John Marshall
@johnm.bsky.social
870 followers 240 following 160 posts
Bioinformatics tools developer at Australia’s Centre for Population Genomics. Will edit GA4GH specifications for food. New Zealander fairly recently returned after a decade in the U.K.
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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?
Reposted by John Marshall
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...
I'm a bit sad to see the PCO is going to end the Legislation.govt.nz RSS feeds, replacing them with an authenticated API.
www.legislation.govt.nz/news.aspx#rs...

APIs are great, but RSS is widely supported and unauthenticated - a much lower barrier to use than having to develop a custom API client.
Reposted by John Marshall
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. 🙏
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.nz
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.
The Govt's stated reason for restricting voter enrolment in the last two weeks of the election has been speeding up the final count.

But the Electoral Commission just told the Justice Select Committee that wouldn't happen - with or without the law change it would take 20 days.

t.co/N0vRXHMbMt
https://www.thepost.co.nz/politics/360835185/controversial-changes-voter-enrolment-wont-speed-final-count-electoral-commission
t.co
Reposted by John Marshall
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...
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
www.bbc.com
Reposted by John Marshall
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.
By creating an Account with Academia.edu, you grant us a worldwide, irrevocable, non-exclusive, transferable license, permission, and consent for Academia.edu to use your Member Content and your personal information (including, but not limited to, your name, voice, signature, photograph, likeness, city, institutional affiliations, citations, mentions, publications, and areas of interest) in any manner, including for the purpose of advertising, selling, or soliciting the use or purchase of Academia.edu's Services.
A modest proposal: Unsuccessful InternetNZ electoral candidates should post to NetHub only in proportion to the percentage of votes they received.
Reposted by John Marshall
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.
Samtools
Samtools
htslib.org
Reposted by John Marshall
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…
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. 🫠
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. 🫠
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.
Reposted by John Marshall
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…
Reposted by John Marshall
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)
Reposted by John Marshall
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...
Unnerving staircasey business
Google map with a red circle around that boxy footbridge about a block along from the city to sea one
(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.