Öffentliches RegisterMittel
Software-GesundheitsberichtSchema 0.27.0 · Metriken 1.13.0 · 2026-07-28 23:42 UTC
edgardomortiz / Captus
Assembly of Phylogenomic Datasets from High-Throughput Sequencing data
edgardomortiz/Captus erreicht einen Gesundheitsindex von 51 von 100 und liegt damit im Bereich Mittel. Am stärksten schneidet es bei Vitality (86/100) ab, am schwächsten bei AI Readiness (11/100). Zuletzt vor 14 Tagen aktualisiert. Ein einzelner Mitwirkender trägt den Großteil der jüngsten Arbeit.
51
gesamt / 100Software-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.
51
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.
Eigentümerschaft
Edgardo M. OrtizPersönliches Konto
84 Follower18 öffentliche Reposseit Okt. 2013Florida Museum of Natural History
Dieses Repository gehört einem persönlichen Konto. Ein Projekt mit nur einem Eigentümer trägt ein höheres Kontinuitätsrisiko als ein organisationsgetragenes.
Metriken nach Kategorie
Vitalität
Lebt das Projekt — wird Code geschrieben und werden Releases ausgeliefert?
86
Wie die Bewertung erfolgt
| 28.8/36 | Push-Aktualität — letzter Push vor 14 Tagen |
| 19.4/36 | Commit-Rhythmus — 28/52 Wochen mit Commits |
| 18/18 | Commit-Volumen — 158 Commits im letzten Jahr |
| 10/10 | OpenSSF Scorecard: Maintained — 30 commit(s) and 7 issue activity found in the last 90 days -- score normalized to 10 |
Verwendete Eingangsdaten
| commits_last_year | 158 |
| human_commit_share | 1 |
| days_since_last_push | 14 |
| active_weeks_last_year | 28 |
Release-Disziplin
100Exzellent
Wie die Bewertung erfolgt
| 27/27 | Liefert Releases aus — 51 Releases veröffentlicht |
| 36/36 | Release-Aktualität — letztes Release vor 14 Tagen |
| 27/27 | Release-Rhythmus — ein Release etwa alle 35 Tage |
| 0/10 | OpenSSF Scorecard: Signed-Releases — keine Daten |
Verwendete Eingangsdaten
| releases_count | 51 |
| latest_release_tag | v1.6.6 |
| releases_from_tags | nein |
| days_since_latest_release | 14 |
| mean_days_between_releases | 35 |
Von der Bewertung ausgeschlossen (keine Daten oder nicht anwendbar): OpenSSF Scorecard: Signed-Releases. Die verbleibenden Gewichte wurden renormalisiert.
Community & Verbreitung
Hat das Projekt Nutzer, Downloads, Aufmerksamkeit und ein einladendes Umfeld für Beitragende?
43
Popularität & Verbreitung
37Gefährdet
Wie die Bewertung erfolgt
| 26.5/60 | Stars — 44 Stars |
| 7/25 | Forks — 8 Forks |
| 3.9/15 | Watcher — 6 Watcher |
Verwendete Eingangsdaten
| forks | 8 |
| stars | 44 |
| watchers | 6 |
| growth_state | unverified |
| growth_factor_pct | 100 |
| growth_unverified_reason | no_history |
Community-Gesundheit
50Mittel
Wie die Bewertung erfolgt
| 22.5/22.5 | README |
| 22.5/22.5 | Lizenz — anerkannte Lizenz (GPL-3.0) |
| 0/18 | CONTRIBUTING-Leitfaden |
| 0/13.5 | Verhaltenskodex |
| 0/7.2 | Issue-Vorlage |
| 0/6.3 | PR-Vorlage |
Verwendete Eingangsdaten
| has_readme | ja |
| has_license | ja |
| has_contributing | nein |
| has_issue_template | nein |
| has_code_of_conduct | nein |
| has_pull_request_template | nein |
Nachhaltigkeit & Governance
Überdauert das Projekt die Menschen, die es tragen — Bus-Faktor, Reaktionsfähigkeit, Trägerschaft und Paketpflege?
42
Maintainer-Resilienz (Bus-Faktor)
22Kritisch
Wie die Bewertung erfolgt
| 9/54 | Bus-Faktor — 1 Beitragende decken die Hälfte aller Commits ab |
| 2.4/22.5 | Commit-Verteilung — wichtigste beitragende Person verfasste 89 % der Commits |
| 4.1/13.5 | Breite der Beitragenden — 3 Beitragende |
| 6/10 | OpenSSF Scorecard: Contributors — project has 2 contributing companies or organizations -- score normalized to 6 |
Verwendete Eingangsdaten
| bus_factor | 1 |
| contributors_sampled | 3 |
| top_contributor_share | 0,894 |
Wie die Bewertung erfolgt
| 14.9/46.8 | Issue-Lösungsquote — 32 % der Issues geschlossen |
| 38.2/38.3 | PR-Annahme — 1/1 entschiedene PRs gemergt |
| 0/15 | OpenSSF Scorecard: Code-Review — Found 0/30 approved changesets -- score normalized to 0 |
Verwendete Eingangsdaten
| merged_prs | 1 |
| open_issues | 30 |
| closed_issues | 14 |
| issue_closed_ratio | 0,318 |
| closed_unmerged_prs | 0 |
Eigentümerschaft & Trägerschaft
56Mittel
Wie die Bewertung erfolgt
| 10/30 | Organisatorische Trägerschaft — persönliches (Nutzer-)Konto |
| 0/20 | Verifizierte Domain — für Nutzerkonten nicht anwendbar |
| 13.9/25 | Reichweite des Inhabers — 84 Follower von edgardomortiz |
| 21.3/25 | Kontohistorie — 18 öffentliche Repos, Kontoalter ca. 12 Jahre |
Verwendete Eingangsdaten
| followers | 84 |
| owner_type | User |
| is_verified | — |
| owner_login | edgardomortiz |
| public_repos | 18 |
| account_age_days | 4.660 |
Von der Bewertung ausgeschlossen (keine Daten oder nicht anwendbar): Verifizierte Domain. Die verbleibenden Gewichte wurden renormalisiert.
Engineering-Qualität
Sind grundlegende Engineering- und Dokumentationspraktiken vorhanden?
41
Engineering-Praktiken
1Kritisch
Wie die Bewertung erfolgt
| 0/24 | CI-Workflows |
| 0/24 | Tests vorhanden |
| 0/16 | Linter-Konfiguration |
| 0/9.6 | Pre-Commit-Hooks |
| 0/6.4 | .editorconfig |
| 0/20 | OpenSSF Scorecard: CI-Tests — keine Daten |
Verwendete Eingangsdaten
| has_ci | nein |
| has_tests | nein |
| has_editorconfig | nein |
| has_linter_config | nein |
| has_precommit_config | nein |
Von der Bewertung ausgeschlossen (keine Daten oder nicht anwendbar): OpenSSF Scorecard: CI-Tests. Die verbleibenden Gewichte wurden renormalisiert.
Dokumentation
100Exzellent
Wie die Bewertung erfolgt
| 30/30 | README |
| 25/25 | Dokumentationsverzeichnis |
| 15/15 | Dokumentations-/Homepage-Site — https://edgardomortiz.github.io/captus.docs/ |
| 10/10 | Repository-Beschreibung |
| 10/10 | Topics — 16 Topics |
| 10/10 | Wiki |
Verwendete Eingangsdaten
| topics | ngs, phylogenomics, alignment, genome-skimming, high-throughput-sequencing, hybridization-capture, next-generation-sequencing, phylogenetics, rna-seq, whole-genome-sequencing, phylotranscriptomics, orthologs, paralogs, target-capture, bioinformatics, busco |
| has_wiki | ja |
| homepage | https://edgardomortiz.github.io/captus.docs/ |
| has_readme | ja |
| has_docs_dir | ja |
| has_description | ja |
Sicherheit
Sind die sichtbaren Sicherheits- und Lieferkettenpraktiken belastbar, ohne ungeklärte Exposition gegenüber Hochrisikojurisdiktionen?
37
Sicherheitslage
37Gefährdet
Wie die Bewertung erfolgt
| 6/7.5 | Binary-Artifacts — binaries present in source code |
| 0/7.5 | Branch-Protection — branch protection not enabled on development/release branches |
| 0/2.5 | CI-Tests — keine Daten |
| 0/2.5 | CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected |
| 0/7.5 | Code-Review — Found 0/30 approved changesets -- score normalized to 0 |
| 1.5/2.5 | Contributors — project has 2 contributing companies or organizations -- score normalized to 6 |
| 0/10 | Dangerous-Workflow — keine Daten |
| 0/7.5 | Dependency-Update-Tool — no update tool detected |
| 0/5 | Fuzzing — project is not fuzzed |
| 2.5/2.5 | Lizenz — license file detected |
| 7.5/7.5 | Maintained — 30 commit(s) and 7 issue activity found in the last 90 days -- score normalized to 10 |
| 0/5 | Packaging — keine Daten |
| 0/5 | Pinned-Dependencies — keine Daten |
| 0/5 | SAST — no SAST tool detected |
| 0/5 | Security-Policy — security policy file not detected |
| 0/7.5 | Signed-Releases — keine Daten |
| 0/7.5 | Token-Permissions — keine Daten |
| 7.5/7.5 | Vulnerabilities — 0 existing vulnerabilities detected |
Verwendete Eingangsdaten
| source | openssf_scorecard |
| checks_evaluated | 12 |
| scorecard_version | v5.5.0 |
| checks_inconclusive | 6 |
| scorecard_aggregate | 3,7 |
Von der Bewertung ausgeschlossen (keine Daten oder nicht anwendbar): ci_tests, dangerous_workflow, packaging, pinned_dependencies, signed_releases, token_permissions. Die verbleibenden Gewichte wurden renormalisiert.
