Публічний реєстр
Звіт про здоров'я програмного забезпеченнясхема 0.27.0 · метрики 1.13.0 · 2026-07-30 20:15 UTC

niekwit / damid-seq

DamMapper: Snakemake workflow for DamID-Seq analysis

Python · RMIT★ 5 зірок⑂ 1 форкз жовт. 2023 р.Переглянути на GitHub ↗

niekwit/damid-seq має індекс здоров’я 51 зі 100, що відповідає смузі «Помірний». Найвищий показник — Vitality (62/100), найнижчий — AI Readiness (17/100). Останнє оновлення було 31 день тому. Більшість нещодавньої роботи виконує один учасник.

51
загалом / 100
Помірний

Індекс здоров'я програмного забезпечення

Метрики згруповано у зважені категорії на шкалі 1–100. Загальна оцінка починається як їхнє середнє; коли публічні дані активують Політику юрисдикцій високого ризику, рейтинг коригується й отримує верхню межу 49 («Під ризиком»). Готовність до ШІ не входить до індексу.

51
Відмінний85-100Зразковий; відповідає практично всім перевіреним критеріям
Добрий70-84Здоровий; незначні прогалини
Помірний50-69Прийнятний, але з помітними прогалинами; рекомендовано перевірку
У зоні ризику30-49Суттєві слабкі місця; впровадження потребує обережності
Критичний1-29Серйозні проблеми (покинутий, єдиний мейнтейнер, без базової гігієни)
ЖиттєздатністьСпільнота тавпровадженняСталість таврядуванняІнженернаякістьБезпекаГотовність доШІ

Профіль оцінок

Кожна вісь — окрема категорія. Форма важить більше, ніж середнє: здоровий об'єкт заповнює всю фігуру, тоді як профіль із піками та провалами означає, що сила в одному вимірі маскує ризик в іншому.

Власність

Niek WitОсобистий обліковий запис
11 підписників60 публічних репозиторіївз лип. 2018 р.University of Cambridge

Цей репозиторій належить особистому обліковому запису. Проєкт з єдиним власником несе більший ризик безперервності, ніж підтримуваний організацією.

Метрики за категоріями

Життєздатність

Чи живий проєкт — чи пишеться код і чи виходять релізи?

62Помірний · 22% загального індексу

Активність розробки

48У зоні ризику
Як обчислюється оцінка
18/36Свіжість push — останній push 31 дн. тому
3.5/36Ритм комітів — 5/52 тижнів із комітами
16.2/18Обсяг комітів — 62 комітів за останній рік
10/10OpenSSF Scorecard: Maintained — 30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10
Використані вхідні дані
commits_last_year62
human_commit_share1
days_since_last_push31
active_weeks_last_year5
Як обчислюється оцінка
27/27Випускає релізи — опубліковано 5 релізів
36/36Свіжість релізів — останній реліз 31 дн. тому
12.6/27Ритм релізів — реліз кожні ~212,4 дн.
0/10OpenSSF Scorecard: Signed-Releases — немає даних
Використані вхідні дані
releases_count5
latest_release_tagv0.7.0
releases_from_tagsні
days_since_latest_release31
mean_days_between_releases212,4
Виключено з оцінювання (немає даних або не застосовно): OpenSSF Scorecard: Signed-Releases. Залишкові ваги перенормовано.

Спільнота та впровадження

Чи має проєкт користувачів, завантаження, увагу та влаштовані умови для контриб’юторів?

29Критичний · 18% загального індексу
Як обчислюється оцінка
9.8/60Зірки — 5 зірок
0/25Форки — 1 форків
0/15Спостерігачі — 1 спостерігачів
Використані вхідні дані
forks1
stars5
watchers1
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history
Як обчислюється оцінка
22.5/22.5README
22.5/22.5Ліцензія — визнана ліцензія (MIT)
0/18Настанови CONTRIBUTING
0/13.5Кодекс поведінки
0/7.2Шаблон issue
0/6.3Шаблон PR
Використані вхідні дані
has_readmeтак
has_licenseтак
has_contributingні
has_issue_templateні
has_code_of_conductні
has_pull_request_templateні

Сталість та врядування

Чи переживе проєкт своїх людей — бас-фактор, реактивність, хто за ним стоїть і як супроводжуються пакети?

48У зоні ризику · 24% загального індексу
Як обчислюється оцінка
9/54Бас-фактор — на 1 контриб’ютор(ів) припадає половина всіх комітів
0/22.5Розподіл комітів — головний контриб’ютор — автор 100% комітів
1.4/13.5Широта контриб’юторів — 1 контриб’юторів
3/10OpenSSF Scorecard: Contributors — project has 1 contributing companies or organizations -- score normalized to 3
Використані вхідні дані
bus_factor1
contributors_sampled1
top_contributor_share1
Як обчислюється оцінка
46.8/46.8Вирішення issue — закрито 100% issue
38.2/38.3Прийняття PR — злито 1/1 вирішених PR
0/15OpenSSF Scorecard: Code-Review — Found 0/16 approved changesets -- score normalized to 0
Використані вхідні дані
merged_prs1
open_issues0
closed_issues1
issue_closed_ratio1
closed_unmerged_prs0
Як обчислюється оцінка
10/30Підтримка власника — особистий (користувацький) обліковий запис
0/20Верифікований домен — не застосовно до користувацьких облікових записів
7.8/25Охоплення власника — 11 підписників у niekwit
25/25Послужний список — 60 публічних репозиторіїв, вік облікового запису ~8 р.
Використані вхідні дані
followers11
owner_typeUser
is_verified
owner_loginniekwit
public_repos60
account_age_days2 936
Виключено з оцінювання (немає даних або не застосовно): Верифікований домен. Залишкові ваги перенормовано.

Інженерна якість

Чи наявні базові інженерні практики та документація?

60Помірний · 20% загального індексу

Інженерні практики

44У зоні ризику
Як обчислюється оцінка
24/24Процеси CI — 3 процес(ів) CI
0/24Наявні тести
0/16Конфігурація лінтера
0/9.6Pre-commit-хуки
0/6.4.editorconfig
20/20OpenSSF Scorecard: CI-Tests — 1 out of 1 merged PRs checked by a CI test -- score normalized to 10
Використані вхідні дані
has_ciтак
has_testsні
has_editorconfigні
has_linter_configні
has_precommit_configні

Документація

85Відмінний
Як обчислюється оцінка
30/30README
25/25Каталог документації
0/15Сайт документації / домашня сторінка
10/10Опис репозиторію
10/10Теми — 3 тем
10/10Wiki
Використані вхідні дані
topicsbioinformatics-pipeline, damid, snakemake-workflow
has_wikiтак
homepage
has_readmeтак
has_docs_dirтак
has_descriptionтак

Безпека

Чи міцні видимі практики безпеки й ланцюга постачання, без непослабленої пов’язаності з юрисдикціями високого ризику?

