John Marshall

Hard to believe how much damage SemVer has done to people’s brains.

Apparently it is difficult to understand that implementations are not necessarily obliged to reject every out-of-spec file and produce a useful diagnostic accordingly.

A few specifications do describe in detail what should happen in error situations. IIRC HTML5 does, but it's not common.

A file format specification (hopefully!) spells out what's valid and invalid. Implementations have choices for how they deal with variously out-of-spec files:
• reject with error message
• reject mysteriously
• accept as an extension, with a well-defined meaning
• accept mysteriously
• crash
• …

Thanks a lot Jon, that's crossed the streams in a really enraging way! 🫠

I assumed they meant zoom appointments with a human, but maybe there's a reason it's been rephrased from “Virtual visits” to “Virtual PCP”. Depressing…

Your version is funnier, but: Primary care physician, which is what they call GPs over there.

So apparently you get a virtual one of those. Yay?

If you ever submit on bills, read legislation on legislation.govt.nz or use its RSS feeds to keep track of new bills, please tell the Parliamentary Counsel Office to make sure the new site keeps RSS. We shouldn't need to have an API key.

Fill in the survey: www.legislation.govt.nz/news.aspx#rs...

Public Webinar - Myth Busting De-Exctinction - Genomics for Aotearoa New Zealand Myth busting de-extinction to sort fact from fiction. In this public talk, Associate Professor Nic Rawlence will provide a New Zealand perspective around claims of de-extinction.

Genomics for Aotearoa New Zealand - Public Webinar 14th October
@nicrawlencenz.bsky.social will be giving a public webinar on myth busting de-exctinction.

The webinar will run from 11:00 am to 12:30 pm including time for questions.

Please boost this to help reach a broad audience. 🙏

I accidentally left my reckons on this point out of my submission. Fortunately there are people submitting in their professional capacity who have done the research and are less forgetful.

Huntington's disease successfully treated for first time One of the most devastating diseases finally has a treatment that could transform lives, tearful doctors tell BBC

Wonderful news. A salutary reminder of the absolute benefits of scientific progress, and the absolute evil of conspiracist bollocks.

Huntington's disease successfully treated for first time www.bbc.com/news/article...

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I'm sorry, worldwide, irrevocable, non-exclusive, transferable permission to my voice and likeness? For what now? In any manner for any purpose???

This is in academia/.edu's new ToS, which you're prompted to agree to on login. Anyway I'll be jumping ship. You can find my stuff at hcommons.org.

A modest proposal: Unsuccessful InternetNZ electoral candidates should post to NetHub only in proportion to the percentage of votes they received.

Is there anyone here at one of the universities in Wellington, NZ, who would want to host me to give a talk around November 10th?

Re “people make mistakes, often”… It does sometimes feel like there's a constant stream of people encountering and reporting the same conda installation issue. But it's important to remember there's a much larger group out there we don't hear from — because it's all just working smoothly for them.

As the designated “someone who admits knowing something about conda”, I've been meaning to write my usual “follow the instructions re channels” answer up into an htslib.org page for a while.

Bioconda packages all theoretically require conda-forge, but samtools et al are unusual in that it's vital.

The htslib.org web site for samtools/htslib/bcftools, or generally get source code from the respective (mostly) GitHub repositories. Build binaries yourself or get them from relatively trusted sources like Linux distributions, brew, or bioconda.

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned

I noticed the “netierh” typo immediately but regretfully noticing the “and his wife” typo took a little longer…

Thanks for the reminder. I'm getting very sick of submitting on stupid bills knowing that my submission will be ignored, but it's easy enough to write something quick and half-arsed that will at least be tallied in the ‘against’ column.

Only forgot to mention about three things this time…

I wish to comment on three aspects of this bill: Firstly, the proposal to close voter registration a fortnight before polling day is a retrograde step that diminishes our democracy. In the last general election, almost 100,000 people enrolled to vote in that last fortnight before polling day. Administratively preventing such people from being able to vote is the opposite of what a modern democracy should be doing. Secondly, the proposed changes to §80(1)(d) (disqualification of people in prison) would change voting disqualification from applying to prisoners serving a term of three years or more to applying to all prisoners. This is obviously a breach of human rights and Te Tiriti o Waitangi, as has been repeatedly established by New Zealand courts. Thirdly, the proposed §218A (provision of food etc near polling places) largely duplicates the existing long-standing §217 regulations around treating. While the existing treating section prohibits the provision of e.g. free food, drink, or entertainment with corrupt intent for the purpose of influencing voters' votes in various ways, the proposed section would prohibit the provision of free food, drink, or entertainment within 100 metres regardless of intent or purpose. I do not believe it is reasonable or equitable to prohibit these activities in general, even when the prohibition is limited to a 100 metre geographical area. The aspect that makes this type of prohibition potentially reasonable is the consideration of the food etc provider's intent and purpose: to my mind, only food etc provision with the intent of corruptly influencing voters is reasonable to prohibit. Clauses 4 to 8's new deadline for the close of registration should be reconsidered. Clause 10's changes to §80(1)(d) should be dropped. Clause 44 seems a good clarification of the rules around treating. However clause 46 inserting §218A should be dropped.

Submitted on the Electoral Amendment Bill with 3 minutes to spare! Was reminded at the last minute that this bill has another go at disenfranchising prisoners (as has been shot down in the courts repeatedly)… so forgot to say that the deadline change likely won't speed up getting results anyway. 🫠

Watching talks on CMake while working out. I truly appreciate the work folks put in to keep trying to explain the "modern" CMake way. But in every case, I quit watching in disgust. CMake is an example of how to do everything wrong, and when cutting your losses is the best course of action.

Naively assumed that with the #InternetNZ election over, we wouldn't be hearing from the spaceman again. But I haven't been back there for long; perhaps he's been invested in spamming them with the same opinion over and over for longer than I realise…

We have endless browser and html extensions, but it maddens me that no one made a common ISP-level protocol to query datacaps that returns:

- Monthly quota (if any)
- Current usage (bytes used)
- Reset date/time
- Throttling policy (what happens when you hit the cap)

Americans, I am once again begging you to consider that sometimes people aren't in America and may be discussing their own bad governments on the niche microblogging website. Please. I am begging.

Are you referring to this rather narrow one — which is apparently also slated for demolition? bsky.app/profile/lynd...

(1) Earthquake risk. (2) Pedestrians will re-learn to know their place, as they once again stare at the six lanes of traffic after they've pressed the button begging to be allowed to cross.

Citation needed, or this is just FUD.

Speaking as someone who has expended a lot of time and effort auditing samtools I/O code and fixing such problems, I can say that all known such problems were fixed years ago.

If you're talking about historical behaviour, please clarify. Otherwise — just FUD.

Turns out this was on Cygwin or some other newlib-using Windows layer, and newlib's <ctype.h> also defines a bunch of bit masks with names like _P. www.cygwin.com/cgit/newlib-...

Obviously we'll be waiting for the dust to settle and it'll be a while before a new pysam release appears anyway.

(I realise it's quixotic to wait for system package availability when the modern way is for everyone to automatically install the latest dependencies via pip during a build anyway…)

Pleased that Debian 13 "trixie" has now been released. Prior to this, by my reckoning Debian was the only remaining major platform that did not package Cython 3.x in its system package repositories.

With Cython 3 available everywhere, pysam can reasonably require it and simplify a few things.

It's a good guess in your field, but less so in bioinformatics. Most of us are operating at a rather different level of abstraction to anything involving C nuts and bolts — often can barely build compiled application code, so unlikely to be building kernel modules or wanting to.