AI Readiness
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.
11
AI-Agentenkontext & Leitlinien
11Kritisch
Wie die Bewertung erfolgt
| 0/45 | Agentenanweisungen — keine CLAUDE.md / AGENTS.md / Editor-Regeln |
| 0/15 | Maschinenlesbare Doku (llms.txt) |
| 11.2/40 | Lesbare Commit-Historie — 21 von 100 menschlichen Commits benennen ihre Absicht (strukturierter Betreff oder erläuternder Text) |
Verwendete Eingangsdaten
| has_llms_txt | nein |
| legible_history_share | 0,21 |
| agent_instruction_files | — |
| agent_instruction_max_bytes | — |
Wie die Bewertung erfolgt
| 0/18 | Bootstrap mit einem Befehl |
| 0/22 | Automatisierte Tests |
| 0/11 | Lint-/Format-Konfiguration |
| 0/11 | Statische Typprüfung |
| 0/10 | Reproduzierbare Umgebung |
| 0/10 | Belegte Agentenpraxis — keine von Agenten verfassten Commits unter den letzten 100 |
| 0/8 | Automatisierte Wartung — keine automatisierten Abhängigkeits-Updates beobachtet |
| 0/10 | OpenSSF Scorecard: Pinned-Dependencies — keine Daten |
Verwendete Eingangsdaten
| has_nix | nein |
| has_tests | nein |
| lockfiles | — |
| has_dockerfile | nein |
| typed_language | nein |
| bootstrap_files | — |
| has_devcontainer | nein |
| has_linter_config | nein |
| typecheck_configs | — |
| agent_commit_share | 0 |
| toolchain_manifests | — |
| dependency_bot_commit_share | 0 |
Von der Bewertung ausgeschlossen (keine Daten oder nicht anwendbar): OpenSSF Scorecard: Pinned-Dependencies. Die verbleibenden Gewichte wurden renormalisiert.
AI-Code-Lesbarkeit für Modelle
40Gefährdet
Wie die Bewertung erfolgt
| 0/45 | Typprüfbarer Code — Python ohne Typprüfungs-Konfiguration |
| 39.8/55 | Handhabbare Dateigrößen — 8/29 Quelldateien über 60 KB |
Verwendete Eingangsdaten
| primary_language | Python |
| largest_source_bytes | 179.292 |
| source_files_sampled | 29 |
| oversized_source_files | 8 |
Eckdaten
44GitHub-Sterne
3Mitwirkende
158Commits, letzte 12 Monate
14Tage seit letztem Push
51Releases
1Bus-Faktor
30offene Issues
PyPIPaket-Ökosysteme
Warnungen zur Datenerhebung
- Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token
- Could not fetch pypi package 'captus' from its registry
Weitere Details
Stern- und Fork-Verlauf 0 ★ / 8 ⇿
0Sterne
8Forks
50Releases
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 1Minor 6Patch 43
Jeder Punkt umfasst 5 Tage.
OpenSSF Scorecard 3.7 / 10
3.7Gesamtwert
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).
| 8 | Binary-Artifacts | binaries present in source code |
| 0 | Branch-Protection | branch protection not enabled on development/release branches |
| k. A. | CI-Tests | no pull request found |
| 0 | CII-Best-Practices | no effort to earn an OpenSSF best practices badge detected |
| 0 | Code-Review | Found 0/30 approved changesets -- score normalized to 0 |
| 6 | Contributors | project has 2 contributing companies or organizations -- score normalized to 6 |
| k. A. | Dangerous-Workflow | no workflows found |
| 0 | Dependency-Update-Tool | no update tool detected |
| 0 | Fuzzing | project is not fuzzed |
| 10 | License | license file detected |
| 10 | Maintained | 30 commit(s) and 7 issue activity found in the last 90 days -- score normalized to 10 |
| k. A. | Packaging | packaging workflow not detected |
| k. A. | Pinned-Dependencies | no dependencies found |
| 0 | SAST | no SAST tool detected |
| 0 | Security-Policy | security policy file not detected |
| k. A. | Signed-Releases | no releases found |
| k. A. | Token-Permissions | No tokens found |
| 10 | Vulnerabilities | 0 existing vulnerabilities detected |
Alle Abhängigkeiten 0
Vollständig aufgelöster Abhängigkeitssatz aus dem GitHub-Abhängigkeitsgraphen: 0 direkte und 0 indirekte (transitive) Pakete. Die transitive Hülle ist vollständig, wenn das Repository eine Lockfile eincheckt.
| Registry | Paket | Version | Beziehung |
|---|
Abhängigkeits-Advisories nicht bewertet
Der Advisory-Abgleich konnte für diesen Bericht nicht ausgeführt werden: No resolved dependencies to assess
JSON-Rohbericht maschinenlesbar
{
"data": {
"repo": {
"topics": [
"ngs",
"phylogenomics",
"alignment",
"genome-skimming",
"high-throughput-sequencing",
"hybridization-capture",
"next-generation-sequencing",
"phylogenetics",
"rna-seq",
"whole-genome-sequencing",
"phylotranscriptomics",
"orthologs",
"paralogs",
"target-capture",
"bioinformatics",
"busco"
],
"is_fork": false,
"size_kb": 81629,
"has_wiki": true,
"homepage": "https://edgardomortiz.github.io/captus.docs/",
"languages": {
"Python": 1167463
},
"pushed_at": "2026-07-14T05:35:50Z",
"created_at": "2020-07-16T22:37:10Z",
"owner_type": "User",
"updated_at": "2026-07-27T18:46:27Z",
"description": "Assembly of Phylogenomic Datasets from High-Throughput Sequencing data",
"is_archived": false,
"is_disabled": false,
"license_spdx": "GPL-3.0",
"default_branch": "master",
"license_spdx_raw": "GPL-3.0",
"primary_language": "Python",
"significant_languages": [
"Python"
]
},
"owner": {
"blog": null,
"name": "Edgardo M. Ortiz",
"type": "User",
"login": "edgardomortiz",
"company": "Florida Museum of Natural History",
"location": "Gainesville, Florida",
"followers": 84,
"avatar_url": "https://avatars.githubusercontent.com/u/5767612?v=4",
"created_at": "2013-10-24T17:36:26Z",
"is_verified": null,
"public_repos": 18,
"account_age_days": 4660
},
"license": {
"state": "standard",
"spdx_id": "GPL-3.0",
"raw_spdx": "GPL-3.0",
"file_present": true,
"scorecard_found": true,
"profile_has_license": true
},
"activity": {
"releases": [
{
"tag": "v1.6.6",
"kind": "patch",
"published_at": "2026-07-14T05:35:50Z"
},
{
"tag": "v1.6.5",
"kind": "patch",
"published_at": "2026-02-27T20:13:42Z"
},
{
"tag": "v1.6.4",
"kind": "patch",
"published_at": "2026-02-23T23:13:36Z"
},
{
"tag": "v1.6.3",
"kind": "patch",
"published_at": "2026-02-22T03:04:38Z"
},
{
"tag": "v1.6.2",
"kind": "patch",
"published_at": "2026-02-21T19:48:20Z"
},
{
"tag": "v1.6.1",
"kind": "patch",
"published_at": "2025-11-07T23:27:18Z"
},
{
"tag": "v1.6.0",
"kind": "minor",
"published_at": "2025-09-29T06:13:49Z"
},
{
"tag": "v1.5.9",
"kind": "patch",
"published_at": "2025-09-12T20:39:50Z"
},
{
"tag": "v1.5.8",
"kind": "patch",
"published_at": "2025-09-08T04:29:30Z"
},
{
"tag": "v1.5.7",
"kind": "patch",
"published_at": "2025-09-02T07:49:16Z"
},
{
"tag": "v1.5.6",
"kind": "patch",
"published_at": "2025-09-01T06:53:32Z"
},
{
"tag": "v1.5.5",
"kind": "patch",
"published_at": "2025-08-28T03:55:55Z"
},
{
"tag": "v1.5.4",
"kind": "patch",
"published_at": "2025-08-15T09:12:23Z"
},
{
"tag": "v1.5.3",
"kind": "patch",
"published_at": "2025-08-04T21:47:11Z"
},
{
"tag": "v1.5.2",
"kind": "patch",
"published_at": "2025-08-03T06:02:41Z"
},
{
"tag": "v1.5.1",
"kind": "patch",
"published_at": "2025-07-15T20:48:41Z"
},
{
"tag": "v1.5.0",
"kind": "minor",
"published_at": "2025-07-08T08:08:44Z"
},
{
"tag": "v1.4.9",
"kind": "patch",
"published_at": "2025-07-03T04:56:54Z"
},
{
"tag": "v1.4.8",
"kind": "patch",
"published_at": "2025-05-31T22:27:47Z"
},
{
"tag": "v1.4.7",
"kind": "patch",
"published_at": "2025-05-26T03:30:23Z"
},
{
"tag": "v1.4.6",
"kind": "patch",
"published_at": "2025-05-18T22:42:13Z"
},
{
"tag": "v1.4.5",
"kind": "patch",
"published_at": "2025-05-18T05:58:31Z"
},
{
"tag": "v1.4.4",
"kind": "patch",
"published_at": "2025-05-16T17:01:55Z"
},
{
"tag": "v1.4.2",
"kind": "patch",
"published_at": "2025-05-13T05:09:16Z"
},
{
"tag": "v1.4.1",
"kind": "patch",
"published_at": "2025-05-04T19:51:31Z"
},
{
"tag": "v1.4.0",
"kind": "minor",
"published_at": "2025-04-16T17:05:38Z"
},
{
"tag": "v1.3.9",
"kind": "patch",
"published_at": "2025-04-15T00:50:27Z"
},
{
"tag": "v1.3.3",
"kind": "patch",
"published_at": "2025-04-09T23:22:48Z"
},
{
"tag": "v1.3.2",
"kind": "patch",
"published_at": "2025-03-19T08:23:45Z"
},
{
"tag": "v1.3.0",
"kind": "minor",
"published_at": "2025-03-16T06:59:38Z"
},
{
"tag": "v1.2.0",
"kind": "minor",
"published_at": "2025-03-09T19:56:20Z"
},
{
"tag": "v1.1.2",
"kind": "patch",
"published_at": "2025-02-24T02:21:49Z"
},
{
"tag": "v1.1.1",
"kind": "patch",
"published_at": "2025-01-29T02:52:59Z"
},
{
"tag": "v1.1.0",
"kind": "minor",
"published_at": "2024-12-23T17:49:26Z"
},
{
"tag": "v1.0.1",
"kind": "patch",
"published_at": "2024-03-02T19:48:29Z"
},
{
"tag": "v1.0.0",
"kind": "major",
"published_at": "2023-11-21T10:57:05Z"
},
{
"tag": "v0.9.99",
"kind": "patch",
"published_at": "2023-11-14T15:47:27Z"
},
{
"tag": "v0.9.98",
"kind": "patch",
"published_at": "2023-10-30T11:03:57Z"
},
{
"tag": "v0.9.97",
"kind": "patch",
"published_at": "2023-09-02T13:56:17Z"
},
{
"tag": "v0.9.96",
"kind": "patch",
"published_at": "2023-08-25T14:57:30Z"
},
{
"tag": "v0.9.95",
"kind": "patch",
"published_at": "2023-08-18T14:52:11Z"
},
{
"tag": "v0.9.93",
"kind": "patch",
"published_at": "2023-06-08T05:49:14Z"
},
{
"tag": "v0.9.92",
"kind": "patch",
"published_at": "2023-05-26T08:52:21Z"
},
{
"tag": "v0.9.91",
"kind": "patch",
"published_at": "2022-12-29T15:52:28Z"
},
{
"tag": "v0.9.90",
"kind": "patch",
"published_at": "2022-12-13T23:34:10Z"
},
{
"tag": "v0.9.89",
"kind": "patch",
"published_at": "2022-11-27T21:32:48Z"
},
{
"tag": "v0.9.88",
"kind": "patch",
"published_at": "2022-11-11T12:51:26Z"
},
{
"tag": "v0.9.86",
"kind": "patch",
"published_at": "2022-07-21T07:14:19Z"
},
{
"tag": "v0.9.85",
"kind": "patch",
"published_at": "2022-07-19T11:00:06Z"
},
{
"tag": "v0.9.84",
"kind": "patch",
"published_at": "2022-07-12T12:30:09Z"
},
{
"tag": "v0.9.83",
"kind": "patch",
"published_at": "2022-07-10T22:04:13Z"
}
],
"recent_commits": [
{
"oid": "7d991867363e701e8e7a1ddf1f43848ffef536d8",
"body": null,
"is_bot": false,
"headline": "Update README.md",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-07-14T04:52:31Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b89a15ce37981e6eb2da569850f057e630047fc8",
"body": null,
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-07-13T05:44:48Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "f6de9c8e88c3b301f8f53feaca6fef0ddfbd30c8",