53Помірний · 16% загального індексу

Стан безпеки

41У зоні ризику
Як обчислюється оцінка
7.5/7.5Binary-Artifacts — no binaries found in the repo
0/7.5Branch-Protection — branch protection not enabled on development/release branches
2.5/2.5CI-Tests — 1 out of 1 merged PRs checked by a CI test -- score normalized to 10
0/2.5CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected
0/7.5Code-Review — Found 0/16 approved changesets -- score normalized to 0
0.8/2.5Contributors — project has 1 contributing companies or organizations -- score normalized to 3
10/10Dangerous-Workflow — no dangerous workflow patterns detected
0/7.5Dependency-Update-Tool — no update tool detected
0/5Fuzzing — project is not fuzzed
2.5/2.5Ліцензія — license file detected
7.5/7.5Maintained — 30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10
0/5Packaging — немає даних
0/5Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
0/5SAST — SAST tool is not run on all commits -- score normalized to 0
0/5Security-Policy — security policy file not detected
0/7.5Signed-Releases — немає даних
0/7.5Token-Permissions — detected GitHub workflow tokens with excessive permissions
7.5/7.5Vulnerabilities — 0 existing vulnerabilities detected
Використані вхідні дані
sourceopenssf_scorecard
checks_evaluated16
scorecard_versionv5.5.0
checks_inconclusive2
scorecard_aggregate4,1
Виключено з оцінювання (немає даних або не застосовно): packaging, signed_releases. Залишкові ваги перенормовано.
Як обчислюється оцінка
35/35Прямі залежності без відомих сповіщень — жодна пряма залежність не має відомих сповіщень
0/25Непрямі залежності без відомих сповіщень — транзитивний набір не відокремлюється від залежностей розробки й тестування в цьому обсязі
0/40Немає задавнених сповіщень — жодне сповіщення не має дати публікації
Використані вхідні дані
sourceosv
advisories0
affected_packages0
assessed_packages2
unassessed_packages0
affected_by_severitynone
direct_affected_packages0
Виключено з оцінювання (немає даних або не застосовно): Непрямі залежності без відомих сповіщень, Немає задавнених сповіщень. Залишкові ваги перенормовано. Звірено 2 резолвлених залежностей із OSV. Цей репозиторій не публікує пакета, який резолвить індекс, тож натомість оцінено граф залежностей репозиторію. Цей граф змішує закріплені версії для розробки й тестування зі справді постачаними залежностями, тож оцінюються лише задекларовані runtime-залежності; транзитивні знахідки подаються як контекст і в оцінку не входять. Досяжність не аналізується.

Готовність до ШІ

Наскільки репозиторій оснащений для розробки та супроводу за участі ШІ-агентів? Незалежний, експериментальний бейдж — вага 0.0, тож він подається окремо і не впливає на загальний індекс здоров'я.

17Критичний · 0% загального індексу
Як обчислюється оцінка
0/45Інструкції для агентів — немає CLAUDE.md / AGENTS.md / правил редактора
0/15Машиночитана документація (llms.txt)
1.6/40Читабельна історія комітів — намір зазначено у 3 з 100 людських комітів (структурований заголовок або пояснювальний текст)
Використані вхідні дані
has_llms_txtні
legible_history_share0,03
agent_instruction_files
agent_instruction_max_bytes
Як обчислюється оцінка
0/18Розгортання однією командою
0/22Автоматизовані тести
0/11Конфігурація лінтера / форматера
0/11Статична перевірка типів
10/10Відтворюване середовище — Dockerfile
4/10Підтверджена практика роботи з агентами — 2 з останніх 100 комітів створено агентом або з його зазначенням
0/8Автоматизоване супроводження — автоматичних оновлень залежностей не виявлено
0/10OpenSSF Scorecard: Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0
Використані вхідні дані
has_nixні
has_testsні
lockfiles
has_dockerfileтак
typed_languageні
bootstrap_files
has_devcontainerні
has_linter_configні
typecheck_configs
agent_commit_share0,02
toolchain_manifests
dependency_bot_commit_share0
Як обчислюється оцінка
0/45Типізований код — Python без конфігурації перевірки типів
55/55Керовані розміри файлів — 0/15 файлів вихідного коду понад 60 КБ
Використані вхідні дані
primary_languagePython
largest_source_bytes3 693
source_files_sampled15
oversized_source_files0

Ключові факти

5зірок GitHub
1контриб'юторів
62комітів за останні 12 місяців
31днів від останнього пушу
5релізів
1бас-фактор
0відкритих issue
PyPIпакетних екосистем

Попередження щодо збору даних

  • Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token

Докладніше

OpenSSF Scorecard 4.1 / 10
4.1сукупно

Незалежна, не прив'язана до інструментів оцінка безпеки від відкритого проєкту OpenSSF Scorecard. Кожна перевірка винагороджує практику безпеки, а не інструмент конкретного постачальника. Перевірки, які Scorecard не зміг визначити, позначено н/д і виключено з оцінки безпеки (вони ніколи не зараховуються як нуль).Scorecard v5.5.0 · 2026-07-30 20:15 UTC

10Binary-Artifactsno binaries found in the repo
0Branch-Protectionbranch protection not enabled on development/release branches
10CI-Tests1 out of 1 merged PRs checked by a CI test -- score normalized to 10
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
0Code-ReviewFound 0/16 approved changesets -- score normalized to 0
3Contributorsproject has 1 contributing companies or organizations -- score normalized to 3
10Dangerous-Workflowno dangerous workflow patterns detected
0Dependency-Update-Toolno update tool detected
0Fuzzingproject is not fuzzed
10Licenselicense file detected
10Maintained30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10
н/дPackagingpackaging workflow not detected
0Pinned-Dependenciesdependency not pinned by hash detected -- score normalized to 0
0SASTSAST tool is not run on all commits -- score normalized to 0
0Security-Policysecurity policy file not detected
н/дSigned-Releasesno releases found
0Token-Permissionsdetected GitHub workflow tokens with excessive permissions
10Vulnerabilities0 existing vulnerabilities detected
Усі залежності 2

Повний розв'язаний набір залежностей із графа залежностей GitHub: 0 прямих і 2 непрямих (транзитивних) пакетів. Транзитивне замикання є повним, коли в репозиторії закомічено lockfile.

РеєстрПакетВерсіяЗв'язок
PyPIsphinx7.3.7непряма
PyPIsphinx-rtd-theme2.0.0непряма
Сповіщення про залежності 0

Цей репозиторій не публікує пакета, який розпізнає індекс, тож оцінено його власний граф залежностей — 2 пакетів, серед яких є й піниї розробки та тестування, що ніколи не постачаються: 0 мають відомі сповіщення, з них 0 прямі.

Жодне відоме сповіщення не стосується оцінених залежностей.

Сповіщення означає, що версія, записана в графі залежностей, потрапляє в уражений діапазон. Досяжність не аналізується, а граф містить піниї розробки й тестування — знахідка може стосуватися інструментів, а не поставленого коду.

