@dalke@toots.nu

Andrew Dalke @dalke@toots.nu · Jul 22, 2026

Replying to @dalke@toots.nu

@lkngrrr@hachyderm.io I also seem to recall a Eugene Garfield essay, perhaps in the 1970s, about the bright future which would allow full-text search to skip some of the issues with machine-based coordinate search. I don't have a link for that one handy.

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Andrew Dalke @dalke@toots.nu · Jul 22, 2026

Replying to @lkngrrr@hachyderm.io

@lkngrrr@hachyderm.io For some history, back in the 1950s people looked to computers as a way to not need single term classification. "The Technical Report and Its Impact on Post–World War II Information Systems", Jana Varlejs, https://web.archive.org/web/20130702201706/https://www.asis.org/History/07-varlejs.pdf quotes Taube (1950) “there cannot be one subject key to bibliographic organization which would serve the librarian, the general reader, and all specialists”, and proposed using computers to handle multiple coordinates. (Nor was he the first to propose it.)

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Andrew Dalke @dalke@toots.nu · Jul 21, 2026

Replying to @fnrd@toots.nu

@fnrd@toots.nu Since then I've found https://vindskyddskartan.se/en/ which is the only one to show both shelters near me. I've also found POI Map, which lets me toggle on/off POIs in OSM, like water and libraries at https://www.flosm.org/en/poimap.html?lat=58.1555709&lon=12.1589731&r=38776.133&st=0&sw=drinkingwater,library

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Andrew Dalke @dalke@toots.nu · Jul 17, 2026

Replying to @hsza@social.tudbut.de

@hsza@social.tudbut.de @Arusekk@infosec.exchange @david_chisnall@infosec.exchange @rosaaeterna@transfem.social "Many people believe that the spirit of the GNU Project is that you should not charge money for distributing copies of software, or that you should charge as little as possible ... This is a misunderstanding. Actually, we encourage people who redistribute free software to charge as much as they wish or can. ... If this seems surprising to you, please read on." Full essay by Stallman at https://www.gnu.org/philosophy/selling.en.html

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Andrew Dalke @dalke@toots.nu · Jul 16, 2026

"Man it's hot. It's like Africa hot." temp here in Sweden = 33°C Algiers = 38 Cairo = 35 Lagos = 27 Kankan = 27 Juba = 33 Kigali = 28 Hmm, looks like I'll need to modify that movie quote to, "it's like Sub-Saharan Africa hot." And if I cheat by heading into winter ... Harare = 22 Windhoek = 24 Cape Town = 18 Huh. Here and today's high also matches Miami's high, .. and every other place I once called home has cooler temps. Feeling cooler now - I twice visited Death Valley. Its high is 45°.

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Andrew Dalke @dalke@toots.nu · Jul 14, 2026

Replying to @Jaak@toots.nu

@Jaak@toots.nu Nej, tyvärr. Jag förväntade dem inte. Efter 3 eller 4 år med Hittaut var den det första gången jag fick fästingar. Området var ganska vilt, och så värmt att jag hade shorts istället för byxor. https://www.openstreetmap.org/#map=15/58.33039/12.28438&layers=P

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Andrew Dalke @dalke@toots.nu · Jul 12, 2026

Replying to @Arapalla@aus.social

@Arapalla@aus.social @fesshole@mastodon.social What about "damn"? Frankly my dear, I don't give a damn. - noun. Damn the torpedoes, full speed ahead! - verb Things are changing too damn fast. - adverb Get in the damn car. - adjective Damn! - exclamation

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Andrew Dalke @dalke@toots.nu · Jul 10, 2026

Replying to @fnrd@toots.nu

@fnrd@toots.nu Whoa, where did that come from‽ I must have not thought of shelters, etc. as "places", even through they clearly are. Thanks! Hmm, only two shelters along the route? And missing the ones just south of here. Last night I found https://pangose.github.io/sheltermap/ which shows more. I found some water maps too, but the "places" option you highlighted is nice as it shows the churches along the way are open for WC and water use. Thanks again!