"body": "Added `--ram` option to `new_targets_from_alignments` to limit the max amount of RAM for mmseqs",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-07-13T05:37:31Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b8283760428e1a679b700247773e03c9237d7104",
"body": null,
"is_bot": false,
"headline": "Change cluster-mode to 2 as default all across",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-06-23T06:21:56Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "8fcd46fa301fb0f53fd5bc3560120506ef31fe43",
"body": null,
"is_bot": false,
"headline": "Update README.md",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-06-13T04:41:14Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "9e2358e9e2b4441abcbae037bc97f67ce146b929",
"body": null,
"is_bot": false,
"headline": "Update settings.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-06-09T04:48:32Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "bde3a2db2b7f423f96244ea66c0c9bd0b4587f77",
"body": "Fix `ctg_mean_depth` formatting",
"is_bot": false,
"headline": "Update extract.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-06-09T04:31:21Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "34692c0c076b8c182c48e65b86997003b402fe1f",
"body": null,
"is_bot": false,
"headline": "Update captus_design.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-06-09T00:44:49Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "8a72672d744d322b53300da967919cc0e975bf7f",
"body": "Cover the case of empty lines in path lists",
"is_bot": false,
"headline": "Improved list consumption",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-06-08T16:13:08Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "484afd4c341f1aa6485c237844e7ae0a758e398c",
"body": "- Changed defaults",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-28T02:29:27Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "ec62d21403385d073045610da8f823528c968eff",
"body": null,
"is_bot": false,
"headline": "Change coverage defaults",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-23T04:51:16Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "af9f667e70b2501c8246279bf2527eda6efbd269",
"body": null,
"is_bot": false,
"headline": "Update align.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-22T18:52:20Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "908c0f90858a686b27942289bf411ccdb2360279",
"body": "-Simply quit if extractions directory(ies) is/are not found",
"is_bot": false,
"headline": "Update align.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-22T18:50:32Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "6e5d32b8aa33212238ee3e2768f15e417a85904d",
"body": "Fixed warning about missing `captus-extract_refs.json` file",
"is_bot": false,
"headline": "Update align.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-22T18:42:56Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "f6256ec279370be419526e072b61b524ce04acd7",
"body": "- Exposed MMseqs' `cluster_mode` and `cov_mode` as additional options for `new_targets_from_alignments`, defaults are still `cluster_mode 2` and `cov_mode 1`.",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-22T15:30:13Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "8ca739fef0c86354e6b71de009a0ebf5547a15cc",
"body": "- Last change of defaults for W and C from 0.6666 to 0.3333",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-21T21:16:37Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "362f1658bec35ed4b4b786b7e96fb8324163d388",
"body": "- Fixed hover menu for sample-wise stats",
"is_bot": false,
"headline": "Update report.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-21T20:25:07Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "6a5a312f08ff0f505352d4bc1e2e483f1e4906d6",
"body": null,
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-21T02:26:40Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "17983aef3908a5961660aee90c8cadd0aa2b97a1",
"body": "- Improved logic for paralog splitting, now PMIN is only added when its total sample proportion is equal or exceeds `min_sample_prop`",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-21T02:13:47Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "84fe98210cdcbe25c686e9cd852e11dac37ff975",
"body": null,
"is_bot": false,
"headline": "Updated in-run explanations",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-15T10:28:59Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "fa26a8b7730a23338f9d1a2eae5e7fadf6f70c51",
"body": "Another fix for reclustering",
"is_bot": false,
"headline": "Update extract.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-14T17:28:42Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "00cb0e9be6746c5fa827caef989b172fadae2838",
"body": "Additional fixes to last commit, the reclustering process matches more closely the logic of `new_targets_from_alignments`",
"is_bot": false,
"headline": "Updated extract.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-14T16:36:57Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "78aa5eab81a455048d8621c1ecefdba8998f410d",
"body": "Another fix",
"is_bot": false,
"headline": "Update extract.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-13T22:49:40Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7cca7151a175cda94efdcf8eafb02908b5bb78d9",
"body": "Linked to last commit",
"is_bot": false,
"headline": "Update extract.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-13T22:29:22Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "c8abafb311ec24ffeb31082d5345d33ef5e5a0aa",
"body": "After reclustering representatives a second check for `min_samples` and `max_copies` must be done",
"is_bot": false,
"headline": "Fixed reclustering of representatives in `captus extract`",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-13T22:21:01Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a0670d79a9a20fa4da08be3d189b176b68f0e24c",
"body": null,
"is_bot": false,
"headline": "Update extract.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-11T13:39:27Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0cf1de386a9427a20ca87389200db6ea581f4ac4",
"body": "Sync variables and drop down menus",
"is_bot": false,
"headline": "Update report.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-11T12:53:33Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "4c052921e14aed3290d2f0bcd521096f0917751f",
"body": "Update function after switching to median for copies",
"is_bot": false,
"headline": "Update align.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-11T12:24:50Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "9fe104592ad9a8bf38a3bc38ce2da818f77d30d3",
"body": null,
"is_bot": false,
"headline": "Ruff run",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-11T11:34:48Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "cbf0ba255dfdf33e8eb315fca2af9b7569727bdc",
"body": "Round `ctg_mean_depth` to 4 decimals",
"is_bot": false,
"headline": "Update bioformats.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-11T09:14:39Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "3a5163faf63e494edcf17fccfda818e06a252b3b",
"body": "Round `ctg_mean_depth` to 4 decimals",
"is_bot": false,
"headline": "Update extract.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-11T09:09:45Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "ca7623431edac16878e52cad8573a96c3ac9c298",
"body": "- `captus align` report median and mean copies\n- Rename column names from avg_ to mean_\n- Rename option `align_min_species` to `clust_min_species`, added option `align_min_samples` to `captusd cluster`\n- Added options `median_copies` and `mean_copies` to `captusd select`\n- Updated all relevant report (review required)",
"is_bot": false,
"headline": "Preferred use of median copies instead of mean",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-11T08:44:06Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d1c36b17e7c0684a05a2ffd92d1b83023fb70759",
"body": "- Expanded description for warnings about bugs in some dependencies",
"is_bot": false,
"headline": "Update README.md",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-07T13:12:32Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "5311062e4f0a2551bd05ac238fbc56ea99555b5e",
"body": "This belongs to previous commit too",
"is_bot": false,
"headline": "Improved `redo_from` in `captus align`",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-07T08:34:48Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "9b008402c6354dd0f36607f97724e41276dfbd78",
"body": "The deletion of folder before redoing steps is now more granular and obeys changes in `markers` and `formats`. For example, an initial set of settings can be used to trim all formats (AA,NT,GE) but then setting can be changed and run with `redo_from` only for GE for example.",
"is_bot": false,
"headline": "Improved `redo_from` in `captus align`",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-07T08:33:46Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "5bd8c25c5c2d1ab3ae468768cc9b0acc572e5f6e",
"body": "Updated preprint title",
"is_bot": false,
"headline": "Update README.md",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-06T14:15:01Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "4ccc1f2bfe8d3a845cda7147edcd33aeee84d3f9",
"body": "- Use the median number of sequences per sample in a cluster instead of the average (missed file in last commit)",
"is_bot": false,
"headline": "Update extract.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-02T17:20:06Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "99d5dadf2a0b3fe73ecbaf6f2be0a0c629fdf3ef",
"body": "- Use the median number of sequences per sample in a cluster instead of the average",
"is_bot": false,