Звіт у форматі JSON машиночитний
{
  "data": {
    "repo": {
      "topics": [
        "bioinformatics-pipeline",
        "damid",
        "snakemake-workflow"
      ],
      "is_fork": false,
      "size_kb": 140060,
      "has_wiki": true,
      "homepage": null,
      "languages": {
        "R": 16919,
        "Perl": 7222,
        "Shell": 644,
        "Python": 112679,
        "Dockerfile": 9761
      },
      "pushed_at": "2026-06-29T09:19:33Z",
      "created_at": "2023-10-21T20:02:14Z",
      "owner_type": "User",
      "updated_at": "2026-06-25T14:51:42Z",
      "description": "DamMapper: Snakemake workflow for DamID-Seq analysis",
      "is_archived": false,
      "is_disabled": false,
      "license_spdx": "MIT",
      "default_branch": "main",
      "license_spdx_raw": "MIT",
      "primary_language": "Python",
      "significant_languages": [
        "Python",
        "R"
      ]
    },
    "owner": {
      "blog": null,
      "name": "Niek Wit",
      "type": "User",
      "login": "niekwit",
      "company": "University of Cambridge",
      "location": "Cambridge, UK",
      "followers": 11,
      "avatar_url": "https://avatars.githubusercontent.com/u/41302859?v=4",
      "created_at": "2018-07-16T17:17:01Z",
      "is_verified": null,
      "public_repos": 60,
      "account_age_days": 2936
    },
    "license": {
      "state": "standard",
      "spdx_id": "MIT",
      "raw_spdx": "MIT",
      "file_present": true,
      "scorecard_found": true,
      "profile_has_license": true
    },
    "activity": {
      "releases": [
        {
          "tag": "v0.7.0",
          "kind": "minor",
          "published_at": "2026-06-29T09:19:33Z"
        },
        {
          "tag": "v0.6.0",
          "kind": "minor",
          "published_at": "2025-05-15T14:58:42Z"
        },
        {
          "tag": "v0.5.0",
          "kind": "minor",
          "published_at": "2024-07-05T12:20:41Z"
        },
        {
          "tag": "v0.4.0",
          "kind": "minor",
          "published_at": "2024-04-12T08:28:20Z"
        },
        {
          "tag": "v0.3.0",
          "kind": "minor",
          "published_at": "2024-03-01T21:53:55Z"
        }
      ],
      "recent_commits": [
        {
          "oid": "5e7a30822c6fe17bbd40af01a04734e3077f7499",
          "body": null,
          "is_bot": false,
          "headline": "removed Zenodo badge",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-25T14:52:52Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "822ee0d13ebd0f98cfc0078f88d02e1fb778b000",
          "body": null,
          "is_bot": false,
          "headline": "point to correct Docker image",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-25T14:52:04Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "71820c16046b90992eac2d80f959b8dca38edf5d",
          "body": null,
          "is_bot": false,
          "headline": "added damidBind ref sample",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T20:10:08Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8b435a2c633ec4dcb5d6a42152cacbafe7f13f55",
          "body": null,
          "is_bot": false,
          "headline": "updated",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T19:55:43Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "12a5ef70ea699a25becde3de167cdc42ebc53375",
          "body": null,
          "is_bot": false,
          "headline": "improved docs, and added info on damidBind",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T19:54:37Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "86738861086f857f3481ce02ff3ca5d64efd59c9",
          "body": null,
          "is_bot": false,
          "headline": "scaffold skip",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T19:54:01Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "72482a9aa00d554d4825bdedc9d911a55629872c",
          "body": null,
          "is_bot": false,
          "headline": "snakefmt formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T19:53:39Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8dc22a78b0a6d5b5ddab498ab48958270290967f",
          "body": null,
          "is_bot": false,
          "headline": "snakefmt formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T19:53:06Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9e2d69d202b573d2b758df9951e8675e6e72a93e",
          "body": null,
          "is_bot": false,
          "headline": "damidBind possible with multiple pairwise comparisons",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T19:21:57Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8df1e82ccd83f1b8009812e4816cef08bbd82db8",
          "body": null,
          "is_bot": false,
          "headline": "output csv with mapping rates for NGS Tracker",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T19:21:34Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8ea72af481b80371c07b1e9e57c2fbdcd7d7c14f",
          "body": null,
          "is_bot": false,
          "headline": "damidBind possible with multiple pairwise comparisons",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T19:21:20Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "8d6540ab2c9f221ddd79569a60b2c6e190b45d24",
          "body": null,
          "is_bot": false,
          "headline": "output csv with mapping rates for NGS Tracker",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T19:13:20Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a5934fbe3f44a01f0db5eff2b77735caf0d4d219",
          "body": null,
          "is_bot": false,
          "headline": "Integration with NGS Tracker and multiple comaprisons with damidBind",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T14:30:56Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d8a3aaf3dc28a2fbae0dcac8541ea30e843344fa",
          "body": null,
          "is_bot": false,
          "headline": "restrict SE test to index_bam rule, full PE test --> reduce runtime",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T07:11:13Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "f32555f1d8bb3652b2a38475d581ee044bea62fa",
          "body": null,
          "is_bot": false,
          "headline": "deleted one replicate to reduce runtime",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T07:10:56Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e9c4351047fb71f0bc4c1ec4c49eb06bca450df6",
          "body": "feat: added damidBind analysis",
          "is_bot": false,
          "headline": "Merge pull request #2 from niekwit/damidbind",
          "author_name": "Niek Wit",
          "author_login": "niekwit",
          "committed_at": "2026-06-24T05:18:07Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "39da6a83034155f5f71d0b15d13f9b79fba4f2f2",
          "body": null,
          "is_bot": false,
          "headline": "lowered stringency for test pe",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T21:29:02Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "64b667aecd176909069376f7a62f15e7f92b92d4",
          "body": null,
          "is_bot": false,
          "headline": "free disk space after se test",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T20:29:40Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "fcfdab95fc3496f8968aeb549f7a4991a2eea28a",
          "body": null,
          "is_bot": false,
          "headline": "use BiocManager::install()",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T19:40:58Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "62f82c694080c1be7076bb577de7a21d211099f4",
          "body": null,
          "is_bot": false,
          "headline": "fixed bug with conda env cache",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T19:40:10Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7ba147a0a34eb1ff7e435e07e3694c2f51149353",
          "body": null,
          "is_bot": false,
          "headline": "activated Perl peak calling for PE test data",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T19:17:25Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ec68cc9fd519f992922e05bcfc3869aa80c91bd9",
          "body": null,
          "is_bot": false,
          "headline": "samples csv included for pe test",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T18:59:12Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "567695fa3bd2223122a8fae954a6ef479c8fb545",
          "body": null,
          "is_bot": false,
          "headline": "added pe test fastq files",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T14:48:26Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "962ad149ed4be8f75c0dbbd089579fb0b0e8a6b6",
          "body": null,
          "is_bot": false,
          "headline": "2 threads for alignment",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T14:19:35Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "28ab5c7a72f01987ac4c9053d2add7aaa61c6fd1",
          "body": null,
          "is_bot": false,
          "headline": "no more use of pipe()",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T14:04:05Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "64730288282fa4f3218965ee33db84785f4ae95a",
          "body": null,
          "is_bot": false,
          "headline": "disable pathway enrichment analysis for Dm data",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T14:03:20Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7fe4ef90a89eb2f4f4aa7aea72eccab1d68f2fe6",
          "body": null,
          "is_bot": false,
          "headline": "fixed broken counter",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T13:53:46Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "f9f7791a84a5dc06d84711c4c007d0d03ef429e1",
          "body": null,
          "is_bot": false,
          "headline": "changed resource cpu counts to 1",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T13:45:24Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0bb461d65aebd15edc13bc9250c1606e1202dc1b",
          "body": null,
          "is_bot": false,
          "headline": "enabled PE testing",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T13:44:52Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c7bfa05ee74f407ee5923838a6606af086befcdd",
