Remote

Peter Cock

@pjacock@fediscience.org

mastodon 4.6.9

#Bioinformatician / #ResearchSoftwareEngineer working in Scotland, initially in plant pathology (including nematodes and Phytophthora). #Python programmer, with a focus on #OpenSource like #Biopython. He/him/his.

737 Followers

428 Following

31 Posts

Joined November 02, 2022

CodeBerg:

https://codeberg.org/peterjc/

Blog:

https://blastedbio.blogspot.com/

ORCID:

https://orcid.org/0000-0001-9513-9993

GitHub:

https://github.com/peterjc/

Peter Cock @pjacock@fediscience.org

· 5mo ago

Replying to

@oantolin@mathstodon.xyz @kickingvegas@sfba.social @jameshowell@fediscience.org @minad@mastodon.world Nah, not just character by character. Japanese IME for example you typically type in a whole sentence phonetically (and see the kana and first choice kanji appear as you go - sometimes that charges as you type in more giving it more context), then manually fix up any wrong inferences (eg left/right cursors to jump to position in sentence, then up/down or space/shift-space to cycle suggestions for that fragment). Then enter to finalise that sentence.

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Peter Cock @pjacock@fediscience.org

· 5mo ago

Replying to

@scottcain@genomic.social @EpicBear@genomic.social @Codeberg@social.anoxinon.de Ditto. I’ve migrated all my personal projects bar those leaning heaving on CI - the power of a “free” integrated service as a lock-in mechanism

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Peter Cock @pjacock@fediscience.org

· 6mo ago

Messing about with my #KeyboardLayout again (that’s half the fun of #QMK or #ZMK etc in a programable #MechanicalKeyboard), this time the mechanism to get capital letters without a dedicated shift key… ⇧

I’m giving #AutoShift another go (long press for capitals), alongside #CapWords (like caps lock, but it turns off at the end of a word), and #MagicCommaShift (comma before letter means shift) 🪄 ⇧

fediscience.org

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Peter Cock @pjacock@fediscience.org

· 6mo ago

Replying to

@lesley@mastodon.gamedev.place @miclgael@hachyderm.io Pragmatic, like my approach. I’ve migrated all my old GitHub stuff without Continuous Integration to CodeBerg, and do same for new stuff. I need to look at their Woodpecker CI, then I can move a load more…

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Peter Cock @pjacock@fediscience.org

· 5mo ago

RE: @mitchellh@hachyderm.io

Throw enough shit at the walls to see what sticks? I do see his point about generating test cases for an API prior to refactoring, likely to have code using it in unintended ways… but I’m not keen #GenAI #slop

Mitchell Hashimoto: "AI slop is good, actually. Slop is what enables f…" - Hachyderm.io

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Peter Cock @pjacock@fediscience.org

· 5mo ago

Replying to

@robho @mbletmathe @tiggy @bytebro @tlayoyo Japanese one and seven have that issue too I find. I cross my sevens.

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Peter Cock @pjacock@fediscience.org

· 6mo ago

Replying to

@maaslalani @fribbledom that’d open up a lot more use cases 👍

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Peter Cock @pjacock@fediscience.org

· 6mo ago

Replying to

@fribbledom @maaslalani Cute but currently a toy limited to 1000 rows https://github.com/maaslalani/sheets/issues/5

Feature request: support for files containing more than 1000 lines · Issue #5 · maaslalani/sheets

Terminal based spreadsheet tool. Contribute to maaslalani/sheets development by creating an account on GitHub.

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Peter Cock @pjacock@fediscience.org

· 6mo ago

Replying to

@atoponce@fosstodon.org sounds like #ForgeJo and thus #Codeberg are ahead of #GitHub with regards to the transition from SHA-1 to SHA-256 - I might give that a test…

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Peter Cock @pjacock@fediscience.org

· 6mo ago

Replying to

@Drmowinckels @emjonaitis I didn’t go as far as wiping the original and its history on GitHub, just added CodeBerg forwarding address and archived. I wonder if #zenodo DOIs can be redirected from GitHub to new hosting… haven’t had to deal with that yet myself.

