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bede

499 karma · joined April 17, 2012

Computational biologist. Oxford, UK https://bede.im b@bede.im
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bede··on Spotify will reduce total headcount by approximately 17%
As a scientist working in public health, this decision burned my faith in Spotify. They were taking down conspiracy theory podcasts daily while bankrolling Rogan to provide a platform with insane reach for cranks like Robert Malone. I cancelled my subscription for a few months in protest.
bede··on [dead]
Title should be suffixed with (2005)
bede··on Aegis Authenticator – Secure 2FA App for Android
Thanks for this, I'm currently using both Duo to Microsoft authenticator, and the lack of firm reassurance about the backup mechanisms in each of these makes me uneasy. I'd frankly prefer a vault with a model similar to BitWarden's, where I can export my private keys.
bede··on My seatbelt rule for judgment
The seatbelt is an excellent example since there are multiple mechanisms with varying observability contributing to its effectiveness. Even after discovering the dynamic locking behaviour, a naive yet inquisitive passenger remains blind to the pretensioning feature that is observable only during a collision.
bede··on Samsung seemingly caught swapping components in its 970 Evo Plus SSDs
As a legal layman, is this possible class action territory?
bede··on Pattern matching accepted for Python
I do editable installs every day with setup.py – what is your point? Poetry is a very interesting third party solution to these issues, but not a best practice. Best practices matter in packaging.
bede··on Pattern matching accepted for Python
Thanks, donated.
bede··on Pattern matching accepted for Python
Core dev Larry Hastings [0] puts it well. The cost-benefit case for this complicated language feature is limited.

"I dislike the syntax and semantics expressed in PEP 634. I see the match statement as a DSL contrived to look like Python, and to be used inside of Python, but with very different semantics. When you enter a PEP 634 match statement, the rules of the language change completely, and code that looks like existing Python code does something surprisingly very different. It also adds unprecedented new rules to Python, e.g. you can replace one expression with another in the exact same spot in your code, and if one has dots and the other doesn’t, the semantics of what the statement expresses changes completely. And it changes to yet a third set of semantics if you replace the expression with a single _.

I think the bar for adding new syntax to Python at this point in its life should be set very high. The language is already conceptually pretty large, and every new feature means new concepts one must learn if one is to read an arbitrary blob of someone else’s Python code. The bigger the new syntax, the higher the bar should become, and so the bigger payoff the new syntax has to provide. To me, pattern matching doesn’t seem like it’s anywhere near big enough a win to be worth its enormous new conceptual load."

This while we have elephants in the room such as packaging. Researching best practices to move away from setup.py right now takes you down a rabbit hole of (excellent) blog posts, and yet you still need a setup.py shim to use editable installs, because the new model simply doesn't yet support this fundamental feature.

I can't afford to spend days immersing myself in packaging to the point of writing a PEP, but would help pay someone to do it well. I can see no way to fund packaging efforts directly on the PSF donations page (edit: see comment). It's great to see Pip improving but there is still not even a coherent guide that I can find for packaging using up-to-date best practices. This appears to be because the best practices are currently slightly broken.

[0] https://discuss.python.org/t/gauging-sentiment-on-pattern-ma...

bede··on Changes to Homebrew adversely affect Python development
Homebrew and its excellent community was once indispensible on the Mac, but various pain points including this flakiness made me switch to (mini)conda for nearly everything, despite initial apprehension. There are some wrinkles and the resolver is slow, but in my hands conda is just so much more reliable than Homebrew ever was.
bede··on Big no on Big Sur: Mullvad disallows Apple apps to bypass firewall
My guess is that this is somehow linked to iCloud device handoff, which does all kinds of questionable stuff [0] on e.g. device wake.

[0] https://arxiv.org/pdf/1904.10600.pdf

bede··on What happened to Firefox Send?
It has been my daily for several years on MacOS and is quite reliable. Lack of true chromeless fullscreen browsing is annoying.
bede··on Dexplot: Python library for data visualization
Great work. This is easily among the most elegant Python plotting APIs for exploratory data analysis. Seaborn is a fantastic tool but I sympathise with the author's frustrations with it.

Excellent documentation, but as others have said docs are everything with charting, so expanding that and adding a gallery are probably the best ways to get people onboard. Looking forward to giving this a try.

bede··on A (possible) solution to Covid-19
The global sequencing effort makes this reasonably straightforward to study. While the prevalance of different strains does vary geographically, new international tranmission events occur so frequently that most places have a handful of circulating strains already [0]

[0] https://nextstrain.org/ncov/europe

bede··on Python Fire – Generates CLIs from any Python object
Fire is an interesting project that's great for testing and hacking. But for crafting Python CLIs from scratch, I fail to understand why Argh[0] doesn't receive more attention.

My only frustrations are a missing default handler for --version, and that I can't use argument names colliding with builtins such as 'input'. All the flexibility of argparse without boilerplate.

[0] https://github.com/neithere/argh

bede··on Zotero: An open-source tool to help collect, organize, cite, and share research
Having recently persuaded my research group leader not to spend >£500 on Endnote licenses, this comment tickled me. It may even be the case that Endnote is now a largely functional piece of software, but its history is too exquisite an exercise in Worse is Better for me to go near it again.
bede··on GM is launching a $5K tiny electric car in China made for city commuters
Perhaps the HN community could avoid sending pageviews to ostensibly homophobic [0], racist [1] and generally vile establishments in the future? I realise this article is none of these things, but it seems unlikely that there would not be a viable alternative source.