          "body": "The old script installed damidBind into the damid conda environment.\ndamidBind now has its own environment (damidbind.yaml) with a dedicated\npost-deploy script, so this file is no longer needed.\n\nCo-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Remove damid.post-deploy.sh (damidBind moved to damidbind env)",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T13:27:56Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "5ed6d571605303590cea4027df80e35b1319cd98",
          "body": null,
          "is_bot": false,
          "headline": "snakefmt formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T13:19:51Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "1ab38ac85373eb876f7f073c56bf6ac32dc2a37c",
          "body": null,
          "is_bot": false,
          "headline": "import resources as alias",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T13:16:51Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "50cad760403440a9180a0226ce48842cbe3f470f",
          "body": "Resolved conflicts in favour of damidbind branch:\n- Dockerfile/README: new damidbind conda env, updated hashes, pinned v1.1.1\n- Snakefile: keep VERSION = \"v0.7.0\"\n- damid.yaml: keep wget, drop r-biocmanager (moved to damidbind env)\n\nCo-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Merge origin/main into damidbind, keeping damidbind changes",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T13:10:19Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "6a8fc6859c0cdff81aeea0f380541718c7a2f34c",
          "body": null,
          "is_bot": false,
          "headline": "damidBind working now with test data",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T12:59:50Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a73acac7b017a3e040aef644c0db59b09ecbf629",
          "body": null,
          "is_bot": false,
          "headline": "pin version to v1.1.1",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T12:59:05Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c02cc82a1bd5caa58b45865df60060fad4b57adb",
          "body": null,
          "is_bot": false,
          "headline": "added wget",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T08:10:25Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "975ba68c92867cca4e8dedee97e976ba80ec934b",
          "body": null,
          "is_bot": false,
          "headline": "do not update other packages when installing BioVenn of damidBind",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-23T08:10:03Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0db9a39c16c3761c1c2efac5cf035c1d8c4a259b",
          "body": null,
          "is_bot": false,
          "headline": "added damidBind",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-19T14:26:04Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "277fc92c748fecd3424541cee31619bc29b8b20f",
          "body": null,
          "is_bot": false,
          "headline": "added damidBind rule",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-19T14:24:27Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "276d151289532397484aa0c44c7e1a82e4f286df",
          "body": null,
          "is_bot": false,
          "headline": "Initial commit",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-19T14:24:06Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "6c9d8bc21312ae37a5d0e4514ee39abe8dafbe73",
          "body": null,
          "is_bot": false,
          "headline": "installation of damidBind",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-19T14:23:42Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7e5614b72f5daa5bf26f6595b181d1ba1afe6332",
          "body": null,
          "is_bot": false,
          "headline": "v0.7.0, keep just one Dockerfile",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-06-19T14:22:34Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "95310a6b67a380bfceb0552dae1b4b9ec189c440",
          "body": "… only",
          "is_bot": false,
          "headline": "added post-deploy script to install damidBind when running with Conda…",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T10:10:05Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "101bb8b99f82f6f440bf2ddb9ff687b2123430d6",
          "body": null,
          "is_bot": false,
          "headline": "fixed error with non-existing command",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T08:57:17Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "963e769767fa551aed5e27415ffb245d621defd1",
          "body": null,
          "is_bot": false,
          "headline": "changed df concatenation to avoid FutureWarning",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T08:56:02Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "85f4f0e5cff0658b769fcf2fe45fd43019c3e095",
          "body": null,
          "is_bot": false,
          "headline": "deleted",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T08:28:26Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "86ae97895fea03c5cb16fcdd02585b1985f368f0",
          "body": null,
          "is_bot": false,
          "headline": "updated",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T08:27:48Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9b39f4c762c7a83907c7f2c3fdadb8f3d7e9a18f",
          "body": null,
          "is_bot": false,
          "headline": "snakefmt formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T08:23:07Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "511e2cb8af4890fdf93c58e0ac43dddf704c6c44",
          "body": null,
          "is_bot": false,
          "headline": "one Dockerfile",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T08:22:22Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ad29d903b04d23c1e774ac9b473c6632079de7a1",
          "body": null,
          "is_bot": false,
          "headline": "added biocmanager",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T08:00:03Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "f58f6caf56b5f32c3c7d4e265155a814333247df",
          "body": null,
          "is_bot": false,
          "headline": "r-base=4.3.2",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T07:47:25Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "cab659bd0d64c9ce467b976e3d1b5ff575d45131",
          "body": null,
          "is_bot": false,
          "headline": "changed dir name",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T07:40:57Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e285842bdd58cdf6e39a9a25f630b90f0af333b6",
          "body": null,
          "is_bot": false,
          "headline": "added missing validations",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T07:40:16Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "cdac1091c4107439e730f413bd836ea08d125e2b",
          "body": null,
          "is_bot": false,
          "headline": "changed replacement string",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T07:39:52Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "597d2b52216017344925d7229bf316e2910fd869",
          "body": null,
          "is_bot": false,
          "headline": "moved code to general_functions.smk",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T07:38:43Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a0fd79ded8d513da51481d058ced2d8613f04e14",
          "body": null,
          "is_bot": false,
          "headline": "bumped to v0.7.0",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2026-05-18T07:36:19Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c86e1bf512f3c64e5d2b1a9927199736c35db9b9",
          "body": "Added citation information for DamMapper.",
          "is_bot": false,
          "headline": "Add citation section to README",
          "author_name": "Niek Wit",
          "author_login": "niekwit",
          "committed_at": "2025-10-15T20:00:16Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "71dad9a10e08174f9bda575aa4953127d49bd2e4",
          "body": null,
          "is_bot": false,
          "headline": "changed git version to 2.49",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-08-29T08:55:10Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d5d2921628c21eeca0aa704b0572abb8f3e3ecc3",
          "body": null,
          "is_bot": false,
          "headline": "changed r version",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-08-29T08:18:05Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "021f73b3166835fb09f8e65676d18f9a4c96f9fa",
          "body": null,
          "is_bot": false,
          "headline": "added git",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-08-29T08:00:10Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "88946ca4ba759b75f1ce01dd9ba8d559b0378e89",
          "body": null,
          "is_bot": false,
          "headline": "point to specific commit",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-08-28T14:37:43Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "f8cf4168ceae10e609ff90906ea7dada00814278",
          "body": null,
          "is_bot": false,
          "headline": "added splash screen",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-08-28T13:21:29Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "1e9cd843fd175f6b6ef9854240b02f6b3daaad1e",
          "body": null,
          "is_bot": false,
          "headline": "replaced damid-seq with DamMapper",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-06-04T09:07:32Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0d7cce4762506e9a6e6fc5156077c16853c981d5",
          "body": null,
          "is_bot": false,
          "headline": "replaced damid-seq with DamMapper",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-06-04T09:02:20Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c072bc27194e45b584b6f5d5a506b36ad6365f4e",
          "body": null,
          "is_bot": false,
          "headline": "updated",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-05-14T07:17:38Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "252ae1d9b0102aa9c1b3da115c4d80ec8ca8f2d0",