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Andrew Dalke @dalke@toots.nu · Jul 09, 2026

Har klarat den sista (av 100) #hittaut #checkpoints i #Trollhättan/#THN. 🎉 Nr 1-10, vid Hjutsjön. Var jobbigt! Gick hela vägen dit och tillbaka från/till stan. Samt fick 7 fästingar. 😠

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Andrew Dalke @dalke@toots.nu · Jul 09, 2026

Replying to @fnrd@toots.nu

@fnrd@toots.nu I don't see any way to show water, toilets or shelters. When I zoom in to where I know there are shelters, I see nothing marked on the map. BRouter using OSM tiles shows shelters, like at https://www.brouter.de/brouter-web/#map=19/58.26723/12.21253/standard&profile=hiking-mountain , but they are hard to spot except when zoomed in. Which means the data is present, somewhere, but I haven't figured the magic to turn it on. BRouter has an option to show extra info, like "wilderness hut" and "shelter", but it just spins with "Running Overpass API query." :(

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Andrew Dalke @dalke@toots.nu · Jul 05, 2026

Where do I get a good outdoors/hiking map which lists where to get water and find shelters and toilets? For Västra Götaland, Sweden. I want to do the Pilgrimsleden Göta Älv, at https://pilgrimsleden-gota-alv.westswedentrails.se/en/kartplaneringsverktyg/pilgrimsleden-gota-alv#googtrans(sv|en) I want to see where there are shelters for sleeping, water points, and toilets. I can't for the life of me find this information. The closest is with brouter.de but I get stuck spinning with "Running Overpass API query ..."

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Andrew Dalke @dalke@toots.nu · Jul 03, 2026

Replying to @jwildeboer@social.wildeboer.net

@jwildeboer@social.wildeboer.net While on the other hand, Västtrafik wants to make it harder to use cash for mass transit - https://www.vasttrafik.se/info/kortlasare-avvecklas/ For certain routes the only cash solution is to buy a period card (like a day ticket), instead of a one-way ticket. This makes us even more dependent on the US and gives the US more power to threaten, say, a Swedish investigator of US war crimes, or trans-rights activist. "That's a nice digital society you live in. I hope you don't force us to shut off your banking."

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Andrew Dalke @dalke@toots.nu · Jul 03, 2026

Replying to @jwz@mastodon.social

@jwz@mastodon.social A termite walks into a bar and asks "Is the bar tender here?" Two guys walk into a bar. The third one ducks. A proton walks into a bar and orders a beer. The bartender says, "are you sure?" The proton answers, "yep, I am positive." An h walks into a bar then starts bawling. The bartender asks "What's wrong?" The ℏ replies "I just lost two pies!" A screwdriver walks into a bar and asks "Can I get a me?" Bartender replies, "Congratulations on your successful defense, Dr. Pepper."

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Andrew Dalke @dalke@toots.nu · Jun 29, 2026

Replying to @nedbat@hachyderm.io

@nedbat@hachyderm.io ... yes? I mean, I mentioned the *args-as-tuple observation from your essay, and tried to build on it by highlighting a case where Python uses a tuple for homogenous data, but unlike with *args it's not so clear that a list could make more sense. I think it's a tuple for the more technical reason that if __bases__ is a (mutable) list then it's very hard if not impossible to prevent an inheritance cycle.

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Andrew Dalke @dalke@toots.nu · Jun 29, 2026

Replying to @nedbat@hachyderm.io

@nedbat@hachyderm.io @Tipa@gamepad.club One of the not-easily-described cases is __bases__, which is a variable-length tuple of types: >>> class Spam: pass ... >>> class Eggs: pass ... >>> class Meal(Eggs, Spam): pass ... >>> Meal.__bases__ (, ) That's a bit more to the "Technical" side than the "*args" case.

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Andrew Dalke @dalke@toots.nu · May 21, 2026

En vecka efter gökotta hörde jag en gök!

Ännu bättre, gök gal i väst.

Fröken västergök är bästergök

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Andrew Dalke @dalke@toots.nu · May 20, 2026

My Cat® feature phone fares poorly in the post-3G world. After 6 months of intermittent connectivity, I bit the bullet and got a new phone, a Mudita Kompakt.

Technically it's Android, but no Google, web browser, or app store in sight. Excellent battery life - looks like 10% battery loss/day at my use level.