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Peter Cock @pjacock@fediscience.org

· 14mo ago

Just added Amos Bairoch's ISMB Accomplishment by a Senior Scientist Award https://www.iscb.org/iscb-awards/accomplishment-senior-scientist-award to his #wikipedia page: https://en.wikipedia.org/wiki/Amos_Bairoch

(It was mentioned at the end of his #ISMBECCB2025) keynote talk

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Peter Cock @pjacock@fediscience.org

· 8mo ago

Replying to

@zerodivision@fediscience.org How exactly are the alignments defined? Simple offsets that apply to the entire feature (easy) or might potentially there be different shifts within a feature (within introns or worse exons)? For the easy case you might use Biopython (shifting locations by an offset is as simple as adding an integer), but would need some familiarity to setup the plumbings. Could probably handle shifting each exon too (sublocations) but more faff. Shifts in CDS meaning due to alignment gaps would be a right pain.

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Peter Cock @pjacock@fediscience.org

· 8mo ago

Replying to

@mitchellh@hachyderm.io or don’t move your hand, switch to your navigation layer (I hold down a right thumb key), and then your home row becomes your cursors (mine are an inverted tee rather than a vi/vim style row of four). Programmable keyboards FTW! (But yeah, keyboard shortcuts can be wonderful)

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Peter Cock @pjacock@fediscience.org

· 10mo ago

Replying to

@Codeberg@social.anoxinon.de I guessed when a git push failed. Looks like a bad one as the website is down too. Thank you to the team & good luck

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Peter Cock @pjacock@fediscience.org

· 10mo ago

Replying to

@etiennebacher@mastodon.social #HelixEditor support https://docs.helix-editor.com/lang-support.html may be relatively easy as it uses the tree sitter LSP model, quoting your README: “Jarl is faster and also easier to link to the Language Server Protocol, which enables its use via VS Code or Positron extensions for instance.”

docs.helix-editor.com

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Peter Cock @pjacock@fediscience.org

· 25mo ago

Replying to

@darkuncle@infosec.exchange @b0rk@social.jvns.ca @phire I know this snippet as #StrictBashMode or #BashStrictMode from http://redsymbol.net/articles/unofficial-bash-strict-mode/ and it’s my default bash header ❤️ And yes, it can need tweaks for things like using grep success vs failure in if-statements.

Bash Strict Mode

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Peter Cock @pjacock@fediscience.org

· 9mo ago

Replying to

@bunnie actually having read your talk abstract about the rust centric design, maybe https://github.com/HaoboGu/rmk is a better fit than Zephyr based ZMK if wanting to use this as a DIY computer keyboard controller?

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Peter Cock @pjacock@fediscience.org

· 9mo ago

Replying to

@bunnie Probably not your target for Xous & Baochip, but might work and be kinda cool for DIY #MechanicalKeyboard designs? Here the Raspberry Pi ARM chips have become very popular for non-Bluetooth designs with #QMK etc firmware (including rust based options). (QMK has very limited Bluetooth support due to licensing incompatibility with closed hardware; Zephyr based #ZMK rules here but the RP’s Bluetooth isn’t supported yet, and I understand not a high priority due to Pi being so power hungry battery life would be poor.)

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Peter Cock @pjacock@fediscience.org

· 9mo ago

Replying to

@bunnie Thanks. I watched your talk video - Raspberry Pi like pin reassignment, clever!

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Peter Cock @pjacock@fediscience.org

· 7mo ago

Replying to

@dalke those are a pain. Running under PyPy or Jython used to reveal a lot of those versus the assumptions with CPython.