          "body": null,
          "is_bot": false,
          "headline": "changed name",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-15T14:23:40Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "15cfeca08063e3e47fee509fbcf3f09466d9d9e2",
          "body": null,
          "is_bot": false,
          "headline": "snakefmt formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T14:49:05Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "50cfe153f52ccf64fb2cf5ef0d3fc3776f38ee4d",
          "body": null,
          "is_bot": false,
          "headline": "fixed path issue attempt 4",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T14:46:57Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "5ad401e4ba84788f8c5fcae6241652d1b3f93642",
          "body": null,
          "is_bot": false,
          "headline": "fixed path issue attempt 3",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T14:37:07Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c9a2253200955995afa44efb963938499108530c",
          "body": null,
          "is_bot": false,
          "headline": "fixed path issue attempt 2",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T14:21:24Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d5de8ded48fede3dfb89b2b858e305b01264f93c",
          "body": null,
          "is_bot": false,
          "headline": "updated name",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T13:26:11Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "154427fe2668ad5f8284acab59472f49f05f83b8",
          "body": null,
          "is_bot": false,
          "headline": "black formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T13:25:18Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "5cb2f9452875cab849deb7f7f333dd38f9161ac8",
          "body": null,
          "is_bot": false,
          "headline": "Air formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T13:24:28Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "86e342944af1cb9b8a91d48ab7b87b91fbfe227d",
          "body": null,
          "is_bot": false,
          "headline": "snakefmt formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T13:18:59Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ebe4205e0ae3399678ef9373de4e892223c1cebe",
          "body": null,
          "is_bot": false,
          "headline": "sort gatc gff file",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T13:18:25Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "076c707704ece74c789ec59d5216997de6fdda33",
          "body": null,
          "is_bot": false,
          "headline": "changed path",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T13:12:39Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d499bd2b774c417cb5ea41ee5c83063e0cd87430",
          "body": null,
          "is_bot": false,
          "headline": "added warning after completion",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-11T13:10:55Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "edeba6a6ca106fe47df429fb948f9c73c401c818",
          "body": null,
          "is_bot": false,
          "headline": "added mm38",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:24:55Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a1b8c47d7cadb39462f5cc1e38f120c632161eaa",
          "body": null,
          "is_bot": false,
          "headline": "added mm38",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:24:35Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "18907a06f937acc19a307d730e107e96100c2427",
          "body": null,
          "is_bot": false,
          "headline": "check for plasmid function",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:24:07Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "78e45e5dd239a5e8aa80f040185f5ade5a0fe72c",
          "body": null,
          "is_bot": false,
          "headline": "simplified frip",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:22:49Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a129736b69864c42f342dc4c4d54f60603cbbc36",
          "body": null,
          "is_bot": false,
          "headline": "updated wrapper to v5.8.3",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:22:35Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9bff7ddda224d4c15ae84c0df194c7b8ce9f591b",
          "body": null,
          "is_bot": false,
          "headline": "simplified frip",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:22:14Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c81f1dd21674ffcb3bacd333b6160f8b1e85bacb",
          "body": null,
          "is_bot": false,
          "headline": "updated wrapper to v5.8.3",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:20:37Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "019132e43da0766a830e075c275f6932d0b9234f",
          "body": null,
          "is_bot": false,
          "headline": "updated wrapper to v5.8.3",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:20:26Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "f2da3fc8a71b596f21c1f670b282375a496a3876",
          "body": null,
          "is_bot": false,
          "headline": "removed redundant code",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:19:49Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "17da854cd478da5014120d6702bfbd0da349a1e8",
          "body": null,
          "is_bot": false,
          "headline": "fixed issues with input/output and added samtools flag",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-07T10:19:11Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "414c13500fd81ba1cefe1bc1a1b9bc40eb01b7e2",
          "body": null,
          "is_bot": false,
          "headline": "Initial commit",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-03T09:54:04Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9fe66b06549280d2507c1c41e2f987288bf59fe1",
          "body": null,
          "is_bot": false,
          "headline": "simplified",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-02T14:27:43Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7c56263b0def4bf7f22fb01ff53ccd1bca79ce82",
          "body": null,
          "is_bot": false,
          "headline": "added pybedtools",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-02T11:17:47Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "813a5dc484a5daf1091a88d0921bbcd88a839afc",
          "body": null,
          "is_bot": false,
          "headline": "added pybedtools",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-02T10:55:05Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9d478360ff4f2977b05651ef7de896c003255818",
          "body": null,
          "is_bot": false,
          "headline": "remove duplicate peaks",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-04-01T13:21:21Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ed0a8cb99f22defa6527eb799f0d54670dca1d97",
          "body": null,
          "is_bot": false,
          "headline": "black formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-03-10T10:52:10Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "deb586c3d549d21b02a32a29f45e0e2643b9cf60",
          "body": null,
          "is_bot": false,
          "headline": "wrapper v5.8.3",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-03-10T10:16:31Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "6a281190424bcd26ea35e1c3adda3e8694546e03",
          "body": null,
          "is_bot": false,
          "headline": "Changed versions of wrappers and Snakemake",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-03-10T10:15:22Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "9061bfb94957721b0a8c7c1d617bcf75327e680f",
          "body": null,
          "is_bot": false,
          "headline": "black formatting",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-03-10T09:16:14Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "237dc19ac6df1d6388e0a2d3713b40c8bcf228f8",
          "body": null,
          "is_bot": false,
          "headline": "deleted",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2025-03-10T08:48:04Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c94e0364796bc6fff37973edbfed5a48b9ce347f",
          "body": null,
          "is_bot": false,
          "headline": "increased CPU count for bowtie2",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2024-11-22T15:32:39Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "da49a6b8e45d554e56fc22d2bf9672e1671b6f6b",
          "body": null,
          "is_bot": false,
          "headline": "lowered CPU count",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2024-11-22T15:12:55Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "457ca120a0ccfc632547ce915af1364a8b54db95",
          "body": null,
          "is_bot": false,
          "headline": "working again",
          "author_name": "niekwit",
          "author_login": "niekwit",
          "committed_at": "2024-11-22T14:58:28Z",
          "body_truncated": false,
          "is_coding_agent": false
        }
      ],
      "releases_count": 5,
      "commits_last_year": 62,
      "latest_release_at": "2026-06-29T09:19:33Z",
      "latest_release_tag": "v0.7.0",
      "releases_from_tags": false,
      "days_since_last_push": 31,
      "active_weeks_last_year": 5,
      "days_since_latest_release": 31,
      "mean_days_between_releases": 212.4
    },
    "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": 1,
      "stars": 5,
      "watchers": 1,
      "fork_history": {
        "days": [
          {
            "date": "2026-04-04",
            "count": 1
          }
        ],
        "complete": true,
        "collected": 1,
        "total_forks": 1
      },
      "star_history": null,
      "open_issues_and_prs": 0
    },
    "ai_readiness": {
      "has_nix": false,
      "example_dirs": [],
      "has_llms_txt": false,
      "has_dockerfile": true,
      "has_mcp_signal": false,
      "bootstrap_files": [],
      "api_schema_files": [],
      "has_devcontainer": false,
      "typecheck_configs": [],
