RasmussenLab/vamb erreicht einen Gesundheitsindex von 56 von 100 und liegt damit im Bereich Mittel. Am stärksten schneidet es bei Community & Adoption (68/100) ab, am schwächsten bei AI Readiness (32/100). Zuletzt vor 85 Tagen aktualisiert. Ein einzelner Mitwirkender trägt den Großteil der jüngsten Arbeit.
56
gesamt / 100
Mittel
Software-Gesundheitsindex
Metriken werden auf einer Skala von 1–100 in gewichtete Kategorien gruppiert. Der Gesamtwert beginnt als ihr Mittel; sobald öffentliche Evidenz die Richtlinie für Hochrisikojurisdiktionen auslöst, wird die Bewertung angepasst und erhält die Obergrenze 49 (Gefährdet). AI Readiness liegt außerhalb.
56
Exzellent85-100Vorbildlich; erfüllt im Wesentlichen alle geprüften Kriterien
Gut70-84Gesund; geringfügige Lücken
Mittel50-69Akzeptabel mit deutlichen Lücken; Überprüfung empfohlen
Gefährdet30-49Erhebliche Schwächen; eine Übernahme erfordert Vorsicht
Kritisch1-29Schwerwiegende Probleme (aufgegeben, nur ein Maintainer, keine Hygiene)
Bewertungsprofil
Jede Achse ist eine Kategorie. Die Form zählt mehr als der Durchschnitt — ein gesundes Projekt füllt die gesamte Fläche, während ein Profil aus Spitzen und Kratern bedeutet, dass Stärke in einer Dimension Risiken in einer anderen verdeckt.
Dieses Repository wird von einer Organisation getragen — geteilte, rechenschaftspflichtige Trägerschaft, die jeden einzelnen Maintainer überdauern kann.
Direkte Abhängigkeiten ohne bekannte Advisories — 1 betroffen: torch 2.6.0 (high 8.8)
25/25
Indirekte Abhängigkeiten ohne bekannte Advisories — keine indirekte Abhängigkeit trägt ein bekanntes Advisory
32.8/40
Keine offenen Advisories — 1 Paket(e) mit Advisory seit über 90 Tagen unbehandelt; ältestes vor 498 Tagen veröffentlicht
Verwendete Eingangsdaten
source
osv
advisories
24
affected_packages
1
assessed_packages
37
unassessed_packages
0
affected_by_severity
high 1
direct_affected_packages
1
Abgeglichen wurde die Laufzeit-Abhängigkeitshülle von pypi:vamb@5.0.4 — das, was die Installation des veröffentlichten Pakets nach sich zieht — mit 37 Paketen. Erreichbarkeit wird nicht analysiert.
Wie gut ist das Repository dafür ausgestattet, mit KI-Coding-Agenten entwickelt und gepflegt zu werden? Ein unabhängiges, experimentelles Badge — Gewicht 0,0, es wird eigenständig ausgewiesen und verändert den Gesamt-Gesundheitswert nicht.
Typprüfbarer Code — Python ohne Typprüfungs-Konfiguration
53.6/55
Handhabbare Dateigrößen — 1/40 Quelldateien über 60 KB
Verwendete Eingangsdaten
primary_language
Python
largest_source_bytes
91.868
source_files_sampled
40
oversized_source_files
1
Eckdaten
330GitHub-Sterne
10Mitwirkende
15Commits, letzte 12 Monate
85Tage seit letztem Push
25Releases
1Bus-Faktor
48offene Issues
PyPIPaket-Ökosysteme
Weitere Details
Stern- und Fork-Verlauf 330 ★ / 51 ⇿
330Sterne
51Forks
25Releases
Wann jeder Stern und Fork hinzugefügt wurde, von GitHub erfasst und nach Tagen gruppiert. Das kumulierte Wachstum steht direkt über den täglichen Zugängen, aus denen es besteht, sodass beide gegeneinander lesbar sind: stetiger organischer Zuwachs sieht ganz anders aus als ein abrupter, kurzlebiger Ausschlag. Wo dieser Unterschied messbar ist, wird er als Wachstumsauthentizität ausgewiesen.
Major 4Minor 2Patch 18
Jeder Punkt umfasst 8 Tage.
