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John Marshall

@johnm.bsky.social
962 followers 321 following 323 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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John Marshall @johnm.bsky.social · 16/09/2026
Overall the unnecessary source code and bundled libraries were substantial, but the biggest component was the out of control GCC debugging symbols, which are particularly bloated for the style of code generated by Cython. I considered ‑g1 but other Cython projects that control this mostly use ‑g0.
Bar chart showing the size reduction in a single representative wheel from version 0.24.0 to last week's 0.24.1: Linux on the left and macOS on the right.

The Linux wheel reduces from ~24 MiB to ~3.5 MiB. The reduction is about 20% excess source code, 20% bundled libraries, and 60% voluminous debug symbols. The libbz2 and liblzma compression libraries are still bundled in 0.24.1 Linux wheels, but they are tiny and should not have the same security concerns as the previous networking libraries.

The macOS wheel reduces from ~8 MiB to ~2.5 MiB, almost entirely due to the removal of excess source code.

Note that these are all the sizes AFTER compression. (Wheels are compressed with zip.)
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John Marshall @johnm.bsky.social · 16/09/2026
Investigating pysam wheel sizes had been on my to-do list for a while. Recently realising that we'd used 6 GiB out of our default 10 GiB PyPI limit and had room for maybe five more releases made it urgent. Last week's 0.24.1 release reduces the per-release total from ~760 MiB to ~150 MiB. 🧬🖥️ 🧵
Bar chart showing total release sizes gradually increasing from 2021's version 0.17.0 to a peak of 760 MiB for the second most recent release (2026's 0.24.0) before dropping to ~150 MiB (between 0.17.0 and 0.18.0 in total size) for the most recent release.

Interesting discontinuities are 0.22.0, which added ARM wheels for macOS, and 0.23.1, which added musl Linux wheels. The sdists are ~5 MiB making a barely visible blue sliver at the bottom of the graph.
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John Marshall @johnm.bsky.social · 24/08/2026
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.
Letter emailed to MP:

I see from the news today that the government finally plans to move ahead with its proposed social media ban for those under 16. RNZ reports that ACT and New Zealand First will not support this bill, and that National will therefore need Labour's support for the bill to progress.

Such bans are ill-considered and I trust Labour will not support the National Party in this. Both on its (lack of) merits, and because it is far too close to the upcoming election for Labour to be supporting any government legislative action. If Labour were to support this bill, I would not be able to support a Labour electoral candidate or the party with my vote in November. As a voter, I am sure I am not alone in this conclusion.

For further background on alternatives to such bans, I would commend to you InternetNZ's submission in response to the Education and Workforce Committee's inquiry in 2025:

[URL follows.] https://internetnz.nz/assets/Archives/Submissions/InternetNZ-Submission-on-Inquiry-into-the-roles-can-the-Government-business-and-society-can-play-in-addressing-online-harms-to-New-Zealands-youth-25-July-2025.pdf
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John Marshall @johnm.bsky.social · 12/08/2026
Live from the prime ministerial lectern! It's riveting stuff…
Radio New Zealand's livestream: “The Prime Minister is due to address media at 12.35pm. Watch a livestream of the announcement…”

It's an empty lectern at 12:40pm.
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John Marshall @johnm.bsky.social · 05/05/2026
Pretty good day yesterday. The Media Council ruling on a particularly egregious headline was released, and a lot of people on here thanked me for taking the time to complain. Thank you all for your kind words — it's much appreciated. Then I got to spend the evening with these colourful characters!
Noel Crombie, Neil Finn, and Tim Finn on stage in Christchurch.Split Enz performing, with an extra large Neil Finn projected behind Eddie Rayner.The Finn brothers on stage.Split Enz signing off after a great concert in Christchurch.
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John Marshall @johnm.bsky.social · 19/03/2026
Perhaps Providence St. Joseph Health should consider not spamming open source maintainers who have nothing whatsoever to do with their application portfolio governance. 🧬🖥️
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.
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John Marshall @johnm.bsky.social · 16/03/2026
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…
Reply to the Stuff Editor's reply to my complaint:

To reiterate, my complaint is about the headline in particular. You write:

[quote] We also want to be clear that Stuff does not advocate for "catching Covid" as a preferred health strategy. The article explicitly reinforces the importance of medical boosters [end quote]