      "toolchain_manifests": [],
      "largest_source_bytes": 3693,
      "source_files_sampled": 15,
      "oversized_source_files": 0,
      "agent_instruction_files": [],
      "agent_instruction_max_bytes": null
    },
    "dependencies": {
      "manifests": [
        "docs/requirements.txt"
      ],
      "advisories": {
        "error": null,
        "scope": "repository_graph",
        "source": "osv",
        "findings": [],
        "collected": true,
        "malicious": [],
        "truncated": false,
        "by_severity": {},
        "advisory_count": 0,
        "affected_count": 0,
        "assessed_count": 2,
        "malicious_count": 0,
        "assessed_package": null,
        "unassessed_count": 0,
        "direct_affected_count": 0
      },
      "ecosystems": [
        "pypi"
      ],
      "dependencies": [],
      "all_dependencies": {
        "error": null,
        "source": "github-sbom",
        "packages": [
          {
            "name": "sphinx",
            "direct": false,
            "version": "7.3.7",
            "ecosystem": "pypi"
          },
          {
            "name": "sphinx-rtd-theme",
            "direct": false,
            "version": "2.0.0",
            "ecosystem": "pypi"
          }
        ],
        "collected": true,
        "truncated": false,
        "total_count": 2,
        "direct_count": 0,
        "indirect_count": 2
      }
    },
    "maintainership": {
      "issues": {
        "open_prs": 0,
        "merged_prs": 1,
        "open_issues": 0,
        "closed_ratio": 1,
        "closed_issues": 1,
        "closed_unmerged_prs": 0
      },
      "bus_factor": 1,
      "bot_contributors": 0,
      "top_contributors": [
        {
          "type": "User",
          "login": "niekwit",
          "commits": 514,
          "avatar_url": "https://avatars.githubusercontent.com/u/41302859?v=4"
        }
      ],
      "contributors_sampled": 1,
      "top_contributor_share": 1
    },
    "quality_signals": {
      "has_ci": true,
      "has_tests": false,
      "ci_workflows": [
        "conventional-prs.yml",
        "main.yml",
        "release-please.yml"
      ],
      "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": 10,
            "reason": "no binaries found in the repo",
            "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": 10,
            "reason": "1 out of 1 merged PRs checked by a CI test -- score normalized to 10",
            "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 0/16 approved changesets -- score normalized to 0",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#code-review"
          },
          {
            "name": "Contributors",
            "score": 3,
            "reason": "project has 1 contributing companies or organizations -- score normalized to 3",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#contributors"
          },
          {
            "name": "Dangerous-Workflow",
            "score": 10,
            "reason": "no dangerous workflow patterns detected",
            "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 0 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": 0,
            "reason": "dependency not pinned by hash detected -- score normalized to 0",
            "documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#pinned-dependencies"
          },
          {
            "name": "SAST",
            "score": 0,
            "reason": "SAST tool is not run on all commits -- score normalized to 0",
            "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": 0,
            "reason": "detected GitHub workflow tokens with excessive permissions",
            "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": "5e7a30822c6fe17bbd40af01a04734e3077f7499",
        "ran_at": "2026-07-30T20:15:44Z",
        "aggregate_score": 4.1,
        "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": "2026-06-29T09:04:38Z",
      "oldest_open_prs": [],
      "last_merged_pr_at": "2026-06-24T05:18:08Z",
      "ci_last_conclusion": "SUCCESS",
      "oldest_open_issues": []
    }
  },
  "config": {
    "disabled_metrics": [],
    "disabled_categories": [],
    "disabled_components": {}
  },
  "source": {
    "url": "https://github.com/niekwit/damid-seq",
    "host": "github.com",
    "name": "damid-seq",
    "owner": "niekwit"
  },
  "metrics": {
    "overall": {
      "key": "overall",
      "band": "moderate",
      "name": "Overall health",
      "note": null,
      "notes": [],
      "value": 51,
      "inputs": {
        "security": 53,
        "vitality": 62,
        "community": 29,
        "governance": 48,
        "engineering": 60
      },
      "components": []
    },
    "categories": [
      {
        "key": "vitality",
        "band": "moderate",
        "name": "Vitality",
        "value": 62,
        "weight": 0.22,
        "metrics": [
          {
            "key": "development_activity",
            "band": "at_risk",
            "name": "Development activity",
            "note": null,
            "notes": [],
            "value": 48,
            "inputs": {
              "commits_last_year": 62,
              "human_commit_share": 1,
              "days_since_last_push": 31,
              "active_weeks_last_year": 5
            },
            "components": [
              {
                "key": "push_recency",
                "name": "Push recency",
                "detail": "last push 31 days ago",
                "points": 18,
                "status": "partial",
                "details": [
                  {
                    "code": "push_recency",
                    "params": {
                      "days": 31
                    }
                  }
                ],
                "max_points": 36
              },
              {
                "key": "commit_cadence",
                "name": "Commit cadence",
                "detail": "5/52 weeks with commits",
                "points": 3.5,
                "status": "partial",
                "details": [
                  {
                    "code": "commit_cadence_weeks",
                    "params": {
                      "weeks": 5
                    }
                  }
                ],
                "max_points": 36
              },
              {
                "key": "commit_volume",
                "name": "Commit volume",
                "detail": "62 commits in the last year",
                "points": 16.2,
                "status": "partial",
                "details": [
                  {
                    "code": "commits_last_year",
                    "params": {
                      "count": 62
                    }
                  }
                ],
                "max_points": 18
              },
              {
                "key": "openssf_scorecard_maintained",
                "name": "OpenSSF Scorecard: Maintained",
                "detail": "30 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10",
                "points": 10,
                "status": "met",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "release_discipline",
            "band": "good",
            "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": 84,
            "inputs": {
              "releases_count": 5,
              "latest_release_tag": "v0.7.0",
              "releases_from_tags": false,
              "days_since_latest_release": 31,
              "mean_days_between_releases": 212.4
            },
            "components": [
              {
                "key": "ships_releases",
                "name": "Ships releases",
                "detail": "5 releases published",
                "points": 27,
                "status": "met",
                "details": [
                  {
                    "code": "releases_published",
                    "params": {
                      "count": 5
                    }
                  }
                ],
                "max_points": 27
              },
              {
                "key": "release_recency",
                "name": "Release recency",
                "detail": "latest release 31 days ago",
                "points": 36,
                "status": "met",
                "details": [
                  {
                    "code": "release_recency",
                    "params": {
                      "days": 31
                    }
                  }
                ],
                "max_points": 36
              },
              {
                "key": "release_cadence",
                "name": "Release cadence",
                "detail": "a release every ~212.4 days",
                "points": 12.6,
                "status": "partial",
                "details": [
                  {
                    "code": "release_cadence",
                    "params": {
                      "gap": 212.4
                    }
                  }
                ],
                "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": 35,
              "days_since_last_human_commit_is_floor": false
            },
            "components": [
              {
                "key": "project_is_still_maintained",
                "name": "Project is still maintained",
                "detail": "last human commit 35 days ago",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "abandonment_maintained",
                    "params": {
                      "days": 35
                    }
                  }
                ],
                "max_points": 100
              }
            ]
          }
        ],
        "description": "Is the project alive — is code being written and are releases shipping?"
      },
      {
        "key": "community",
        "band": "critical",
        "name": "Community & Adoption",
        "value": 29,
        "weight": 0.18,
        "metrics": [
          {
            "key": "popularity",
            "band": "critical",
            "name": "Popularity & adoption",
            "note": null,