OpenSSF Scorecard 3.6 / 10
3.6Gesamtwert
Unabhängige, werkzeugneutrale Sicherheitsbewertung durch das quelloffene OpenSSF Scorecard. Jede Prüfung honoriert eine Sicherheits-Praxis, nicht das Werkzeug eines bestimmten Anbieters. Prüfungen, die Scorecard nicht ermitteln konnte, sind mit k. A. markiert und vom Sicherheitswert ausgeschlossen (nie als null gezählt).Scorecard v5.5.0 · 2026-07-22 05:43 UTC
Vollständig aufgelöster Abhängigkeitssatz aus dem GitHub-Abhängigkeitsgraphen: 10 direkte und 0 indirekte (transitive) Pakete. Die transitive Hülle ist vollständig, wenn das Repository eine Lockfile eincheckt.
Registry
Paket
Version
Beziehung
PyPI
dadaptation
3.2
direkt
PyPI
loguru
0.7.3
direkt
PyPI
networkx
3.4.2
direkt
PyPI
numpy
1.26.4
direkt
PyPI
pycoverm
0.6.2
direkt
PyPI
pyhmmer
0.10.15
direkt
PyPI
pyrodigal
3.6.3
direkt
PyPI
scikit-learn
1.6.1
direkt
PyPI
torch
2.6.0
direkt
PyPI
vambcore
0.1.2
direkt
Abhängigkeits-Advisories 1
Die Installation von pypi:vamb@5.0.4 zieht 37 Pakete nach sich, direkt und transitiv: 1 tragen bekannte Advisories, davon 1 direkte Abhängigkeiten.
Paket
Version
Beziehung
Schweregrad
Advisories
Behoben in
torch
2.6.0
direkt
hoch
24
2.13.0
Ein Advisory bedeutet, dass die im Abhängigkeitsgraphen erfasste Version in den betroffenen Bereich eines Advisories fällt. Erreichbarkeit wird nicht analysiert, und der Graph enthält Entwicklungs- und Test-Pins — ein Fund kann das Werkzeug betreffen und nicht die ausgelieferte Software.
JSON-Rohbericht maschinenlesbar
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"body": "Previously, the VAEVAE's batch size and epochs were used. Also, delete the -pq\noption, which was never used, even when set.",
"is_bot": false,
"headline": "Fix: In TaxVamb, use Taxometer CLI options for Taxometer (#444)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-04-29T11:16:00Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "23dfdef95d6ae1e6026d3b6b572051a5784f56ec",
"body": "* Print in scientific notation, to allow small losses to not round to zero\n* Print the epoch number so people know how far the network has come\n* Indent the loss lines similar to the VAE loss's log lines",
"is_bot": false,
"headline": "Improve printing of VAEVAE loss in log (#443)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-04-29T09:21:20Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "782c2425668f4d7dbda04ee2d82c0453b16a7a84",
"body": "Previously, it got parsed as `[\"\"]`.",
"is_bot": false,
"headline": "Bugfix: Parse empty taxonomy as empty list (#441)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-04-25T08:42:31Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7b5d46541cfd1b20766d90a7c47db3c7c8e7af0c",
"body": null,
"is_bot": false,
"headline": "Update CI (#442)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-04-25T08:33:56Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7ce46fa53c7d3015e451f248c54266120d7c64c4",
"body": "When parsing a Taxonomy object, each seq in the input file needs to be matched\nwith the existing seq in the CompositionMetaData. However, seqs may be filtered\nfrom the latter, if they fall below the minimum length.\nSo, when we encounter a seq in the taxonomy file not present in the composition,\nhow \n[…]\nthe composition, but then check that the\n taxonomy contained all the sequences in the composition.\n Thus, do less validation than would be optimal, but no breakage\n\nThis commit goes with option 3.",
"is_bot": false,
"headline": "Allow taxonomy to contain filtered contigs (#439)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-04-08T11:35:05Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "f27691adc4bd2afd8a64f384fbb73efef557d02c",
"body": null,
"is_bot": false,
"headline": "Docs: Add how to run on example data (#436)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-04-07T11:56:32Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "2fa0a675113705a2552cecf7fe00e6cf0373e7ee",
"body": "Users have often installed old versions of Vamb (see e.g. results presented in\nHan, Wang & Zhu, Nat Commun 16, 2025)\nThis is unfortunate, and may be due to Conda having old versions.\nMaybe this doc change can convince some users to upgrade, and can be used as\na reference to persuade people in the future.",
"is_bot": false,
"headline": "Add figure comparing Vamb versions (#432)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-04-01T07:33:59Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "8687abd494a58a788516319a63bcf6f8493d6acb",
"body": "This was left out from db35c11 by accident",
"is_bot": false,
"headline": "Remove Cython from pyproject (#431)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-03-30T18:20:53Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "db35c116519982c9fe1347dda215dfc5425e093d",