"headline": "`cl_max_copies` is now median",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-02T17:16:05Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "9cbf53ff59531c0f7a1c305e02b15f72f9b58865",
"body": "Cosmetic changes",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-01T17:21:47Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0483967f2b5dfce0cb80f5b99b2a2ded32885d34",
"body": "- Don't overcount split paralogs",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-01T16:12:50Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "30fcf802910440349c83f970bc57d857a701f960",
"body": "Using median copies, changed defaults",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-01T05:33:31Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e99404b0c7aabca40f9a49bf02f410d18d1e4366",
"body": "- Switch to using median copies instead of average copies",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-01T04:51:22Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "3402186bb3c98b2763da6b689524c886cbead189",
"body": "Fixing the logic of paralog-splitting",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-01T03:14:35Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e39aff0600ea3321a1d6c4cc49746f446c2d4b2f",
"body": "- Add 'low_copy_only' too",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-01T02:38:55Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "51c99f68d594ea7ada57270604ba9d7567639198",
"body": "- Add option to remove low copy loci, useful for optimizing paralog-splitting parameters",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-05-01T02:31:35Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "aadb6ced77fcffc2afb7d90fb40a2638df73d600",
"body": "- Changed default of `min_depth_proportion` from 0.55 to 0.33",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-30T18:39:48Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "2555078c9f5fc9b18b693b2f87f934e87d7552cd",
"body": null,
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-29T20:11:24Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "43ff43cb422a294614e7e6d41d77147eed8b16e4",
"body": "- Calculate 'sample_pct' even when not splitting paralogs",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-29T20:07:47Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "965c8fde9fdd456378a9f8a8f27f75bed465f37c",
"body": "Remove empty alignment columns after removing reference target sequences",
"is_bot": false,
"headline": "Update align.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-29T15:29:26Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "9200d2ece2fd33ce88b32c69b4e81a106a474f53",
"body": null,
"is_bot": false,
"headline": "Locate refs.json automatically if possible",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-29T08:46:17Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "6e4d09266f7798197e261ed01d4d7151fe5f0b07",
"body": null,
"is_bot": false,
"headline": "Update captus_assembly.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-29T07:47:12Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "c1e765cf8f9084c47caf2234d3600f81db778dbe",
"body": "`--cl_max_copies` changed to 3 from 6, this means every sample is allowed to have at most 3 sequences in a cluster, increase if your assemblies are highly fragmented, in a cluster an extra sequence doesn't become an additional copy directly and instead could be a non-overlapping fragment.",
"is_bot": false,
"headline": "Default change",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-29T05:41:26Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "5915638caa727d1adf4043eb490ee79afe3f11d6",
"body": "- Rename PAR0 to PMIN to indicate a paralog composed of minor alleles",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-28T21:43:48Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "66078cfeb7c12408aa23e6b55b2e81984ca65163",
"body": "Changed some defaults",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-28T18:43:24Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "bbd321ec88e2eec8988725582534130dc0b7b731",
"body": "- Added per target info (% samples in locus retained, copies)",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-28T18:38:30Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "289bbfdb23a8bd2df8c9612b142d9df0c781cfd4",
"body": null,
"is_bot": false,
"headline": "Minor fixes",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-27T19:31:51Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "3c3672f04366e626101a7dadee163e9199e9fc6f",
"body": "- Sanitize sequence names during importation, replace `:`, `(`, or `)` with `_`",
"is_bot": false,
"headline": "Sanitize sequence names",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-27T06:25:45Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "40f1e7c0b7ce3627981ec93c63ec447c1b298e60",
"body": null,
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-27T01:45:19Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d39860e163c9c58ffd0a510b5787c2c1a2dac6e7",
"body": "Cosmetic changes",
"is_bot": false,
"headline": "Update extract.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-26T21:55:13Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "11b3ac8accf7f8071254d5ea5b268091337c443f",
"body": null,
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-26T20:32:32Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "3a5d8a5aa9af636f4628eafbd46ad3f54ed124f5",
"body": "- Save an additional table with run statistics for easy concatenation across several runs",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-26T18:54:20Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "14653364b9d147e600b7c94d6a64057ff939f8ee",
"body": "- Added `--retain_samples` to retain a list of samples even if the don't pass the `--min_depth_proportion` threshold, useful if a small group of sequences is very divergent and consistently produces small clusters, like for example in the case of an outgroup",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-26T17:51:43Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e4e17c625f33381d11419bb7dfb600e4583ae0c3",
"body": null,
"is_bot": false,
"headline": "Update extract.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-25T05:00:37Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b37526f8c9a456d34e7c93d1dfebc150f86430be",
"body": "- Show assembly and extraction directories not found",
"is_bot": false,
"headline": "Update extract.py and align.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-25T04:58:31Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "70529e63703b3b3a201600fe575441bd97eea4ab",
"body": "Improved explanations",
"is_bot": false,
"headline": "Cosmetic changes",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-24T06:45:56Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "33f0bb4206b23a6466bb67d2ff0010f6f15eba17",
"body": null,
"is_bot": false,
"headline": "Cosmetic changes",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-24T06:07:51Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "791d2710892f005f8263b83ca8530e73af5991b5",
"body": "- You can use a list of paths to individual sample extraction folders (ending in __captus-ext) to `captus align`. Useful when your extractions are in separate captus extractions folders or just need align subsets of samples\n- The name in symbolic links are honored",
"is_bot": false,
"headline": "List of paths allowed in `captus align`",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-24T05:53:59Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "485e8074965fb969ab604a361139994aa145ff50",
"body": "- You can use a list of paths to individual sample assembly folders (ending in __captus-asm) to `captus extract`. Useful when your assemblies are in separate captus assembly folders\n- The name in symbolic links are honored\n- Reduced default `--min_coverage` to 0.2 in `captus align`",
"is_bot": false,
"headline": "Lists of paths allowed in `captus extract`",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-24T03:58:06Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "cdfe144e574949d036bd616e34c5f0cfab138309",
"body": null,
"is_bot": false,
"headline": "Update settings.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-21T21:59:01Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "821c598c5c91cdb628406a3fbfa8d6dd2c5c64aa",
"body": "- Added `--min_length` to `captus clean`\n- Added new ClipKIT's modes to Captus' choices (`gappyout`, `block-gappy`, `composition-bias`, `heterotachy`)",
"is_bot": false,
"headline": "Added options",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-21T21:38:56Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a8456da485e79f416f84f3f28894516a2dc4b455",
"body": "- Fixed a bug caused by comparing versions as decimal numbers",
"is_bot": false,
"headline": "Check minimum versions correctly",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-21T17:04:35Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "680ecd96199efe1adebfa8a89f0240970b813ce2",
"body": null,
"is_bot": false,
"headline": "Update align.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-20T07:56:15Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "015bd65360c929a92ac9a81f60ae8674e10c959c",
"body": null,
"is_bot": false,
"headline": "Update align.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-20T07:53:13Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7740fb669df5176aae215c885fd9d10d25858ad3",
"body": "Skip alignment of loci with many copies",
"is_bot": false,
"headline": "Added `max_average_copies` to `captus align`",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-20T07:50:32Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "ea928252ff5ff0ae504a59e97ff8dbd742c4e8b4",
"body": null,
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-19T22:35:03Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e9ec187c5f3a04db110fa436a8c82c25e4cc158c",
"body": null,
"is_bot": false,