            "notes": [],
            "value": 10,
            "inputs": {
              "forks": 1,
              "stars": 5,
              "watchers": 1,
              "growth_state": "unverified",
              "growth_factor_pct": 100,
              "growth_unverified_reason": "no_history"
            },
            "components": [
              {
                "key": "stars",
                "name": "Stars",
                "detail": "5 stars",
                "points": 9.8,
                "status": "partial",
                "details": [
                  {
                    "code": "stars",
                    "params": {
                      "count": 5
                    }
                  }
                ],
                "max_points": 60
              },
              {
                "key": "forks",
                "name": "Forks",
                "detail": "1 forks",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "forks",
                    "params": {
                      "count": 1
                    }
                  }
                ],
                "max_points": 25
              },
              {
                "key": "watchers",
                "name": "Watchers",
                "detail": "1 watchers",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "watchers",
                    "params": {
                      "count": 1
                    }
                  }
                ],
                "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 (MIT)",
                "points": 22.5,
                "status": "met",
                "details": [
                  {
                    "code": "license_standard",
                    "params": {}
                  },
                  {
                    "code": "license_spdx",
                    "params": {
                      "spdx": "MIT"
                    }
                  }
                ],
                "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": 48,
        "weight": 0.24,
        "metrics": [
          {
            "key": "maintainer_resilience",
            "band": "critical",
            "name": "Maintainer resilience (bus factor)",
            "note": null,
            "notes": [],
            "value": 13,
            "inputs": {
              "bus_factor": 1,
              "contributors_sampled": 1,
              "top_contributor_share": 1
            },
            "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 100% of commits",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "top_contributor_share",
                    "params": {
                      "share": 100
                    }
                  }
                ],
                "max_points": 22.5
              },
              {
                "key": "contributor_breadth",
                "name": "Contributor breadth",
                "detail": "1 contributors",
                "points": 1.4,
                "status": "partial",
                "details": [
                  {
                    "code": "contributors_sampled",
                    "params": {
                      "count": 1
                    }
                  }
                ],
                "max_points": 13.5
              },
              {
                "key": "openssf_scorecard_contributors",
                "name": "OpenSSF Scorecard: Contributors",
                "detail": "project has 1 contributing companies or organizations -- score normalized to 3",
                "points": 3,
                "status": "partial",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "responsiveness",
            "band": "excellent",
            "name": "Issue & PR responsiveness",
            "note": null,
            "notes": [],
            "value": 85,
            "inputs": {
              "merged_prs": 1,
              "open_issues": 0,
              "closed_issues": 1,
              "issue_closed_ratio": 1,
              "closed_unmerged_prs": 0
            },
            "components": [
              {
                "key": "issue_resolution",
                "name": "Issue resolution",
                "detail": "100% of issues closed",
                "points": 46.8,
                "status": "met",
                "details": [
                  {
                    "code": "issues_closed_share",
                    "params": {
                      "share": 100
                    }
                  }
                ],
                "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 0/16 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": 54,
            "inputs": {
              "followers": 11,
              "owner_type": "User",
              "is_verified": null,
              "owner_login": "niekwit",
              "public_repos": 60,
              "account_age_days": 2936
            },
            "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": "11 followers of niekwit",
                "points": 7.8,
                "status": "partial",
                "details": [
                  {
                    "code": "owner_followers",
                    "params": {
                      "count": 11,
                      "login": "niekwit"
                    }
                  }
                ],
                "max_points": 25
              },
              {
                "key": "track_record",
                "name": "Track record",
                "detail": "60 public repos, account ~8 yr old",
                "points": 25,
                "status": "met",
                "details": [
                  {
                    "code": "public_repos",
                    "params": {
                      "count": 60
                    }
                  },
                  {
                    "code": "account_age_years",
                    "params": {
                      "years": 8
                    }
                  }
                ],
                "max_points": 25
              }
            ]
          }
        ],
        "description": "Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?"
      },
      {
        "key": "engineering",
        "band": "moderate",
        "name": "Engineering Quality",
        "value": 60,
        "weight": 0.2,
        "metrics": [
          {
            "key": "engineering_practices",
            "band": "at_risk",
            "name": "Engineering practices",
            "note": null,
            "notes": [],
            "value": 44,
            "inputs": {
              "has_ci": true,
              "has_tests": false,
              "has_editorconfig": false,
              "has_linter_config": false,
              "has_precommit_config": false
            },
            "components": [
              {
                "key": "ci_workflows",
                "name": "CI workflows",
                "detail": "3 workflow(s)",
                "points": 24,
                "status": "met",
                "details": [
                  {
                    "code": "ci_workflows",
                    "params": {
                      "count": 3
                    }
                  }
                ],
                "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": "1 out of 1 merged PRs checked by a CI test -- score normalized to 10",
                "points": 20,
                "status": "met",
                "details": [],
                "max_points": 20
              }
            ]
          },
          {
            "key": "documentation",
            "band": "excellent",
            "name": "Documentation",
            "note": null,
            "notes": [],
            "value": 85,
            "inputs": {
              "topics": [
                "bioinformatics-pipeline",
                "damid",
                "snakemake-workflow"
              ],
              "has_wiki": true,
              "homepage": null,
              "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": null,
                "points": 0,
                "status": "missed",
                "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": "3 topics",
                "points": 10,
                "status": "met",
                "details": [
                  {
                    "code": "topics_count",
                    "params": {
                      "count": 3
                    }
                  }
                ],
                "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": "moderate",
        "name": "Security",
        "value": 53,
        "weight": 0.16,
        "metrics": [
          {
            "key": "security_posture",
            "band": "at_risk",
            "name": "Security posture",
            "note": "Excluded from scoring (no data or not applicable): Packaging, Signed-Releases. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "packaging",
                    "signed_releases"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 41,
            "inputs": {
              "source": "openssf_scorecard",
              "checks_evaluated": 16,
              "scorecard_version": "v5.5.0",
              "checks_inconclusive": 2,
              "scorecard_aggregate": 4.1
            },
            "components": [
              {
                "key": "binary_artifacts",
                "name": "Binary-Artifacts",
                "detail": "no binaries found in the repo",
                "points": 7.5,
                "status": "met",
                "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": "1 out of 1 merged PRs checked by a CI test -- score normalized to 10",
                "points": 2.5,
                "status": "met",
                "details": [],
                "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 0/16 approved changesets -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "contributors",
                "name": "Contributors",
                "detail": "project has 1 contributing companies or organizations -- score normalized to 3",