"body": "Remove the Cython backend _vambtools in favor of a separately installable Rust\npackage.\nThis is a reversible change, since it does not alter Vamb's API. If things go\nhorribly wrong, we can switch it back to the Cython version.\n\nThe advantages of the new backend are:\n* Hopefully, the inevitable insta\n[…]\n Vamb are not really in the Python parts anyway.\n\n* Python scripts like the ones in src/ can depend on vambcore instead of the\n whole of Vamb, and will therefore load faster and consume less memory.",
"is_bot": false,
"headline": "Switch Cython backend to vambcore package (#423)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-03-17T10:12:11Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "79ae2facc7aa7488b0e6596209b15c40282d741c",
"body": "Fix a bug in TaxVamb where a typo caused an error when instantiating a new DataLoader during a batch step. Also test this code path in the CLI args.",
"is_bot": false,
"headline": "Bugfix: Batchsteps for TaxVamb (#427)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-03-17T07:41:25Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "2b1e34fae658cef8196e64f6f5d30aa54d7fc716",
"body": "Some models in Vamb used dataloaders with `drop_last=True`. One rationale for\nthis is that the last mini batch, having fewer elements, is likely to give\ninflated gradients, which will disrupt training.\nHowever, since Vamb uses rather large batch sizes, this can easily result in a\nsituation where the\n[…]\nons is smaller than the batch size,\nwhich will result in an error, as no samples can be loaded from the dataset.\n\nHere, we only set `drop_last` if there are more observations than one mini\nbatch size.",
"is_bot": false,
"headline": "Only drop_last with enough elements in data loaders (#425)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-03-15T11:16:41Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "c2a05d68f528abf49003d0fd78d6b8fe49ffa3d3",
"body": "* Do not allow hash comments in FASTA files, which do not support this normally\n* Remove dead code\n* Clean up help strings in argument parser\n* Simplify FASTA parser and hopefully make it more robust",
"is_bot": false,
"headline": "Misc cleanup (#421)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-03-12T09:58:51Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "c7f225f3c771f95ffcb2069aaff3a4929874ffe6",
"body": "Missed a check for invalidly formatted input files.",
"is_bot": false,
"headline": "merge_aemb.py: Check duplicate headers (#420)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-03-12T09:32:18Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "27f8df9430da1ff9b5c423d8e72fad53092409ac",
"body": "The try-statement was meant to catch an iterator of non-bytes, as it's a common\nmistake to pass iterators of strings into the FASTA iterator.\nInstead, just check if the iterated object is an instance of `bytes`.",
"is_bot": false,
"headline": "Remove dubious use of try/catch in byte_iterfasta (#419)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-03-11T09:23:47Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0bd0df2524869c86a6e73ecb2a922dcf86af4a0a",
"body": null,
"is_bot": false,
"headline": "Bump Ruff linting CI",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-03-07T12:27:11Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "25b2f503ecde9c4936f52cef6913ac8a3deba92f",
"body": "To improve user friendliness of Vamb, it's important to be clear about the format\nof all input files, and to provide clear error messages to users when they\nviolate the assumed formats.",
"is_bot": false,
"headline": "Various improvements to parser error messages",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-03-07T12:27:11Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "adc76f7f641deaa75d2edce9fd44f91dabdac229",
"body": "* Use paths instead of strings\n* Check for invalid sample names",
"is_bot": false,
"headline": "Improve src/merge_aemb.py",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-03-07T12:27:11Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "9c06e8485527cd5d00a5dd6d994bef691e95ad63",
"body": "I'm generally wary of adding scripts, because they are hard to test.\nHowever, I'm making an exception here, because:\n1. Creating the input abundance TSV file from --aemb inputs is the recommended\n way of creating abundances in Vamb, and it's important that it's easy\n2. This script does not depend on Vamb and will not break when Vamb changes.\n In fact, it uses only numpy and stdlibs, and only reads and produces dirt\n simple, well-specified files making breakage unlikely.",
"is_bot": false,
"headline": "Add src/merge_aemb.py script to merge AEMB to abundance TSV",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-03-06T09:06:09Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "3e135a3b10ac9eeecf8597bfb2f0676c1425837b",