For the first time in a long time I felt happy after reading the terms&conditions! Easy to read and doesn't confuse consent with permission for surveillance capitalism.

#muditakompakt .

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Andrew Dalke @dalke@toots.nu · May 17, 2026

USA kallar "radically pro-transgender" folk som terrorister.

USA har stängt av internet och bankkort tjänster till svenskar som de stämplade som terrorister.

När kommer USA att stänga av Apple/ Google/ Microsoft/ Visa/MasterCard till transmänniskor i Sverige?

Och sen .. abortdoktorer? Forskare om amerikanska brott mot folkrätten?

app + kontantfri => USA få mer kraft över alla som bor i Sverige.

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Andrew Dalke @dalke@toots.nu · May 13, 2026

Planen e att göra Pilgrimsleden mellan Göteborg o Vänersborg. Ca. 14 mil. Ha börjat träna. 6 km idag, varav 3 km i skogen med upp-och-ner.

Förhoppningsvis kommer jag att klara hela Edsvidsleden (14 km) på en gång, inom flera veckor. Sen bytter jag till den stora ryggsäcken och mer vikt.

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Andrew Dalke @dalke@toots.nu · May 01, 2026

Har bekräftat att #SocialDemokraterna i stan vill spara pengar med att minska möljigheten för att kunna åka kollektivt för folk som inte har bankkort eller app. Den kommer att påverka några

- äldre
- hemlösa
- nya immigranter & besökare från flera länder
- ungdomar
- flyktingar
- svenskar på USA:s "specially designated national" lista

samt

- de med höga krav på integritet, som skulle åka anonymt
- de som bojkottar USA och vill inte vara beronde på USA för sitt vardagligt liv

S omfamnar USA.

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Andrew Dalke @dalke@toots.nu · May 01, 2026

Replying to @itamarst@hachyderm.io

@itamarst@hachyderm.io @trs@metasocial.com @glyph@mastodon.social When I used OpenMP to parallelize my code I found that single-threaded processing became slower. I ended up using some C macros shenanigans to double-include the relevant C code, once for the single-thread case (no OpenMP) and once for multiple threads (OpenMP). If you do OMP_NUM_THREADS=1 then it avoids using OpenMP completely.

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Andrew Dalke @dalke@toots.nu · Apr 28, 2026

My wife is on a sociology class trip to Rome. I suggested she install #OrganicMaps to get around. She found it easy to install and download the Rome map for offline use.

When the got to the hostel, turns out they were delivered to the wrong building. The right was 1 km away. Easy walk, no need for a roaming plan. When they are told to meet at a given plaza after lunch? Done.

Some of her classmates don't have working data on their phones. They like her map, but oddly haven't installed the app??

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Andrew Dalke @dalke@toots.nu · Apr 27, 2026

Jag ringde #Västtrafik och fick bekräftelse att i framtiden kommer de två lösningarna att betala kontant att vara: 1) pappersbilljet, som måste köps när butiken eller ombud har öppet, och är kan inte förköps, och 2) periodkort, som är mycket dyrare för oss som sällan åker.

De har inga planer för #hemlösa, #flyktningar, nya #immigranter, besökare, ungdomar, osv som saknar bankkonto och betalkort och måste använda kontant för att åka kollektivt! (t.ex, till/från sjukhuset)

Vsg och skicka vidare!

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Andrew Dalke @dalke@toots.nu · Apr 21, 2026

Replying to @mhoye@cosocial.ca

@mhoye I believe the answer may found in the Book of Job.

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Andrew Dalke @dalke@toots.nu · Apr 20, 2026

I have withdrawn my submission to the Journal of #Cheminformatics due to poor response by the editors for concerns I raised about possible ethical violations, and due to Springer denying my request for fee waiver, which I made in the submission process, on the grounds that it was made too late and should have been part of the submission process. I got this notification last week, three months after submission, and after two rounds of peer review.

I do not recommend people publish in J.Cheminf.