[0] https://twitter.com/moranicly/status/908710539500642304

[1] https://leftfootforward.org/2015/05/daily-mails-racial-scare...

bede··on How to Generate FiveThirtyEight Graphs in Python
I agree – it's interesting how one is initially drawn to, yet eventually tires of these sorts of plot styles. While Seaborn strikes a good balance, clear and simple monochrome plots never go out of fashion. This is just as much the case when building fancy interactive plots using Shiny/Plotly etc.
bede··on Bootstrapped – A Python library to generate confidence intervals
While on the topic of confidence intervals, has anyone encountered a package capable of generating multinomial confidence intervals similar to CRAN's MultinomialCI? I've yet to find a Python solution.
bede··on Microsoft to acquire LinkedIn for $26B
Perhaps LinkedIn will use fewer evil antipatterns now that its ownership has something resembling a reputation to uphold.
bede··on Soundcloud for the Desktop
Is anybody aware of plans for a web API to allow reassignment of media keys? Clearly it would require strict permissions so as not to be abused, but it could be really useful.
bede··on GCHQ-built phone voice encryption has massive backdoor
I feel obliged to once again refer to Home Secretary Theresa May's on-record statement to a government committee only seven days ago:

"The UK does not undertake mass surveillance".

Make of this what you will.

bede··on Did European Court Just Outlaw “Massive Monitoring of Communications” in Europe?
Given that our Home Secretary recently stated that 'the UK does not undertake mass surveillance' to the investigatory powers government committee, I can't see this having any semblance of an effect (over here, at least).
bede··on Fuzzy string matching using cosine similarity
> It might serve to partition search space for another more expensive algorithm

This is what we're doing. We're working on approaches for performing nucleotide sequence alignment using approximate time series representations of vectorised DNA sequences. There are some really elegant lower bounding similarity search methods for time series which generate no false negative alignments, allowing use of more expensive alignment algorithms later on in the search to prune out the false positives.

We've tested a few transformations including Haar wavelets, DFT and PAA and implemented an indexing structure in C++.

Preprint: https://www.academia.edu/12575290/Alignment_by_numbers_seque... (slightly outdated... Email me for more info)

bede··on AT&T fined $100M after slowing down its ‘unlimited’ data
T-Mobile UK (now largely assimilated by the EE mothership) comprehensively denied the existence of an 18-hours-a-day 4mbps throttle placed on its unlimited plans [1] for several years before getting in trouble with the regulators. As far as I'm aware they weren't even punished, which is a shame given how blatantly deceptive their practices were.

This strikes me as a reasonable fine. Well done FCC.

[1] http://www.techradar.com/news/phone-and-communications/mobil...

bede··on Where are the self-tuning systems?
Self-tuning systems are inherently complex and opaque. Execution tends to be non-deterministic and irreproducible, and so the burden of testing is far greater.

It takes some discipline to write elegant, loosely coupled code that is self-tuning. I work on scientific software, where reproducibility and reusability is (…or at least should be) paramount, and where black boxes are evil. It's hard not to build black boxes when you're writing self-tuning software.

bede··on Show HN: Exa, a replacement for ls written in Rust
Although many packages are still source only, Homebrew has an initiative for packaging (or 'bottling') larger tools into binaries for convenience. It can always be overridden with --build-from-source
bede··on The rise of fake engine noise
Living in Manchester, this amuses me too.

This discussion is very reminiscent of the debate over skeuomorphic user interfaces. As with the transition from physical interfaces to virtual ones, which has drawn interface designers towards the use of skeuomorphic elements to varying extents over the years, we are in another period of technological transition away from normally aspirated internal combustion towards quieter, more efficient means of making motion. To ease the transition for the conservative masses, some degree of skeuomorphism will be needed at first (although I personally think that creating synthetic engine noise is a horrible, horrible idea!).

bede··on Snap webcam photos whenever your app crashes
Yes, this seems to be necessary for using Imagesnap with more recent Apple devices.
bede··on Dr. Dre, Jimmy Iovine Would Both Join Apple in Beats Deal
Yes – I had a good listen to a friend's Studio headphones in 2010. They were not bad and I understand why the sound appeals to some – I just thought they represented terrible value for money. IIRC they cost >£200 in 2010. This particular pair was stored in a hard case yet snapped due to fatigue in the plastic headband after a few months, although I expect their construction has improved a fair bit since then.

In response to your edit, the difference between the two companies is that Apple generally backs up the superficial appeal of its products with very good, if not market leading user experience, engineering and manufacturing. The iPhone is relatively expensive (part of the reason I own a Nexus device), but its quality is undeniable.

bede··on Dr. Dre, Jimmy Iovine Would Both Join Apple in Beats Deal
Does anyone else feel that this deal tarnishes their perception of the Apple brand? I struggle to think of a brand of consumer electronics for which I have more contempt than Beats Electronics (and Monster Cable, who once manufactured all Beats products, between tricking the naive masses into buying hundred dollar HDMI cables…).

The cultural values of these two companies couldn't be much more different. While both are extremely image-conscious and fashionable, Apple has nevertheless built its reputation by delivering innovation and quality to its customers. Beats on the other hand has a built a reputation by selling very expensive headphones of highly questionable quality whose value, I would argue, is primarily superficial.

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