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Peter Cock @pjacock@fediscience.org

· 5mo ago

Replying to

@bortzmeyer @b0rk @pulkomandy Then just in case, you can easily snapshot releases on GitHub to Zenodo and get a DOI as well - https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content

Referencing and citing content - GitHub Docs

Referencing and citing content - GitHub Docs

You can use third-party tools to cite and reference content on GitHub.

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Peter Cock @pjacock@fediscience.org

· 2mo ago

Today Microsoft #Excel differences on Windows to macOS (missing menus just ribbon) got me thinking: can I not just run a #SpreadSheet in the #Linux #terminal for basic data work and visualisation? I want something akin to the original text only #Lotus123 (which I used for school work on DOS), but ideally with in-terminal graphics for #DataViz. There is https://github.com/andmarti1424/sc-im (must self compile, not trivial), several apparently abandoned tools like https://www.syntax-k.de/projekte/teapot/ - and multiple vibe-coded rust tools I'd rather avoid... Suggestions please?

GitHub - andmarti1424/sc-im: sc-im - Spreadsheet Calculator Improvised -- An ncurses spreadsheet program for terminal

sc-im - Spreadsheet Calculator Improvised -- An ncurses spreadsheet program for terminal - andmarti1424/sc-im

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Peter Cock @pjacock@fediscience.org

· 6mo ago

Replying to

@manchicken@defcon.social @mntmn@mastodon.social That could be very tempting! I’d like to buy their 15mm spaced keycaps with captions (to build a smaller kid’s #MechanicalKeyboard), have only found the blank MNT Pocket keycaps for sale…

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Peter Cock @pjacock@fediscience.org

· 5mo ago

Replying to

@FlockOfCats@famichiki.jp visit https://shop.yushakobo.jp/en if you’re in/near Tokyo - at very least you can try the feeling of a bunch of different switches and keycaps, and see some cool kits (but I guess you’re looking for prebuilt - they’re more the DIY end).

shop.yushakobo.jp

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Peter Cock @pjacock@fediscience.org

· 8mo ago

Replying to

@zerodivision@fediscience.org try searching for annotation lift over or transfer tools (but you may need to convert your genes into GTF or GFF format first)?

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Peter Cock @pjacock@fediscience.org

· 5mo ago

Replying to

@LeafyEricScott@hachyderm.io @adamhsparks@rstats.me are these optional columns at the end of each line? Otherwise seems horribly heuristic.

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Peter Cock @pjacock@fediscience.org

· 8mo ago

Replying to

@taydev@hachyderm.io that’s basically what I do too, but the details differ. I hold down space with right thumb, and use what would be Qwerty’s JKIL for an inverted tee cursor set - like https://dreymar.colemak.org/layers-extend.html

dreymar.colemak.org

DreymaR's Big Bag of Kbd Tricks - Extend Extra Extreme

A treasure trove of keyboard wisdom. Layout tips, tricks, modifications and additions await in the Big Bag! Centered around but not limited to the Colemak layout.

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Peter Cock @pjacock@fediscience.org

· 5mo ago

Replying to

@cks@mastodon.social and just like breaking UI conventions can be justified in exceptional cases, you should start with standard conventions for user facing configuration files (eg INI files)? KISS, principle of least surprise, etc.

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Peter Cock @pjacock@fediscience.org

· 5mo ago

Replying to

@gedankenstuecke@scholar.social @cameronneylon@hcommons.social @florian@bsd.network Sadly not - I left all my spare Codeberg and Forgejo stickers at the Dundee state of the map conference 🗺️ I’d seen the "notice: butlerian jihad is the moderate position" design and agree it is an excellent sticker 👌

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Peter Cock @pjacock@fediscience.org

· 5mo ago

Replying to

@pkal@social.sdfeu.org @cks@mastodon.social I think that’s true - perhaps more common on cross platform tools that UNIX first? I’ve seen a bunch that superficially at least look like INI files: https://docs.helix-editor.com/configuration.html Or key=value without sections: https://ghostty.org/docs/config

docs.helix-editor.com

Configuration

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