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Andrew Dalke @dalke@toots.nu · Apr 16, 2026

Replying to @dalke@toots.nu

@molecule

EState atom typing is 30% faster with the new SMARTS extension.

old time: 15.32 (EState atom typing with recursive SMARTS) new time: 10.59 (EState atom typing with my new notation) other time: 18.38 (Python startup/overhead and parse time)

Nicer to read too, for orbital configuration patterns. Compare:

[PX3#-3H2] [PX3#-3H1] [PX3#-3H0] [PX4#-3#=1H0]

vs

[PX3H2]-[!#1] PX3H1-[!#1] PX3H0(-)- PX4H0(-)(-)-*

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Andrew Dalke @dalke@toots.nu · Apr 15, 2026

Replying to @molecule@mstdn.science

@molecule With my modifications to the RDKit SMARTS matcher:

mol = Chem.MolFromSmiles("FS(F)(F)(F)(F)N(S(F)(F)(F)(F)(F))S(F)(F)(F)(F)(F)") pat = Chem.MolFromSmarts("[$(d6()()()()*)]") print(len(mol.GetSubstructMatches(pat))) 2 pat = Chem.MolFromSmarts("[d6#-6]") print(len(mol.GetSubstructMatches(pat))) 3

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Andrew Dalke @dalke@toots.nu · Apr 15, 2026

Replying to @dalke@toots.nu

@molecule .... and here's a diff which adds that to RDKit. (Incomplete. Doesn't do the full function registration or handle MolToSmarts or have tests.) https://paste.sr.ht/~dalke/e3748ccea2bf3b58c04abd8fa9aaebb57953ce13 With it, something like [!$(*#*)&!D1] can be replaced with [##0!D1], and make HasSubstructMatch twice as fast. BTW, my has-a-double-or-triple-bond SMARTS should be "[!#=0,!##0]" (with "," not ";"). :) To go further than this POC and add it to RDKit would require evidence of of utility that I can't provide.

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Andrew Dalke @dalke@toots.nu · Apr 14, 2026

Replying to @molecule@mstdn.science

@molecule Nice. 6! = 720 hence only 2 matches with a default max of 1,000. Looks like "d" is an RDKit extension for non-hydrogen degree. I didn't know about it. I've been toying with a new SMARTS extension: '#' ('-' | '=' | '#' | ':') = for n single (implicit and explicit), double, triple, or aromatic bonds Your pattern might then be written "[d6#-6]", since I don't think you need to match aromatic bonds. "Atom with at least one a double or triple bond" would be "[!#=0;!##0]".

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Andrew Dalke @dalke@toots.nu · Apr 10, 2026

Replying to @aartaka@merveilles.town

@aartaka I think you'll enjoy https://en.wikipedia.org/wiki/Polynesian_navigation and learning more about Mau Piailug (https://en.wikipedia.org/wiki/Mau_Piailug) and his influence on the Second Hawaiian Renaissance and revival of Polynesian wayfinding. Eg, http://www.forsea.org/wp-content/uploads/2019/09/f9u1A300-navigating.pdf and https://daily.jstor.org/pius-mau-piailug-master-navigator-of-micronesia/ . Then take everything you may have learned about Polynesian migration from Thor Heyerdahl's exciting "Kon-Tiki" account and throw it out the window as white supremacist Eurocentric hyperdiffusionism trash.

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Andrew Dalke @dalke@toots.nu · Apr 10, 2026

Replying to @aartaka@merveilles.town

@aartaka Yes. I know traditional Polynesian navigation included many methods to help infer island location further than 8 miles away, and out of line of sight, like observing:

wave patterns (which are reflected and refracted by the island);
bird flight and habits (a diurnal bird in the morning with a fish in its mouth is likely heading to its nest);
cloud patterns above the island

But note how position uncertainty and visual confusion lead to the name "False Bay", https://en.wikipedia.org/wiki/False_Bay

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Andrew Dalke @dalke@toots.nu · Apr 10, 2026

Replying to @aartaka@merveilles.town

@aartaka The statement 'This may sound a little outdated, but this system was perfected to such an extent that in the second half of the eighteenth century it was almost as accurate as the present-day GPS.' remains me of the discussion on mapping in "The Ring of Truth" by the Morrisons in the late 1980s. The image from the book, https://archive.org/details/ringoftruthinqui00morrrich/page/138/mode/2up?q=gps compares a 1798 position (off by 8 miles), the 1980s position using old methods, and GPS (within 50 feet). Video at https://archive.org/details/TheRingofTruth/Ring.of.Truth.S01E03.Mapping.1987.VHSRip.AAC2.0.x264-rattera.mp4 .

