - File->Path everywhere for NIO file system plugins - Proper CRAM/CRAI indexing - CSI index support for many formats - Non-trivial performance improvements

In which someone's AI suggests exactly the same thing as I did seven years ago… …except that it suggests adding a note to the instructions rather than a contextually adjusted note to the end of the build log, because it doesn't understand no one ever reads the instructions.

If you live overseas and been there for less that 3 years or have visited recently you can still vote, if you are not enrolled you MUST do it before Sunday, don't delay you can do it online: vote.nz/enrolling/en...

Looks like I picked the right week to quit bundling security & certificate infrastructure libraries.

Somewhat embarrassed to have emailed my Labour candidate this morning on the basis of the uncorrected article. Thanks a lot RNZ! Still, good for him for replying within an hour, which is more than his predecessor has managed since I emailed her on this topic back in August.

Well the time I and other experts sent both submitting and then talking to labour ministers about why this is a terrible idea unsupported by facts was clearly well spent. Dear Labour: Campaigning on "we'll ignore experts, just like National!" may not be the winner you expect it to be. #nzpol

Kia ora NZ make sure you remind every 18-24 year old you know to get registered to vote by 25 October! #nzpol

NATIONALISE PAYWAVE www.rnz.co.nz/news/busines...

SCOOP: A majority of Cabinet wanted New Zealand to back a vote on a new UN pandemic treaty but Winston Peters made the call not to, @samsachdeva.bsky.social reports. NZ and Paraguay were only countries to abstain, US, Israel and Argentina voted against. newsroom.co.nz/2026/10/13/p...

Python 3.15 final has now been released. We built pysam 0.24.1 with 3.15 RC2 (which is guaranteed to be ABI-compatible with the eventual final release) so the next entry in this table is minus 1 month (3.15) 🎉

ah damn, RIP Margaret Hamilton. she took safety-critical software engineering seriously, and got people to the moon and back. news.mit.edu/2026/margare...

Twenty years ago, on October 7, 2006, Anna Politkovskaya was murdered by Putin’s henchmen. She had warned about the true nature of the russian regime and urged that it not be allowed to continue until it was too late. Western leaders chose to listen to the appeasers—or succumbed to corruption.

In Python function definitions, parameters before / are positional-only; parameters after * are keyword-only. The * is old, and even / has been around since 3.8 so no longer counts as newfangled. (Noted here so I might remember it clearly in future…)

What's worse than a drive-by pull request from some rando with no interest in your project who merely pointed their AI at one of your open issues? That same drive-by PR, but when the issue reporter (and their cybernetic friend) has already opened a superior PR fixing the problem.

Wondering where the Python Standard Library documentation's sections on built-in functions, constants, types, and exceptions went? They were moved to a new top-level Built-ins section alongside Library/Language/etc three weeks ago. Now I regularly need to look at two index pages instead of one…

Seacliff farm sheds, North Dunedin #Nikon #Rural I've always been a fan of this fangled new 'hyper localism', a reaction to 'influencer photographers' all travelling to the same insanely beautiful 'secret' location to get iconic shots. Celebrating the local rocks my boat too

I'm at Unity Bookshop Wellington for the Nicky Hager book launch. The event is not due to start until 6 pm, but the room is mostly full already and filling up fast.

Today's pysam 0.24.1 release bundles htslib, samtools, and bcftools 1.24 and has pre-built wheels on PyPI for Python 3.9 through 3.15. Wheels are much smaller than in previous releases. It includes type hint fixes, some speed optimisations, and a new reverse_complement() utility function. 🧬🖥️

Probably the biggest organisational change we've made in pysam for a while: Dynamically load libcurl and libcrypto in order to subvert Linux wheel repair and avoid these libraries being bundled into the final wheels. (This organisational change affects only the pre-built Linux wheels.)

A week later, and no response from my electorate MP other than the autoreply from her office. I also emailed Reuben Davidson asking if the public are allowed to read his reported “79 questions” letter… 🦗🦗 Labour really working hard to earn every vote here… 🙄

Days since I've been screwed by SELinux: 0 I spent years reflexively removing the selinux packages whenever I upgraded Fedora. Was hoping not to have to go back to that…

Just reflecting on the fact that when a Kiwi was seized and detained for weeks by the US regime, our Minister of Foreign Affairs (who also leads a party in govt) responded by sharing an elaborate and obvious lie that it was her own fault- -and it has disappeared down the memory hole already. 1/

What I have spent the last hour writing.

Very disappointed to see the govt proposing a ban on under-16s using social media. While we agree there is work to be done, a ban is the wrong approach and interferes with young people's rights to communicate with family, each other, and the wider world. www.rnz.co.nz/news/politic...

Surely (surely…!) Labour would not offer support to the government on a contentious topic less than three months before an election. I've told my Labour MP what will happen to my vote if the party supports this, and I hope they get a deluge of such letters.

Wait what, synthID requires access to the secret key used to encode the watermark? And we just have to trust the person with the secret to say yes or no? I know DRM is pretty useless, but this is next level useless.

There was no cholera in ancient or medieval Europe; it’s a 19th century arrival to Europe

Spot the literal criminal offence.

First #InternetNZ AGM motion vote at 7.30, scheduled for a minute or two after 6:55 — we're only running half an hour late after two hours elapsed!

Currently ~900 people in the InternetNZ AGM meeting. Early days yet, still just testing the voting system — if memory serves, we spent AGES doing this last year!

Tēnā koutou, e hoa and #InternetNZ folks! Here are my thoughts on Motions 2–5 and Motion 9, and what they could actually require of Ipurangi Aotearoa: bit.ly/3St9A2E.

It's going to be proper Red Wedding if it's Winston who comes out