"headline": "Bug fixes",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-19T18:05:24Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "9b636f712b3fbeb935e2e3ea4b374e230ebe6a45",
"body": "- Changed query= to target= in output sequences",
"is_bot": false,
"headline": "Cosmetic changes",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-19T01:33:37Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e9c32f63b0bb054c5991392fcd4996e5ccd22d30",
"body": "- Add a cleanup for IQ-TREE output files\n- Fixed bug in `new_targets_from_alignments`",
"is_bot": false,
"headline": "IQ-TREE cleanup",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-18T22:23:17Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "1e9e69af7cb6c5e6903be56f02350de2c95338c0",
"body": null,
"is_bot": false,
"headline": "Update copyright date",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-18T07:37:06Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "5103798a5596f23a07dec0b7fcf19dbf8aee0d22",
"body": "Help is shown if no options are provided",
"is_bot": false,
"headline": "Improved accessory scripts",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-18T07:28:54Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7b84ea47bde34deb47f824b54c65006f69fef565",
"body": null,
"is_bot": false,
"headline": "Allow symbolic links to import assemblies",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-18T07:24:01Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "47a8006d72861b32d628f093441e8d3268399a30",
"body": "Also allow symbolic links for imported FASTA assemblies",
"is_bot": false,
"headline": "Tidy up `phylo_commands`",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-18T06:51:45Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d9f407a3fa52c4e11035a308b1667e89fc53da9e",
"body": "Fixed message about skipped empty/corrupt FASTQs",
"is_bot": false,
"headline": "Update assemble.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-18T05:05:14Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d0b1d21b44ec12ddcb7b2fa9f0979eea4ce3f5d6",
"body": null,
"is_bot": false,
"headline": "Update extract.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-17T23:36:13Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "be2d10447e4718b316948856bbf2775fc350a50a",
"body": null,
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-17T17:15:11Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "6ab1fb538ff6e649a7c9b919d6eba309ca31e5a7",
"body": "- New default `cl_mode` for `captus extract` is 1, new `cl_min_coverage` is 50, relaxed `cl_max_copies` to 6",
"is_bot": false,
"headline": "Changed clustering defaults",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-17T16:56:08Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a8bff1f04e82a0e9fc8e23f4cb5bebb6c6e712de",
"body": null,
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-17T14:27:50Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "c0e959db158a5ea379a1196601ac90904b1c339e",
"body": null,
"is_bot": false,
"headline": "Warning messages for empty FASTQs",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-17T04:06:01Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "867acc62aaba0333b6b2acb35b977a8d526ed2b0",
"body": null,
"is_bot": false,
"headline": "Update README.md",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-16T21:06:09Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "998d2b96908d16639cead88868b059786be4f784",
"body": null,
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-16T16:52:34Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "6ccbeb1f1d75768cc0c72019af746df2e30f13a8",
"body": null,
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-16T06:12:25Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "40a82d9be1a1f8429626bed97be20acafbfd0288",
"body": "Add warnings about buggy versions",
"is_bot": false,
"headline": "Update README.md",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-16T03:02:10Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "027e7305da66b7af94bc0984667fd2ccc1472cb0",
"body": "Additional bug fixes",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-16T02:40:32Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "46770a55e84d21e09e881380d7e8842083a0f166",
"body": "Small bug fixes",
"is_bot": false,
"headline": "Update new_targets_from_alignments.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-15T20:07:24Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "530e452ce2dc861278e8f04589f16b4ab8a2429b",
"body": "- Added empty/corrupted file check for FASTQs\n- Added `sample_bases_target` to `captus assemble`\n- Added value check for paralog tolerances parameters (transform percentages to proportions automatically)\n- Improvements to `phylo_commands`, added some IQTREE options\n- Changed minimum read length from\n[…]\nlt Salmon kmer size for indexing\n- `new_targets_from_alignments` has been completely rewritten, workflow is better explained during execution, it can auto-split paralogous loci into new separate loci.",
"is_bot": false,
"headline": "Updating to v1.6.6",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-04-15T17:32:35Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "73290b4a0d83fc5e87a3f765adc5611bf25a1c87",
"body": "- Fix for `min_data_per_column`, sometimes the percentage didn't remove the exact number of columns expected because of a rounding error.",
"is_bot": false,
"headline": "Minor fixes",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-03-27T06:29:07Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "f197f38b97b1efa60a684cfa007060afd8474075",
"body": "- Baits are created faster, less to deduplicate.\n- RAM and CPUs better assigned during loci extraction.",
"is_bot": false,
"headline": "Optimization and speedups",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-03-19T18:15:23Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "4b6396824ac4b3bdf65d3eacfe4d2f0ff6503466",
"body": null,
"is_bot": false,
"headline": "Changed hit region determination formula",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-03-03T05:59:37Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e6afee88d33506c8e263d1caaf3aa175c03cb021",
"body": "Fix directories dictionaries",
"is_bot": false,
"headline": "Update align.py",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-03-01T18:09:23Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "caaecd2f43a5a31312b165c85470685201e15fa1",
"body": "The function to find FASTAs now takes into account MARKER and FORMAT",
"is_bot": false,
"headline": "Granular selection of alignments",
"author_name": "Edgardo M. Ortiz",
"author_login": "edgardomortiz",
"committed_at": "2026-03-01T18:04:45Z",
"body_truncated": false,
"is_coding_agent": false
}
],
"releases_count": 51,
"commits_last_year": 158,
"latest_release_at": "2026-07-14T05:35:50Z",
"latest_release_tag": "v1.6.6",
"releases_from_tags": false,
"days_since_last_push": 14,
"active_weeks_last_year": 28,
"days_since_latest_release": 14,
"mean_days_between_releases": 35
},
"community": {
"has_readme": true,
"has_license": true,
"has_description": true,
"has_contributing": false,
"health_percentage": 42,
"has_issue_template": false,
"has_code_of_conduct": false,
"has_pull_request_template": false
},
"ecosystem": {
"packages": []
},
"popularity": {
"forks": 8,
"stars": 44,
"watchers": 6,
"fork_history": {
"days": [
{
"date": "2021-11-06",
"count": 1
},
{
"date": "2022-02-28",
"count": 1
},
{
"date": "2022-07-11",
"count": 1
},
{
"date": "2023-05-18",
"count": 1
},
{
"date": "2023-08-09",
"count": 1
},
{
"date": "2025-03-13",
"count": 1
},
{
"date": "2025-10-13",
"count": 1
},
{
"date": "2026-07-14",
"count": 1
}
],
"complete": true,
"collected": 8,
"total_forks": 8
},
"star_history": null,
"open_issues_and_prs": 30
},
"ai_readiness": {
"has_nix": false,
"example_dirs": [],
"has_llms_txt": false,
"has_dockerfile": false,
"has_mcp_signal": false,
"bootstrap_files": [],
"api_schema_files": [],
"has_devcontainer": false,
"typecheck_configs": [],
"toolchain_manifests": [],
"largest_source_bytes": 179292,
"source_files_sampled": 29,
"oversized_source_files": 8,
"agent_instruction_files": [],
"agent_instruction_max_bytes": null
},
"dependencies": {
"manifests": [
"setup.py"
],
"advisories": {
"error": "No resolved dependencies to assess",
"scope": "repository_graph",
"source": null,
"findings": [],
"collected": false,
"malicious": [],
"truncated": false,
"by_severity": {},
"advisory_count": 0,
"affected_count": 0,
"assessed_count": 0,
"malicious_count": 0,
"assessed_package": null,
"unassessed_count": 0,
"direct_affected_count": 0
},
"ecosystems": [
"pypi"
],
"dependencies": [],
"all_dependencies": {
"error": null,
"source": "github-sbom",
"packages": [],
"collected": true,
"truncated": false,
"total_count": 0,
"direct_count": 0,
"indirect_count": 0
}
},
"maintainership": {
"issues": {
"open_prs": 0,
"merged_prs": 1,
"open_issues": 30,
"closed_ratio": 0.318,
"closed_issues": 14,
"closed_unmerged_prs": 0
},
"bus_factor": 1,
"bot_contributors": 0,
"top_contributors": [
{
"type": "User",
"login": "edgardomortiz",
"commits": 551,
"avatar_url": "https://avatars.githubusercontent.com/u/5767612?v=4"
},
{
"type": "User",
"login": "shigita",
"commits": 63,
"avatar_url": "https://avatars.githubusercontent.com/u/40628880?v=4"
},
{
"type": "User",
"login": "SethMusker",
"commits": 2,
"avatar_url": "https://avatars.githubusercontent.com/u/16952350?v=4"
}
],
"contributors_sampled": 3,
"top_contributor_share": 0.894
},
"quality_signals": {
"has_ci": false,
"has_tests": false,
"ci_workflows": [],
"has_docs_dir": true,
"linter_configs": [],
"has_editorconfig": false,
"has_linter_config": false,
"has_precommit_config": false
},
"security_signals": {
"lockfiles": [],
"scorecard": {
"checks": [
{
"name": "Binary-Artifacts",
"score": 8,
"reason": "binaries present in source code",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#binary-artifacts"