                "points": 0.8,
                "status": "partial",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "dangerous_workflow",
                "name": "Dangerous-Workflow",
                "detail": "no dangerous workflow patterns detected",
                "points": 10,
                "status": "met",
                "details": [],
                "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 0 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": "dependency not pinned by hash detected -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "sast",
                "name": "SAST",
                "detail": "SAST tool is not run on all commits -- score normalized to 0",
                "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": "detected GitHub workflow tokens with excessive permissions",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "vulnerabilities",
                "name": "Vulnerabilities",
                "detail": "0 existing vulnerabilities detected",
                "points": 7.5,
                "status": "met",
                "details": [],
                "max_points": 7.5
              }
            ]
          },
          {
            "key": "dependency_advisories",
            "band": "excellent",
            "name": "Dependency advisories",
            "note": "Excluded from scoring (no data or not applicable): Indirect dependencies free of known advisories, No advisories left outstanding. Remaining weights renormalized. Matched 2 resolved dependencies against OSV. This repository publishes no package the index resolves, so the repository dependency graph was assessed instead. That graph mixes development and test pins with shipped dependencies, so only the declared runtime dependencies are scored; transitive findings are reported as context and excluded from the score. Reachability is not analyzed.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "indirect_dependencies_free_of_known_advisories",
                    "no_advisories_left_outstanding"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              },
              {
                "code": "advisories_scope_repository",
                "params": {
                  "assessed": 2
                }
              },
              {
                "code": "advisories_repo_graph_caveat",
                "params": {}
              },
              {
                "code": "advisories_reachability",
                "params": {}
              }
            ],
            "value": 100,
            "inputs": {
              "source": "osv",
              "advisories": 0,
              "affected_packages": 0,
              "assessed_packages": 2,
              "unassessed_packages": 0,
              "affected_by_severity": "none",
              "direct_affected_packages": 0
            },
            "components": [
              {
                "key": "direct_dependencies_free_of_known_advisories",
                "name": "Direct dependencies free of known advisories",
                "detail": "no direct dependency carries a known advisory",
                "points": 35,
                "status": "met",
                "details": [
                  {
                    "code": "no_direct_advisories",
                    "params": {}
                  }
                ],
                "max_points": 35
              },
              {
                "key": "indirect_dependencies_free_of_known_advisories",
                "name": "Indirect dependencies free of known advisories",
                "detail": "transitive set not separable from development and test dependencies in this scope",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "advisories_scope_not_separable",
                    "params": {}
                  }
                ],
                "max_points": 25
              },
              {
                "key": "no_advisories_left_outstanding",
                "name": "No advisories left outstanding",
                "detail": "no advisory carries a publication date",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "advisories_no_publication_date",
                    "params": {}
                  }
                ],
                "max_points": 40
              }
            ]
          },
          {
            "key": "malicious_dependencies",
            "band": "excellent",
            "name": "Malicious dependencies",
            "note": null,
            "notes": [],
            "value": 100,
            "inputs": {
              "source": "osv",
              "meaning": "reported as a malicious package by the OpenSSF corpus; the remedy is removal or moving off the compromised name, never an upgrade of the same artifact. Versions the registry has since pulled are listed but not scored",
              "packages": [],
              "red_flag": false,
              "assessed_packages": 2,
              "malicious_packages": 0,
              "direct_malicious_packages": 0,
              "withdrawn_malicious_packages": 0,
              "installable_malicious_packages": 0
            },
            "components": [
              {
                "key": "no_dependency_reported_as_a_malicious_package",
                "name": "No dependency reported as a malicious package",
                "detail": "no dependency is reported as a malicious package",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "no_malicious_dependencies",
                    "params": {}
                  }
                ],
                "max_points": 100
              }
            ]
          },
          {
            "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": 2
            },
            "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": 17,
        "weight": 0,
        "metrics": [
          {
            "key": "ai_agent_context",
            "band": "critical",
            "name": "Agent context & guidance",
            "note": null,
            "notes": [],
            "value": 2,
            "inputs": {
              "has_llms_txt": false,
              "legible_history_share": 0.03,
              "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": "3 of 100 human commits state their intent (structured subject or explanatory body)",
                "points": 1.6,
                "status": "partial",
                "details": [
                  {
                    "code": "legible_history",
                    "params": {
                      "legible": 3,
                      "sampled": 100
                    }
                  }
                ],
                "max_points": 40
              }
            ]
          },
          {
            "key": "ai_verify_loop",
            "band": "critical",
            "name": "Verify loop (build / test / typecheck)",
            "note": null,
            "notes": [],
            "value": 14,
            "inputs": {
              "has_nix": false,
              "has_tests": false,
              "lockfiles": [],
              "has_dockerfile": true,
              "typed_language": false,
              "bootstrap_files": [],
              "has_devcontainer": false,
              "has_linter_config": false,
              "typecheck_configs": [],
              "agent_commit_share": 0.02,
              "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": "Dockerfile",
                "points": 10,
                "status": "met",
                "details": [
                  {
                    "code": "file_list",
                    "params": {
                      "files": "Dockerfile"
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "demonstrated_agent_practice",
                "name": "Demonstrated agent practice",
                "detail": "2 of the last 100 commits agent-authored or agent-credited",
                "points": 4,
                "status": "partial",
                "details": [
                  {
                    "code": "agent_authored_commits",
                    "params": {
                      "count": 2,
                      "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": "dependency not pinned by hash detected -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 10
              }
            ]
          },
          {
            "key": "ai_code_legibility",
            "band": "moderate",
            "name": "Code legibility for models",
            "note": null,
            "notes": [],
            "value": 55,
            "inputs": {
              "primary_language": "Python",
              "largest_source_bytes": 3693,
              "source_files_sampled": 15,
              "oversized_source_files": 0
            },
            "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": "0/15 source files over 60KB",
                "points": 55,
                "status": "met",
                "details": [
                  {
                    "code": "oversized_source_files",
                    "params": {
                      "kb": 60,
                      "sampled": 15,
                      "oversized": 0
                    }
                  }
                ],
                "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"
  ],
  "report_type": "repository",
  "generated_at": "2026-07-30T20:15:58.825981Z",
  "schema_version": "0.27.0",
  "badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/n/niekwit/damid-seq.svg",
  "full_name": "niekwit/damid-seq",
  "license_state": "standard",
  "license_spdx": "MIT"
}

Оцінки — це сигнали, а не гарантії. Вони відображають публічно видимі практики на GitHub — це не аудит коду й не гарантія безпеки.

Відсутні дані виключаються, а ваги перенормовуються — нуль за відсутність ніколи не ставиться. Методологія версіонована й відкрита: метрики v1.13.0, схема v0.27.0 — повна методологія · вікі метрик.

Як окремий результат виглядає на тлі всього реєстру: сукупна статистика.