"body": "Based on a discussion with Lasse, I've reorganized the documentation to be more\ncomprehensive, and hopefully also easier to follow.\nRemove most of the information from the README in order to direct users to the\ndocumentation instead.",
"is_bot": false,
"headline": "Re-organise documentation and trim down README",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-03-05T12:41:56Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b3a58cd88eb823555a1720dabd7c00090e9eba52",
"body": "Mostly just formatting changes",
"is_bot": false,
"headline": "Small touchups to documentation and README",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-03-05T11:29:54Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "fb5c7d879beb6657fa3ab6ffd023ae53b564c2cb",
"body": "Add slightly more content in the how to run section.",
"is_bot": false,
"headline": "Expand on how to run",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-03-05T10:31:05Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "dae4cdf5066ff1f5ee8394e3e4b956713d64b07d",
"body": "* Add automatic help, which is more robust\n* Normalize path before checking parent to address edge cases like \"a/\"\n* Correctly close file handles on exception",
"is_bot": false,
"headline": "Slightly clean up concatenate script",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-03-05T09:51:25Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "26df8cda5bfae05476a1bc48b012d593d0d1ca33",
"body": "Prevents some annoying compat issues with NumPy v2.",
"is_bot": false,
"headline": "Bump deps, limit NumPy to v1",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-03-03T15:50:51Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "33aae5ab1c1aeb377adc747708f6d57eb1eb076c",
"body": "The medoid cache stores at least 4 * n_contigs bytes per entry, and often much\nmore. Without a limit, it may quickly consume multiple gigabytes of memory.\nHere, restrict the size to 64, which is approximately 3 times the size of the\nlatent space.\nThat might be too generous a size, but it should solve the problem experienced\nby our users at the moment.",
"is_bot": false,
"headline": "Limit medoid cache size to 64",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-03-03T15:48:46Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "f028bdd6119c48693b297d2218084923fdd8719d",
"body": "Don't mention the outdated Taxometer branch in installation instructions.",
"is_bot": false,
"headline": "Fixup README",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-02-28T11:45:55Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "03be8b1b84aa692e2e51f010e2d01eb7850a2d9e",
"body": "Commit d35788c introduced a bug, where sample_medoid was being called repeatedly\non the currently best medoid, instead of the different medoid candidates.\nThis effectively disables medoid wandering, therefore degrading clustering.\nFix this.",
"is_bot": false,
"headline": "Fix: Don't re-sample sample medoid candidate repeatedly",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-02-14T12:55:52Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "3fa8bf72feef26d021aa847845f9b343881826c3",
"body": "Several parts of TaxVamb's and Taxometer's handling of taxonomies have some\nimplicit assumptions which are not checked. Perhaps the restrictions could be\nlifted, but for now, let's check it when we parse the input files.\nIn particular, taxons are referred to by their name in the code, which means\nth\n[…]\non with a given name must always appear on the same rank\n* A taxon with a given name must always have a parent with the same name\nI believe this should be sufficient to ensure the tree is well-formed.",
"is_bot": false,
"headline": "Enforce well-behaved taxonomy annotations on tax construction",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-02-14T11:27:31Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "fc43b4550e37445c4f7d4bb868724e21e5b6634e",
"body": null,
"is_bot": false,
"headline": "Bump ruff format",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-02-11T09:21:01Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "38803bc527e645602f9944a3341324062eaba108",
"body": "We keep getting CI failures where the split fails because there is not enough\nfields. I can't debug why as it only fails in CI.\nMaybe a better error message will help me track it down",
"is_bot": false,
"headline": "Improve error on tax file splitting",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-02-11T09:21:01Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "02a9a6ec16e7db7bca4812f6f5b074e25f5aa444",
"body": "Mask short contigs when loading TSV abundance\r\n\r\nPreviously, the TSV file was expected to only contain the retained contigs.\r\nThis is confusing for users, since they natually assume the TSV file should\r\ncontain the same contigs as the composition or the FASTA file.\r\nSo, also mask the TSV file with the composition metadata mask when loading it.",