},
{
"name": "Branch-Protection",
"score": 0,
"reason": "branch protection not enabled on development/release branches",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#branch-protection"
},
{
"name": "CI-Tests",
"score": null,
"reason": "no pull request found",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#ci-tests"
},
{
"name": "CII-Best-Practices",
"score": 0,
"reason": "no effort to earn an OpenSSF best practices badge detected",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#cii-best-practices"
},
{
"name": "Code-Review",
"score": 0,
"reason": "Found 0/30 approved changesets -- score normalized to 0",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#code-review"
},
{
"name": "Contributors",
"score": 6,
"reason": "project has 2 contributing companies or organizations -- score normalized to 6",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#contributors"
},
{
"name": "Dangerous-Workflow",
"score": null,
"reason": "no workflows found",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#dangerous-workflow"
},
{
"name": "Dependency-Update-Tool",
"score": 0,
"reason": "no update tool detected",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#dependency-update-tool"
},
{
"name": "Fuzzing",
"score": 0,
"reason": "project is not fuzzed",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#fuzzing"
},
{
"name": "License",
"score": 10,
"reason": "license file detected",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#license"
},
{
"name": "Maintained",
"score": 10,
"reason": "30 commit(s) and 7 issue activity found in the last 90 days -- score normalized to 10",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#maintained"
},
{
"name": "Packaging",
"score": null,
"reason": "packaging workflow not detected",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#packaging"
},
{
"name": "Pinned-Dependencies",
"score": null,
"reason": "no dependencies found",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#pinned-dependencies"
},
{
"name": "SAST",
"score": 0,
"reason": "no SAST tool detected",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#sast"
},
{
"name": "Security-Policy",
"score": 0,
"reason": "security policy file not detected",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#security-policy"
},
{
"name": "Signed-Releases",
"score": null,
"reason": "no releases found",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#signed-releases"
},
{
"name": "Token-Permissions",
"score": null,
"reason": "No tokens found",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#token-permissions"
},
{
"name": "Vulnerabilities",
"score": 10,
"reason": "0 existing vulnerabilities detected",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#vulnerabilities"
}
],
"commit": "7d991867363e701e8e7a1ddf1f43848ffef536d8",
"ran_at": "2026-07-28T23:42:23Z",
"aggregate_score": 3.7,
"scorecard_version": "v5.5.0"
},
"has_codeql_workflow": false,
"has_security_policy": false,
"has_dependabot_config": false
},
"contribution_flow": {
"collected": true,
"ci_last_run_at": null,
"oldest_open_prs": [],
"last_merged_pr_at": "2023-06-09T15:17:07Z",
"ci_last_conclusion": null,
"oldest_open_issues": [
{
"number": 1,
"created_at": "2023-02-22T19:35:56Z",
"last_comment_at": "2023-02-23T15:27:54Z",
"last_comment_author": "edgardomortiz"
},
{
"number": 3,
"created_at": "2023-06-01T21:44:48Z",
"last_comment_at": "2023-06-06T07:56:25Z",
"last_comment_author": "edgardomortiz"
},
{
"number": 4,
"created_at": "2023-11-24T06:56:37Z",
"last_comment_at": "2023-12-05T05:21:08Z",
"last_comment_author": "korjent"
},
{
"number": 5,
"created_at": "2024-01-29T00:55:29Z",
"last_comment_at": "2024-03-04T20:48:27Z",
"last_comment_author": "EdBiffin"
},
{
"number": 6,
"created_at": "2024-02-29T15:20:46Z",
"last_comment_at": "2024-02-29T16:41:38Z",
"last_comment_author": "veronicamb"
},
{
"number": 8,
"created_at": "2024-04-03T09:19:35Z",
"last_comment_at": "2024-04-05T11:41:24Z",
"last_comment_author": "edgardomortiz"
},
{
"number": 10,
"created_at": "2024-05-14T12:54:42Z",
"last_comment_at": "2024-08-20T04:02:54Z",
"last_comment_author": "edgardomortiz"
},
{
"number": 12,
"created_at": "2024-06-28T00:53:35Z",
"last_comment_at": "2024-08-05T23:12:40Z",
"last_comment_author": "EdBiffin"
},
{
"number": 13,
"created_at": "2024-06-28T18:23:51Z",
"last_comment_at": "2024-09-24T03:51:54Z",
"last_comment_author": "edgardomortiz"
},
{
"number": 14,
"created_at": "2024-09-02T15:31:19Z",
"last_comment_at": "2025-04-01T18:32:43Z",
"last_comment_author": "edgardomortiz"
},
{
"number": 15,
"created_at": "2024-09-21T14:58:18Z",
"last_comment_at": "2024-09-28T11:08:44Z",
"last_comment_author": "Kailin-Sun"
},
{
"number": 20,
"created_at": "2025-01-15T11:13:53Z",
"last_comment_at": "2025-02-17T11:55:03Z",
"last_comment_author": "vincianem"
},
{
"number": 22,
"created_at": "2025-04-01T15:37:40Z",
"last_comment_at": "2025-04-01T15:42:31Z",
"last_comment_author": "edgardomortiz"
},
{
"number": 24,
"created_at": "2025-05-01T20:29:09Z",
"last_comment_at": "2025-05-05T16:10:59Z",
"last_comment_author": "CaroSci"
},
{
"number": 25,
"created_at": "2025-05-13T09:10:20Z",
"last_comment_at": "2025-05-21T01:54:08Z",
"last_comment_author": "edgardomortiz"
},
{
"number": 26,
"created_at": "2025-05-14T15:02:55Z",
"last_comment_at": "2025-09-18T15:38:08Z",
"last_comment_author": "edgardomortiz"
},
{
"number": 29,
"created_at": "2025-07-24T17:35:00Z",
"last_comment_at": "2026-05-01T20:31:31Z",
"last_comment_author": "edgardomortiz"
},
{
"number": 30,
"created_at": "2025-08-11T18:21:54Z",
"last_comment_at": "2025-08-12T16:10:07Z",
"last_comment_author": "edgardomortiz"
},
{
"number": 31,
"created_at": "2025-10-06T15:19:16Z",
"last_comment_at": "2025-10-09T17:03:19Z",
"last_comment_author": "edgardomortiz"
},
{
"number": 32,
"created_at": "2025-10-10T00:58:15Z",
"last_comment_at": "2025-10-22T17:49:41Z",
"last_comment_author": "edgardomortiz"
}
]
}
},
"config": {
"disabled_metrics": [],
"disabled_categories": [],
"disabled_components": {}
},
"source": {
"url": "https://github.com/edgardomortiz/Captus",
"host": "github.com",
"name": "Captus",
"owner": "edgardomortiz"
},
"metrics": {
"overall": {
"key": "overall",
"band": "moderate",
"name": "Overall health",
"note": null,
"notes": [],
"value": 51,
"inputs": {
"security": 37,
"vitality": 86,
"community": 43,
"governance": 42,
"engineering": 41
},
"components": []
},
"categories": [
{
"key": "vitality",
"band": "excellent",
"name": "Vitality",
"value": 86,
"weight": 0.22,
"metrics": [
{
"key": "development_activity",
"band": "good",
"name": "Development activity",
"note": null,
"notes": [],
"value": 76,
"inputs": {
"commits_last_year": 158,
"human_commit_share": 1,
"days_since_last_push": 14,
"active_weeks_last_year": 28
},
"components": [
{
"key": "push_recency",
"name": "Push recency",
"detail": "last push 14 days ago",
"points": 28.8,
"status": "partial",
"details": [
{
"code": "push_recency",
"params": {
"days": 14
}
}
],
"max_points": 36
},
{
"key": "commit_cadence",
"name": "Commit cadence",
"detail": "28/52 weeks with commits",
"points": 19.4,
"status": "partial",
"details": [
{
"code": "commit_cadence_weeks",
"params": {
"weeks": 28
}
}
],
"max_points": 36
},
{
"key": "commit_volume",
"name": "Commit volume",
"detail": "158 commits in the last year",
"points": 18,
"status": "met",
"details": [
{
"code": "commits_last_year",
"params": {
"count": 158
}
}
],
"max_points": 18
},
{
"key": "openssf_scorecard_maintained",
"name": "OpenSSF Scorecard: Maintained",
"detail": "30 commit(s) and 7 issue activity found in the last 90 days -- score normalized to 10",
"points": 10,
"status": "met",
"details": [],
"max_points": 10
}
]
},
{
"key": "release_discipline",
"band": "excellent",
"name": "Release discipline",
"note": "Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Signed-Releases. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"openssf_scorecard_signed_releases"
]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 100,
"inputs": {
"releases_count": 51,
"latest_release_tag": "v1.6.6",
"releases_from_tags": false,
"days_since_latest_release": 14,
"mean_days_between_releases": 35
},
"components": [
{
"key": "ships_releases",
"name": "Ships releases",
"detail": "51 releases published",
"points": 27,
"status": "met",
"details": [
{
"code": "releases_published",
"params": {
"count": 51
}
}
],
"max_points": 27
},
{
"key": "release_recency",
"name": "Release recency",
"detail": "latest release 14 days ago",
"points": 36,
"status": "met",
"details": [
{
"code": "release_recency",
"params": {
"days": 14
}
}
],
"max_points": 36
},
{
"key": "release_cadence",
"name": "Release cadence",
"detail": "a release every ~35 days",
"points": 27,
"status": "met",
"details": [
{
"code": "release_cadence",
"params": {
"gap": 35
}
}
],
"max_points": 27
},
{
"key": "openssf_scorecard_signed_releases",
"name": "OpenSSF Scorecard: Signed-Releases",
"detail": "no releases found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 10
}
]
},
{
"key": "abandonment",
"band": "excellent",
"name": "Abandonment",
"note": null,
"notes": [],
"value": 100,
"inputs": {
"cap": null,
"state": "maintained",
"guards": [],
"signals": [],
"red_flag": false,
"multiplier_pct": 100,
"declared_reason": null,
"unverified_reason": null,
"unanswered_open_prs": null,
"unanswered_open_issues": null,
"days_since_last_merged_pr": null,
"days_since_last_human_commit": 14,
"days_since_last_human_commit_is_floor": false
},
"components": [
{
"key": "project_is_still_maintained",
"name": "Project is still maintained",
"detail": "last human commit 14 days ago",
"points": 100,
"status": "met",
"details": [
{
"code": "abandonment_maintained",
"params": {
"days": 14
}
}
],
"max_points": 100
}
]
}
],
"description": "Is the project alive — is code being written and are releases shipping?"