The headline makes the statement “catching the virus is basically our new booster”. With particular reference to principle 6 of the NZ Media Council Principles, do you consider that the headline accurately reflects the article as you have described it in the quote above?
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John Marshall @johnm.bsky.social · 17/01/2026
Fairly sure this is the only band tee shirt I have ever owned. Got it at their concert in London which we went to a few days after first hearing them, when they wowed John Peel on his radio show.
Melt Banana T-shirt, with what appears to be one anime character exploding another via the power of her voice. My shirt was black print on light blue.
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John Marshall @johnm.bsky.social · 06/01/2026
LOL 🤣
Dialog box in the ManageMyHealth iOS app saying “Manage My Health is temporarily directing users to the Web Application to ensure consistent access to information and support, following the cyber security incident.
To launch the Web Application, tap the ‘Help and Support’ button or log in by visiting
www.managemyhealth.co.nz”.
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John Marshall @johnm.bsky.social · 11/09/2025
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.
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John Marshall @johnm.bsky.social · 07/06/2025
… And also two very thoughtful jars of homemade jam — not sure how they divined how much I like feijoas — and some damson plum gin in the hip flask. Top work, Santa!
Binoculars and a hip flask in front of two jars of jam.
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John Marshall @johnm.bsky.social · 07/06/2025
Foolishly I hadn't given my #MWSecretSantaAoNZ person any hints as to suitable gifts, but they've done spectacularly well nonetheless. My partner and I have one pair of binoculars for watching birds and other wildlife, so a second little pair so we can both look at once is perfect. …
Two jars of jam, a pair of binoculars, and a silver hip flask peeking out from behind a card with a googly-eyed cat in a party hat.
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John Marshall @johnm.bsky.social · 05/04/2025
Stuff reporting on an Antonov An-124 cargo plane arriving in Auckland tonight. Stay classy, Stuff! The single An-225 Mriya ever built was destroyed three years ago, when Russia attacked Hostomel Airport on the outskirts of Kyiv. If only you'd read just a little more of that Wikipedia article…
Last paragraph of Stuff's article: “The biggest plane in the world currently is the An-225 Mriya, an enlarged version of the An-124, which has a maximum take-off weight of 640 tonnes.”
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John Marshall @johnm.bsky.social · 18/03/2025
Definitely less annoying to be at my desk today.
Lake Wānaka from Bremner Bay, with the low lake level typical for this time of year. Overcast and between rain showers.
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John Marshall @johnm.bsky.social · 15/03/2025
Definitely a day to be outside rather than looking at pysam or pybwa code just now 😎 ☀️
Lake Wānaka from Roy’s Bay.
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John Marshall @johnm.bsky.social · 09/02/2025
Sitting on my balcony doing some pysam hacking… just glanced up at the right time to see some tourists en route to the Bay of Islands.
Cruise ship Carnival Splendor passing Rangitoto on an overnight voyage to the Bay of Islands.
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John Marshall @johnm.bsky.social · 03/02/2025
Took lunch up Devonport's North Head / Maungauika today to watch the retiring Hercules farewell Auckland on today's tour of the country. www.nzdf.mil.nz/media-centre...
Three planes approach Auckland's Sky Tower while on a final tour of New Zealand.Three planes turning over the Auckland War Memorial Museum while on a final tour of New Zealand.Three planes over Devonport Naval Base flying towards the Auckland Harbour Bridge.
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John Marshall @johnm.bsky.social · 04/01/2025
One of my better photos from tonight’s aurora activity.
Aurora, looking towards the Cardrona Valley from Wānaka.
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John Marshall @johnm.bsky.social · 12/11/2024
More scenery, in keeping with my previous postings here. However given the current influx of people following me for some reason, and given that hoping for birdsite recovery no longer seems tenable, the time is ripe to start posting more bioinformatics over here.
Rangitoto from Cheltenham Beach, Auckland.
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John Marshall @johnm.bsky.social · 22/08/2023
Stripes
Treble Cone reflected in Bremner Bay, at low lake levels.
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John Marshall @johnm.bsky.social · 04/07/2023
A glorious winter’s day today
Snow-covered Black Peak over Lake Wānaka
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