"is_bot": false,
"headline": "Mask short contigs when loading TSV abundance (#389)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-01-22T11:11:45Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "8fa32805d7267e50446b0220c7f0288480d8393e",
"body": "This is generally useful, and in particular helps with a current CI issue where\r\nthe wrong file is seemingly loaded in CI",
"is_bot": false,
"headline": "Log the file taxonomy is loaded from (#386)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-01-09T12:18:25Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a0c1a2afebe13431a54b0e4d69420ca2bd1cd004",
"body": null,
"is_bot": false,
"headline": "Bump dependencies and support Python 3.13 (#385)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-01-09T08:57:24Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "dfc17ae9b47be851398dadf1aa8a243d0274af8d",
"body": "In commit 905115, the bin files were renamed by adding a prefix in order to\r\nresolve a file name conflict between the Z and Y space clusters.\r\nHowever, this meant that the bin/cluster names now did not correspond to the\r\nfile names of the bins.\r\nInstead, in this commit, rename the bins themselves.",
"is_bot": false,
"headline": "Also add bin prefix to AAE cluster names (#384)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-01-08T14:08:45Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "f3fe7e03bc042dbc458a1feb99aa4baaff22aac9",
"body": "For some reason the old one didn't work, and didn't alert us to the fact that\r\nit didn't.",
"is_bot": false,
"headline": "Fix Ruff linting CI (#383)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-01-08T07:58:52Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "905115c5ce5d1e39562daf95532acf26dda326b6",
"body": "The AVAMB ensemble model produces bins from the Z space, the Y space and the\r\nordinary VAE model. When the FASTA bins are written with the --minfasta flag,\r\nthe bins derived from the three models would erroneously overwrite each other.\r\n\r\nNow, the written bins may be given an optional prefix to avo\n[…]\nng bins from the AAE Z and Y spaces - the\r\nVAE and VAEVAE models use no prefix.\r\n\r\nSo, now the bins created using the --minfasta flag with the AAE model will be\r\ncalled e.g. `z_S5C9` or `y_S12C51402`.",
"is_bot": false,
"headline": "Resolve bin name clashes between Z and Y space in AAE (#382)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2025-01-08T07:47:08Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "77e1cba32a3ad869b76b13844e5b35c70667f469",
"body": "Previously, TaxVamb incorrectly used the inert splitter instead of the one\r\nspecified on command-line, when loading its composition.\r\nSince the binsplitter is properly initialized in `calc_tnf`, such that it will\r\nnot attempt to binsplit on 'C' if this separator is not present, the use of an\r\ninert splitter skipped this initialization.\r\nThis caused a bug where the lack of a separator was not detected until the data\r\nwas clustered, far too late.",
"is_bot": false,
"headline": "Use the correct binsplitter in TaxVamb (#377)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2024-12-10T16:08:44Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "95f11550068c66ce7a735334984fcbaa4ffc3fa1",
"body": null,
"is_bot": false,
"headline": "Some documentation updates (#375)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2024-12-04T12:58:03Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "589194e5491a743a2b0de143859f37f5061405a2",
"body": "More consistently differentiate between unrefined and refined taxonomy.\r\n* Taxometer requires an unrefined, and errors on a refined one\r\n* Recluster DBScan can take either, but will warn if passed a refined one, and\r\n not `--no_predictor`. If refinement is needed and the requisite comp and ab\r\n ar\n[…]\nb, since this is always required for TaxVamb.\r\n\r\nAlso minor fixes in logging\r\nAlso some changes to the DBScan algorithm - the old algo has not yet been\r\nvalidated, so this is not a high-impact change.",
"is_bot": false,
"headline": "Make taxonomy more consistently used (#374)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2024-12-03T11:46:06Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "6c97ece140c806ffb2a425301a9588d146d26d29",
"body": "Packing the indices of a ClusterGenerator shifts the meaning of the integers\r\nin its cache, invalidating it.\r\nI suppose they could be updated in the cache, but that'd be a complex piece of\r\ncode a clustering implementation which is already too complex for its own good.\r\nInstead, clear the cache when packing.\r\n\r\nThis should happen a neglible amount of times compared to how often we already\r\nclear the cache.",