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Andrew Dalke @dalke@toots.nu · Apr 03, 2026

Replying to @me_@sueden.social

@me_ @Unixbigot I remember using elvis to open the directory. Not a list of the files in the directory, but the content of the directory inode.

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Andrew Dalke @dalke@toots.nu · Apr 03, 2026

Replying to @Unixbigot@aus.social

@Unixbigot @me_ FWIW, from 1st ed. 1987,

A UNIX file system uses 1024-byte blocks and 16-bit disk addresses. The i-node holds 8 disk addresses for data blocks, one single indirect block address, and one double-indirect block address. What is the maximum file size? Think carefully.
Three different protection mechanisms that we have discusses are capabilities, access control lists, and the UNIX rwx bit. For each of the following protection problems, tell me [...] which can be used ...

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Andrew Dalke @dalke@toots.nu · Mar 29, 2026

Replying to @gvwilson@mastodon.social

@gvwilson@mastodon.social I have no pointers to such a language, merely an observation that perl's "taint" seems like a mechanism to capture the intent that "this string needs input validation before general use."

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Andrew Dalke @dalke@toots.nu · Mar 21, 2026

Replying to @dalke@toots.nu

To make it more fun, add more possible matches

pat = Chem.MolFromSmarts("[$(CX4(-)-CX4(-)-CX4(-)-CX4(-)-CX4-*)]") print(len(mol.GetSubstructMatches(pat, maxMatches=25000))) 46 print(len(mol.GetSubstructMatches(pat, maxMatches=30000))) 50

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Andrew Dalke @dalke@toots.nu · Mar 21, 2026

Replying to @dalke@toots.nu

The answer is 42. When the pattern CD4H0X4(-)(-)-*) matches an atom, there are 24 possible ways for it to match (that's 4! = 4 * 3 * 2 * 1 because there are 4 places for the first *, 3 for the second, etc.).

RDKit's GetSubstructMatches by default matches at most maxMatches=1000 times.

1000/24 = 41.666...

Changing maxMatches to 2000 finds all 50 expected matches.

This means RDKit's recursive SMARTS matcher does all matches, rather than stop at first match.

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Andrew Dalke @dalke@toots.nu · Mar 20, 2026

Replying to @cdk@fosstodon.org

@cdk The OEChem equivalent also finds 50, as does my eyeball interpretation. The question is, what does RDKit return, with the secondary question "why"?

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Andrew Dalke @dalke@toots.nu · Mar 20, 2026

Here's an #RDKit #cheminformatics quiz for you all. What do you think this code will output?

from rdkit import Chem
mol = Chem.MolFromSmiles("C" + "C(C)(C)" * 50 + "C")
pat = Chem.MolFromSmarts("[$([CD4H0X4](-*)(-*)(-*)-*)]")
print(len(mol.GetSubstructMatches(pat)))

No cheating by actually running the code! :) Feel free to explain your reasoning in the comments.

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Andrew Dalke @dalke@toots.nu · Mar 10, 2026

Replying to @wackJackle@norden.social

@wackJackle@norden.social @adapalmer@wandering.shop I don't understand the economics. If I print 300 books for the cost of one copy of the book, and I sell seven copies, doesn't that mean I've made a big profit? Even if the 293 remaining copies just sit there? Or were manuscript copies by scribes sold at a big loss? And https://en.wikipedia.org/wiki/Gutenberg_Bible says the full print run of 158 or 180 copies seems to have sold out immediately, including sales outside modern Germany, so how did poor distribution result in bankruptcy?

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Andrew Dalke @dalke@toots.nu · Mar 06, 2026

Replying to @egonw@social.edu.nl

@egonw@social.edu.nl I don't think that's the case here. Fingerprints are no longer a hot topic. People read, study, and ponder their field intensely, but pick up related fields by a sort of osmosis. As more people used binary ECFP/Morgan/circular fps, the viewpoint progressed from "interesting", to "a good baseline", "standard practice", and "best practice", even "gold standard." Using something else requires justification and extra work. A tutorial doesn't have the weight to change that perception.