},
{
"key": "community",
"band": "at_risk",
"name": "Community & Adoption",
"value": 43,
"weight": 0.18,
"metrics": [
{
"key": "popularity",
"band": "at_risk",
"name": "Popularity & adoption",
"note": null,
"notes": [],
"value": 37,
"inputs": {
"forks": 8,
"stars": 44,
"watchers": 6,
"growth_state": "unverified",
"growth_factor_pct": 100,
"growth_unverified_reason": "no_history"
},
"components": [
{
"key": "stars",
"name": "Stars",
"detail": "44 stars",
"points": 26.5,
"status": "partial",
"details": [
{
"code": "stars",
"params": {
"count": 44
}
}
],
"max_points": 60
},
{
"key": "forks",
"name": "Forks",
"detail": "8 forks",
"points": 7,
"status": "partial",
"details": [
{
"code": "forks",
"params": {
"count": 8
}
}
],
"max_points": 25
},
{
"key": "watchers",
"name": "Watchers",
"detail": "6 watchers",
"points": 3.9,
"status": "partial",
"details": [
{
"code": "watchers",
"params": {
"count": 6
}
}
],
"max_points": 15
}
]
},
{
"key": "community_health",
"band": "moderate",
"name": "Community health",
"note": null,
"notes": [],
"value": 50,
"inputs": {
"has_readme": true,
"has_license": true,
"has_contributing": false,
"has_issue_template": false,
"has_code_of_conduct": false,
"has_pull_request_template": false
},
"components": [
{
"key": "readme",
"name": "README",
"detail": null,
"points": 22.5,
"status": "met",
"details": [],
"max_points": 22.5
},
{
"key": "license",
"name": "License",
"detail": "recognized license (GPL-3.0)",
"points": 22.5,
"status": "met",
"details": [
{
"code": "license_standard",
"params": {}
},
{
"code": "license_spdx",
"params": {
"spdx": "GPL-3.0"
}
}
],
"max_points": 22.5
},
{
"key": "contributing_guide",
"name": "CONTRIBUTING guide",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 18
},
{
"key": "code_of_conduct",
"name": "Code of conduct",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 13.5
},
{
"key": "issue_template",
"name": "Issue template",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.2
},
{
"key": "pr_template",
"name": "PR template",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 6.3
}
]
}
],
"description": "Does the project have users, downloads, attention, and a welcoming setup for contributors?"
},
{
"key": "governance",
"band": "at_risk",
"name": "Sustainability & Governance",
"value": 42,
"weight": 0.24,
"metrics": [
{
"key": "maintainer_resilience",
"band": "critical",
"name": "Maintainer resilience (bus factor)",
"note": null,
"notes": [],
"value": 22,
"inputs": {
"bus_factor": 1,
"contributors_sampled": 3,
"top_contributor_share": 0.894
},
"components": [
{
"key": "bus_factor",
"name": "Bus factor",
"detail": "1 contributor(s) cover half of all commits",
"points": 9,
"status": "partial",
"details": [
{
"code": "bus_factor",
"params": {
"count": 1
}
}
],
"max_points": 54
},
{
"key": "commit_distribution",
"name": "Commit distribution",
"detail": "top contributor authored 89% of commits",
"points": 2.4,
"status": "partial",
"details": [
{
"code": "top_contributor_share",
"params": {
"share": 89
}
}
],
"max_points": 22.5
},
{
"key": "contributor_breadth",
"name": "Contributor breadth",
"detail": "3 contributors",
"points": 4.1,
"status": "partial",
"details": [
{
"code": "contributors_sampled",
"params": {
"count": 3
}
}
],
"max_points": 13.5
},
{
"key": "openssf_scorecard_contributors",
"name": "OpenSSF Scorecard: Contributors",
"detail": "project has 2 contributing companies or organizations -- score normalized to 6",
"points": 6,
"status": "partial",
"details": [],
"max_points": 10
}
]
},
{
"key": "responsiveness",
"band": "moderate",
"name": "Issue & PR responsiveness",
"note": null,
"notes": [],
"value": 53,
"inputs": {
"merged_prs": 1,
"open_issues": 30,
"closed_issues": 14,
"issue_closed_ratio": 0.318,
"closed_unmerged_prs": 0
},
"components": [
{
"key": "issue_resolution",
"name": "Issue resolution",
"detail": "32% of issues closed",
"points": 14.9,
"status": "partial",
"details": [
{
"code": "issues_closed_share",
"params": {
"share": 32
}
}
],
"max_points": 46.75
},
{
"key": "pr_acceptance",
"name": "PR acceptance",
"detail": "1/1 decided PRs merged",
"points": 38.2,
"status": "met",
"details": [
{
"code": "decided_prs_merged",
"params": {
"merged": 1,
"decided": 1
}
}
],
"max_points": 38.25
},
{
"key": "openssf_scorecard_code_review",
"name": "OpenSSF Scorecard: Code-Review",
"detail": "Found 0/30 approved changesets -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 15
}
]
},
{
"key": "stewardship",
"band": "moderate",
"name": "Ownership & stewardship",
"note": "Excluded from scoring (no data or not applicable): Verified domain. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"verified_domain"
]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 56,
"inputs": {
"followers": 84,
"owner_type": "User",
"is_verified": null,
"owner_login": "edgardomortiz",
"public_repos": 18,
"account_age_days": 4660
},
"components": [
{
"key": "ownership_backing",
"name": "Ownership backing",
"detail": "personal (user) account",
"points": 10,
"status": "partial",
"details": [
{
"code": "owner_personal",
"params": {}
}
],
"max_points": 30
},
{
"key": "verified_domain",
"name": "Verified domain",
"detail": "not applicable to user accounts",
"points": 0,
"status": "excluded",
"details": [
{
"code": "not_applicable_to_user_accounts",
"params": {}
}
],
"max_points": 20
},
{
"key": "owner_reach",
"name": "Owner reach",
"detail": "84 followers of edgardomortiz",
"points": 13.9,
"status": "partial",
"details": [
{
"code": "owner_followers",
"params": {
"count": 84,
"login": "edgardomortiz"
}
}
],
"max_points": 25
},
{
"key": "track_record",
"name": "Track record",
"detail": "18 public repos, account ~12 yr old",
"points": 21.3,
"status": "partial",
"details": [
{
"code": "public_repos",
"params": {
"count": 18
}
},
{
"code": "account_age_years",
"params": {
"years": 12
}
}
],
"max_points": 25
}
]
}
],
"description": "Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?"
},
{
"key": "engineering",
"band": "at_risk",
"name": "Engineering Quality",
"value": 41,
"weight": 0.2,
"metrics": [
{
"key": "engineering_practices",
"band": "critical",
"name": "Engineering practices",
"note": "Excluded from scoring (no data or not applicable): OpenSSF Scorecard: CI-Tests. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"openssf_scorecard_ci_tests"
]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 1,
"inputs": {
"has_ci": false,
"has_tests": false,
"has_editorconfig": false,
"has_linter_config": false,
"has_precommit_config": false
},
"components": [
{
"key": "ci_workflows",
"name": "CI workflows",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 24
},
{
"key": "tests_present",
"name": "Tests present",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 24
},
{
"key": "linter_config",
"name": "Linter config",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 16
},
{
"key": "pre_commit_hooks",
"name": "Pre-commit hooks",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 9.6
},
{
"key": "editorconfig",
"name": ".editorconfig",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 6.4
},
{
"key": "openssf_scorecard_ci_tests",
"name": "OpenSSF Scorecard: CI-Tests",
"detail": "no pull request found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 20
}
]
},
{
"key": "documentation",
"band": "excellent",
"name": "Documentation",
"note": null,
"notes": [],
"value": 100,
"inputs": {
"topics": [
"ngs",
"phylogenomics",
"alignment",
"genome-skimming",
"high-throughput-sequencing",
"hybridization-capture",
"next-generation-sequencing",
"phylogenetics",
"rna-seq",
"whole-genome-sequencing",
"phylotranscriptomics",
"orthologs",
"paralogs",
"target-capture",
"bioinformatics",
"busco"
],
"has_wiki": true,
"homepage": "https://edgardomortiz.github.io/captus.docs/",
"has_readme": true,
"has_docs_dir": true,
"has_description": true
},
"components": [
{
"key": "readme",
"name": "README",
"detail": null,
"points": 30,
"status": "met",
"details": [],
"max_points": 30
},
{
"key": "documentation_directory",
"name": "Documentation directory",
"detail": null,
"points": 25,
"status": "met",
"details": [],
"max_points": 25
},
{
"key": "documentation_homepage_site",
"name": "Documentation / homepage site",
"detail": "https://edgardomortiz.github.io/captus.docs/",
"points": 15,
"status": "met",
"details": [],
"max_points": 15
},
{
"key": "repository_description",
"name": "Repository description",
"detail": null,
"points": 10,
"status": "met",
"details": [],
"max_points": 10
},
{
"key": "topics",
"name": "Topics",
"detail": "16 topics",
"points": 10,
"status": "met",
"details": [
{
"code": "topics_count",
"params": {
"count": 16
}
}
],
"max_points": 10
},
{
"key": "wiki",
"name": "Wiki",
"detail": null,
"points": 10,
"status": "met",
"details": [],
"max_points": 10
}
]
}
],
"description": "Are baseline engineering and documentation practices in place?"