"is_bot": false,
"headline": "Clear invalidated medoid cache on packing (#373)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2024-11-28T09:13:37Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "21bdcdd7f607c67781ce26691b2275b42cb66b05",
"body": null,
"is_bot": false,
"headline": "Fix small formatting issues in log file (#371)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2024-11-19T10:28:27Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "003735d5f6d2ff1876b8e30a86c4a71d5f2f7960",
"body": "It's often useful to know which medoid was used to generate a cluster.\r\nRemarkably, we didn't think to output it earlier.",
"is_bot": false,
"headline": "Write medoid to cluster metadata file (#369)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2024-11-18T15:48:58Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "3828e3dcc41181c8147a1fb235adf5d76aff47bb",
"body": null,
"is_bot": false,
"headline": "Update README.md (#367)",
"author_name": "Ben J Woodcroft",
"author_login": "wwood",
"committed_at": "2024-11-11T09:42:30Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "11272380f5016192f3e16354c4a96fa5a9162d08",
"body": "This large commit is a rewrite of reclustering, along with a variety of related \r\nfixes and changes:\r\n\r\n* Add a new `taxonomy` module which includes the `ContigTaxonomy` previously\r\n stored in vambtools. Also include new types `PredictedTaxonomy` and `Taxonomy`\r\n to more clearly encapsulate the di\n[…]\nproperly tested. That is\r\nbecause following this commit, we will do a more thorough performance testing\r\nof Vamb before release v5, and I expect that this process will cause a series\r\nof fixes anyway.",
"is_bot": false,
"headline": "Rewrite reclustering (#340)",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
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"body": "Update the README.md with new TaxVamb link, and fill in the TaxVamb \"how to run\" section.",
"is_bot": false,
"headline": "chore: TaxVAMB README (#366)",
"author_name": "Svetlana Kutuzova (Galkina)",
"author_login": "sgalkina",
"committed_at": "2024-10-30T09:35:09Z",
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"body": null,
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"headline": "fix: cuda utilization",
"author_name": "Svetlana Kutuzova",
"author_login": "sgalkina",
"committed_at": "2024-09-23T09:20:59Z",
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{
"oid": "bdd14d12855081dbe0ab0c42c3cd7d948f997943",
"body": "The previous defaults were conflicting, since the default number of epochs\nwas smaller than the last steps.\nPrevious runs have indicated that no steps is a good option, though I believe\nwe have never done any optimization on this.",
"is_bot": false,
"headline": "Set default taxometer batch steps to no steps",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2024-09-10T06:31:09Z",
"body_truncated": false,
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"oid": "9810ef047ef41f986b7ddcfdd3dc06947ee0ab6c",
"body": "In issue 355, a user requested to bring back the --jgi option, suc that users\ncan pass in precomputed abundances. That's completely reasonable, and it's not\ngreat that the currently recommended way is to use the internal Python types\nto create an Abundance object.\n\nInstead of bringing back the JGI p\n[…]\nmade a more generic TSV parser.\nTSV is a simple, straightforward format also used elsewhere in Vamb. Also, since\nit's easy to convert the output from --aemb to TSV format, I removed the --aemb\noption.",
"is_bot": false,
"headline": "Replace AEMB parser with generic TSV parser",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
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"oid": "bb2388dadad8c3736da75ff0c3533477278c7069",
"body": "The dependency pyhmmer is compiled with -funsafe-math-optimizations. Loading a\nlib compiled with that flag will set some flags in the CPU for the whole\nprocess, which changes float subnormal behaviour.\nThis is detected when loading NumPy, raising a warning.\nI believe this is not an issue for Vamb, so I just silence the warning for now.\nI'm not too happy with this \"solution\".",
"is_bot": false,
"headline": "Silence NumPy warning about float subnormals",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2024-09-04T08:35:52Z",
"body_truncated": false,
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{
"oid": "c9233476543254e2f685f519f0a4b92e7637bf04",
"body": "I didn't use this script, do not want to maintain it, and generally don't trust\nthat it provides reliable answers.",
"is_bot": false,
"headline": "Remove abundance.py script",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2024-07-22T12:30:11Z",
"body_truncated": false,