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Andrew Dalke @dalke@toots.nu · Mar 06, 2026

Replying to @egonw@social.edu.nl

@egonw@social.edu.nl Thanks for looking! I do not know why count fingerprints are seemingly so rarely used over their binary counterparts.

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Andrew Dalke @dalke@toots.nu · Mar 05, 2026

Replying to @ThePSF@fosstodon.org

@ThePSF

I and others have highlighted problems in the survey. No wonder mostly new Python programmers answer it.

need to agree to a 10 page legal document
which say you pay a fine if you discuss the survey before publication!
biased towards professional software developers, ie, the target audience of JetBrains, not "the Python community"
the prize is a $100 card from anti-labor, pro-Trump Amazon

The PSF account has never replied to any comment.

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Andrew Dalke @dalke@toots.nu · Mar 03, 2026

Replying to @egonw@social.edu.nl

@egonw@social.edu.nl @cdk@fosstodon.org Good point. I can't search on GH w/o a Microsoft/GH login. Other services let me do some searches. "getCountFingerprint" shows almost no hits, neither for CDK nor RDKit's GetCountFingerprint. So, not for this chemfp release. I don't get why people aren't experimenting more with count fingerprints.

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Andrew Dalke @dalke@toots.nu · Mar 03, 2026

Replying to @cdk@fosstodon.org

@cdk@fosstodon.org I'll update chemfp for "Allow the ExtendedFingerprinter to setHashExplicitHydrogens". BTW, any idea of how often people use the count versions of these fingerprints?

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Andrew Dalke @dalke@toots.nu · Feb 24, 2026

I've been an emacs user since the early 1990s.

My introduction to Unix-like systems was with Minux in 1990, where the class used elvis.

I then became one of those "I know just enough vi to compile emacs" people, on IRIX.

Today is the first time I've used TRAMP (the Transparent Remote Access, Multi-Protocol), so I could edit files on a remote computer using the emacs on my laptop.

Usually I just ssh in and use emacs locally as text-only.

I guess I decided to be adventurous today. :)

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Andrew Dalke @dalke@toots.nu · Feb 24, 2026

Replying to @dalke@toots.nu

After 5 hours, found the problem. I have a function which creates a generator and returns a generator, like: def f(filename): it = g(filename) def process_it(): for value in it: yield value*2 return process_it() I needed def process_it(): try: for value in it: yield value*2 finally: it.close() I used traceback.print_stack() to help figure out if I was in a normal close() or in gc close, since it's a few levels deep.

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Andrew Dalke @dalke@toots.nu · Feb 21, 2026

The #cheminformatics fingerprint tool #chemfp version 5.1b1 is out! https://chemfp.com/

The big feature is integration of the new "superimposed" count simulation method to RDKit byte fingerprint generation.

Use it if you want Tanimoto similarity of count fingerprints, but don't want to toss out all of your existing byte fingerprint tools for similarity search, clustering, etc. nor take a big performance loss.

Instead, use superimposed and get a ~0.95 recall using "normal" byte fps.

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Andrew Dalke @dalke@toots.nu · Feb 20, 2026

Replying to @dalke@toots.nu

Now my test suite says there's a file handle I forgot to close. It generates a warning to stderr. Some of my tests check stderr to ensure it's empty. I've been staring at the code, and as far as I can tell it's in a context manager which should always close it. Annoying. And the relevant code hasn't changed in months, which means it's a garbage collection timing thing where new tests changed when gc is run. I don't think I'm being happy enough. ;)

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Andrew Dalke @dalke@toots.nu · Feb 19, 2026

Ahh, the joy of writing the documentation which summarizes all of the new features, then realizing that I forgot to implement two functions. Added functions. Added tests.

Then to update the documentation for a command-line "--help" and learn that "--help" doesn't work. Turns out I forgot to define a metavar that click needs. Added tests.

Now to figure out why the SEC fingerprints changed in the latest RDKit version.

Happy, happy, joy, joy.

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