},
{
"key": "security",
"band": "at_risk",
"name": "Security",
"value": 37,
"weight": 0.16,
"metrics": [
{
"key": "security_posture",
"band": "at_risk",
"name": "Security posture",
"note": "Excluded from scoring (no data or not applicable): CI-Tests, Dangerous-Workflow, Packaging, Pinned-Dependencies, Signed-Releases, Token-Permissions. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"ci_tests",
"dangerous_workflow",
"packaging",
"pinned_dependencies",
"signed_releases",
"token_permissions"
]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 37,
"inputs": {
"source": "openssf_scorecard",
"checks_evaluated": 12,
"scorecard_version": "v5.5.0",
"checks_inconclusive": 6,
"scorecard_aggregate": 3.7
},
"components": [
{
"key": "binary_artifacts",
"name": "Binary-Artifacts",
"detail": "binaries present in source code",
"points": 6,
"status": "partial",
"details": [],
"max_points": 7.5
},
{
"key": "branch_protection",
"name": "Branch-Protection",
"detail": "branch protection not enabled on development/release branches",
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.5
},
{
"key": "ci_tests",
"name": "CI-Tests",
"detail": "no pull request found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 2.5
},
{
"key": "cii_best_practices",
"name": "CII-Best-Practices",
"detail": "no effort to earn an OpenSSF best practices badge detected",
"points": 0,
"status": "missed",
"details": [],
"max_points": 2.5
},
{
"key": "code_review",
"name": "Code-Review",
"detail": "Found 0/30 approved changesets -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.5
},
{
"key": "contributors",
"name": "Contributors",
"detail": "project has 2 contributing companies or organizations -- score normalized to 6",
"points": 1.5,
"status": "partial",
"details": [],
"max_points": 2.5
},
{
"key": "dangerous_workflow",
"name": "Dangerous-Workflow",
"detail": "no workflows found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 10
},
{
"key": "dependency_update_tool",
"name": "Dependency-Update-Tool",
"detail": "no update tool detected",
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.5
},
{
"key": "fuzzing",
"name": "Fuzzing",
"detail": "project is not fuzzed",
"points": 0,
"status": "missed",
"details": [],
"max_points": 5
},
{
"key": "license",
"name": "License",
"detail": "license file detected",
"points": 2.5,
"status": "met",
"details": [],
"max_points": 2.5
},
{
"key": "maintained",
"name": "Maintained",
"detail": "30 commit(s) and 7 issue activity found in the last 90 days -- score normalized to 10",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
},
{
"key": "packaging",
"name": "Packaging",
"detail": "packaging workflow not detected",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 5
},
{
"key": "pinned_dependencies",
"name": "Pinned-Dependencies",
"detail": "no dependencies found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 5
},
{
"key": "sast",
"name": "SAST",
"detail": "no SAST tool detected",
"points": 0,
"status": "missed",
"details": [],
"max_points": 5
},
{
"key": "security_policy",
"name": "Security-Policy",
"detail": "security policy file not detected",
"points": 0,
"status": "missed",
"details": [],
"max_points": 5
},
{
"key": "signed_releases",
"name": "Signed-Releases",
"detail": "no releases found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 7.5
},
{
"key": "token_permissions",
"name": "Token-Permissions",
"detail": "No tokens found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 7.5
},
{
"key": "vulnerabilities",
"name": "Vulnerabilities",
"detail": "0 existing vulnerabilities detected",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
}
]
},
{
"key": "high_risk_jurisdiction_exposure",
"band": "excellent",
"name": "High-Risk Jurisdiction Exposure",
"note": "Only high-confidence self-published location evidence affects this multiplier. Ambiguous matches are review-only; country evidence is not proof of nationality, citizenship, legal registration, malicious intent, or sanctions status.",
"notes": [
{
"code": "jurisdiction_evidence_limits",
"params": {}
}
],
"value": 100,
"inputs": {
"meaning": "self-published location evidence; not nationality or citizenship",
"red_flag": false,
"exposures": [],
"policy_countries": [
"Russia",
"Iran",
"North Korea"
],
"review_only_matches": 0,
"assessed_self_published_locations": 3
},
"components": [
{
"key": "policy_exposure_multiplier",
"name": "Policy exposure multiplier",
"detail": "no confirmed policy-scope location match",
"points": 100,
"status": "met",
"details": [
{
"code": "jurisdiction_no_match",
"params": {}
}
],
"max_points": 100
}
]
}
],
"description": "Are visible security and supply-chain practices strong, with no malicious dependency and no unresolved high-risk jurisdiction exposure?"
},
{
"key": "ai_readiness",
"band": "critical",
"name": "AI Readiness",
"value": 11,
"weight": 0,
"metrics": [
{
"key": "ai_agent_context",
"band": "critical",
"name": "Agent context & guidance",
"note": null,
"notes": [],
"value": 11,
"inputs": {
"has_llms_txt": false,
"legible_history_share": 0.21,
"agent_instruction_files": [],
"agent_instruction_max_bytes": null
},
"components": [
{
"key": "agent_instructions",
"name": "Agent instructions",
"detail": "no CLAUDE.md / AGENTS.md / editor rules",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_agent_instructions",
"params": {}
}
],
"max_points": 45
},
{
"key": "machine_readable_docs_llms_txt",
"name": "Machine-readable docs (llms.txt)",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 15
},
{
"key": "legible_commit_history",
"name": "Legible commit history",
"detail": "21 of 100 human commits state their intent (structured subject or explanatory body)",
"points": 11.2,
"status": "partial",
"details": [
{
"code": "legible_history",
"params": {
"legible": 21,
"sampled": 100
}
}
],
"max_points": 40
}
]
},
{
"key": "ai_verify_loop",
"band": "critical",
"name": "Verify loop (build / test / typecheck)",
"note": "Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Pinned-Dependencies. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"openssf_scorecard_pinned_dependencies"
]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 1,
"inputs": {
"has_nix": false,
"has_tests": false,
"lockfiles": [],
"has_dockerfile": false,
"typed_language": false,
"bootstrap_files": [],
"has_devcontainer": false,
"has_linter_config": false,
"typecheck_configs": [],
"agent_commit_share": 0,
"toolchain_manifests": [],
"dependency_bot_commit_share": 0
},
"components": [
{
"key": "one_command_bootstrap",
"name": "One-command bootstrap",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 18
},
{
"key": "automated_tests",
"name": "Automated tests",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 22
},
{
"key": "lint_format_config",
"name": "Lint / format config",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 11
},
{
"key": "static_type_checking",
"name": "Static type checking",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 11
},
{
"key": "reproducible_environment",
"name": "Reproducible environment",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
},
{
"key": "demonstrated_agent_practice",
"name": "Demonstrated agent practice",
"detail": "no agent-authored commits among the last 100",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_agent_authored_commits",
"params": {
"sampled": 100
}
}
],
"max_points": 10
},
{
"key": "automated_maintenance",
"name": "Automated maintenance",
"detail": "no automated dependency updates observed",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_dependency_automation",
"params": {}
}
],
"max_points": 8
},
{
"key": "openssf_scorecard_pinned_dependencies",
"name": "OpenSSF Scorecard: Pinned-Dependencies",
"detail": "no dependencies found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 10
}
]
},
{
"key": "ai_code_legibility",
"band": "at_risk",
"name": "Code legibility for models",
"note": null,
"notes": [],
"value": 40,
"inputs": {
"primary_language": "Python",
"largest_source_bytes": 179292,
"source_files_sampled": 29,
"oversized_source_files": 8
},
"components": [
{
"key": "type_checkable_code",
"name": "Type-checkable code",
"detail": "Python without a type-check config",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_typecheck_config_language",
"params": {
"language": "Python"
}
}
],
"max_points": 45
},
{
"key": "manageable_file_sizes",
"name": "Manageable file sizes",
"detail": "8/29 source files over 60KB",
"points": 39.8,
"status": "partial",
"details": [
{
"code": "oversized_source_files",
"params": {
"kb": 60,
"sampled": 29,
"oversized": 8
}
}
],
"max_points": 55
}
]
}
],
"description": "How well is the repo equipped to be developed and maintained with AI coding agents? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score."
}
],
"metrics_version": "1.13.0"
},
"warnings": [
"Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token",
"Could not fetch pypi package 'captus' from its registry"
],
"report_type": "repository",
"generated_at": "2026-07-28T23:42:33.522561Z",
"schema_version": "0.27.0",
"badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/e/edgardomortiz/Captus.svg",
"full_name": "edgardomortiz/Captus",
"license_state": "standard",
"license_spdx": "GPL-3.0"
}Bewertungen sind Signale, keine Garantien. Sie spiegeln öffentlich sichtbare Praxis auf GitHub wider — kein Code-Audit und keine Sicherheitsgarantie.
Fehlende Daten werden ausgeschlossen und die Gewichte neu normiert, nie als null bewertet. Die Methodik ist versioniert und offen: Metriken v1.13.0, Schema v0.27.0 — vollständige Methodik · Metriken-Wiki.
Wie ein einzelnes Ergebnis im Gesamtregister steht: aggregierte Statistiken.