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"oid": "5e8ce14741f0f878823ebd91be67c2475c100f3b",
"body": null,
"is_bot": false,
"headline": "Minor tweaks to CLI args",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2024-07-19T13:20:24Z",
"body_truncated": false,
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{
"oid": "06b21362a2f273e85834153cfdfa10bd7cf753cc",
"body": "Most of the changes are internal, i.e. show no changed behaviour. Instead, the\ncode should be more robust and maintainable. This is achieved by:\n\n* Choosing composition over inheiritance\n* Leaning even further into static typing, with the different combinations of\n options being encoded in a sum t\n[…]\nposed to the user, such that only the\n flags actually used by each command is exposed.\n* Changed the grouping of command-line flags to be more sensible\n* Added the `--version` flag to all subcommands",
"is_bot": false,
"headline": "Refactor __main__.py",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2024-07-19T10:49:17Z",
"body_truncated": true,
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{
"oid": "7612296536053326c259eab11b7d306bb761fcac",
"body": "Also mask lower bits of VAE's latent, to save disk space.",
"is_bot": false,
"headline": "Save VAEVAE latent as compressed npz",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2024-07-18T08:55:30Z",
"body_truncated": false,
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{
"oid": "8401be0cecae4150606ca169744e77465a800ec8",
"body": "In 62baa358, I added `@logger.catch` to `run` in order for Loguru to catch and\nlog any errors emitted by Vamb.\nHowever, I did not notice that this will cause any caught errors to exit Vamb\nwith a return code of zero.\nThis broke CI and undoubtedly will break snakemake pipelines relying on Vamb.",
"is_bot": false,
"headline": "Do not ingore errors caught by Loguru",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2024-07-18T07:31:53Z",
"body_truncated": false,
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{
"oid": "7bdc15cfe3c16838344732c465c93064a720e43e",
"body": "* RPKM is more obscure, technical terminology\n* It's technically wrong, since we don't require the abundance to be expressed\n in terms of reads per kilobase per million mapped reads.\n* We call the output file `abundance.npz`\n* \"Abundance\" is the standard terminology for this feature in the literature",
"is_bot": false,
"headline": "More consistently rename RPKM to abundance",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2024-07-18T06:57:53Z",
"body_truncated": false,
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"oid": "c049fbd01783e784e1476c052bd4c07e7cdec010",
"body": "Previously, the taxonomy format input to TaxVamb was poorly defined, and did not\ncorrespond to the format output by Taxometer.\nThis had a couple of bad consequences:\n1. It made it more difficult to specify what format the user should format the\n supplied taxonomy with\n2. The taxonomy format was to\n[…]\nhese changes, we have:\n* Three command-line arguments removed\n* __main__.py no longer depends on Pandas, it is also thoroughly statically\n analyzable\n* More robust parsing with better error messages.",
"is_bot": false,
"headline": "Make TaxVamb taxonomy output format well-defined",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2024-07-17T05:36:03Z",
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"oid": "34b91bd97e33ca91f7e01ccd5fc9a9309637bbfe",
"body": "Add the ability of Vamb to detect marker genes. This is done using pyrodigal\nto predict genes in the contigs, and pyhmmer to find marker genes in the\npredicted genes.\n\nThe marker genes are currently not used in Vamb, so future commits need to add\nthe ability of Vamb to enhance binning based on these marker genes.",
"is_bot": false,
"headline": "Add marker gene detection",
"author_name": "Jakob Nybo Nissen",
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"oid": "a33b1b8bd9442e49762b7cb57a121350ef4b10b3",
"body": "Let's be real, what are the chances a Vamb user is going to experiment with tweaking\nalpha or the latent space size?\nIt's nice to have these flags when testing, but we don't need to display them\nin the help menu. All they do is confuse users and drown out the actually\nimportant parameters users need to set.",
"is_bot": false,
"headline": "Hide several less-used CLI options",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
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"body": null,
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"headline": "Remove link to deleted tutorial in README",
"author_name": "Jakob Nybo Nissen",
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"oid": "43144d0968d0648e5b46e8bfffdd043dc9dbb381",
"body": "We decided not to support these for users, since they are hard to maintain.",
"is_bot": false,
"headline": "Delete TaxVamb-related workflows",
"author_name": "Jakob Nybo Nissen",
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"body": "Remove tutorial - Vamb's Python interface has been internal since v4, and I\nreally don't want to keep it up to date. That takes too much time.\nAdd new sections in Documentation, and move some material from the README to\nthese doc pages.\nSmall tweaks to the documentation.\n\nThe docs are not done yet, grep for \"TODO\" before v5 launch, including:\n* No link to TaxVamb preview in README\n* No description of how to run AVAMB and TaxVamb\n* No description of the Taxonomy input to TaxVamb or Taxometer",
"is_bot": false,
"headline": "Initial docs update before v5",
"author_name": "Jakob Nybo Nissen",
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"body": "Since around the D-adaptation commit, the avamb tests have begun failing.\nIt looks like the AAE doesn't really work with D-adaptation.\nInstead of digging into this, I've decided to just revert the D-adaptation\nfor the AAE in particular.",
"is_bot": false,
"headline": "Disable D-adaptation for AVAMB",
"author_name": "Jakob Nybo Nissen",
"author_login": "jakobnissen",
"committed_at": "2024-07-05T11:32:39Z",
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"oid": "40b19af03cebaea3fddc205df02c480a0d9de56c",
"body": "These files are redundant w.r.t. composition.npz. Although it takes more memory\nto load the latter, it's unlikely that storing the composition briefly is going\nto be a problem, since if it was, Vamb would cause OOM elsewhere anyway.",
"is_bot": false,
"headline": "Do not make files lengths.npz and contignames",
"author_name": "Jakob Nybo Nissen",
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"body": "* Add `Abundance.from_aemb` function\n* Add `--aemb` flag on command line, similar to `--bamdir`\n* Update README and elsewhere that we recommend using strobealign --aemb",
"is_bot": false,
"headline": "Switch to strobealign --aemb as default abundance estimator",
"author_name": "Jakob Nybo Nissen",
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"body": "This lets us use the same tool for both linting and formatting, simplifying\nthings. Also, Ruff is faster, and installs with no dependencies.",
"is_bot": false,
"headline": "Switch Black formatter to Ruff",
"author_name": "Jakob Nybo Nissen",
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"headline": "Update changelog and fix a missing f-string",
"author_name": "Jakob Nybo Nissen",
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"body": "This optimizer is more efficient, and makes the learning rate obsolete, which\nis nice from a UI standpoint.",
"is_bot": false,
"headline": "Use Dadaptation for all DL models",
"author_name": "Jakob Nybo Nissen",
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"body": "For now, it's quite basic. It could go into stuff like unit testing, but it's\nhard not to write this kind of thing without it turning into a course in research\nsoftware engineering.",
"is_bot": false,
"headline": "Add CONTRIBUTING.md and issue template",
"author_name": "Jakob Nybo Nissen",
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"body": "This commit adds a cache to the sampling of the medoid in clustering. This allows\nthe clusterer to fetch the results from a dict, if it's been previously computed.\nThis will get merged only if benchmarks have verified that clustering actually\nruns faster - it's probable that so few medoids are sampled multiple times that\nthe cache wastes more time in overhead than it saves in computation.",
"is_bot": false,
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"body": "Float32 has 23 bits of precision, which is more than necessary for Vamb.\nWe can mask out the lower bits, probably with no loss of performance.\nThis helps reducing the disk space usage of Vamb's output",
"is_bot": false,
"headline": "Mask out low bits of input float arrays",
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{
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{
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{
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"key": "package_maintenance",
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{
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{
"key": "fuzzing",
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Verwandte Einträge
Geprüfte Repositories, die Katalog-Tags oder Ökosysteme mit RasmussenLab/vamb teilen. Nebeneinander lesen →
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Fehlende Daten werden ausgeschlossen und die Gewichte neu normiert, nie als null bewertet. Die Methodik ist versioniert und offen: Metriken v1.13.0, Schema v0.26.0 — vollständige Methodik · Metriken-Wiki.
