JSON-Rohbericht maschinenlesbar
{
"data": {
"repo": {
"topics": [
"structure-prediction",
"3d-structure",
"protein",
"protein-complexes"
],
"is_fork": false,
"size_kb": 19375,
"has_wiki": true,
"homepage": "http://evcouplings.org",
"languages": {
"Python": 973487,
"Jupyter Notebook": 1112585
},
"pushed_at": "2026-04-20T13:02:50Z",
"created_at": "2016-07-20T18:15:45Z",
"owner_type": "Organization",
"updated_at": "2026-07-22T16:01:41Z",
"description": "Evolutionary couplings from protein and RNA sequence alignments",
"is_archived": false,
"is_disabled": false,
"license_spdx": null,
"default_branch": "develop",
"license_spdx_raw": "NOASSERTION",
"primary_language": "Jupyter Notebook",
"significant_languages": [
"Jupyter Notebook",
"Python"
]
},
"owner": {
"blog": "https://marks.hms.harvard.edu/",
"name": "Debora Marks Lab",
"type": "Organization",
"login": "debbiemarkslab",
"company": null,
"location": "Boston, MA",
"followers": 135,
"avatar_url": "https://avatars.githubusercontent.com/u/8976419?v=4",
"created_at": "2014-09-30T19:46:58Z",
"is_verified": null,
"public_repos": 33,
"account_age_days": 4316
},
"license": {
"state": "custom",
"spdx_id": null,
"raw_spdx": "NOASSERTION",
"file_present": true,
"scorecard_found": true,
"profile_has_license": true
},
"activity": {
"releases": [
{
"tag": "v0.2.1",
"kind": "patch",
"published_at": "2024-11-05T11:16:06Z"
},
{
"tag": "v0.1.1",
"kind": "patch",
"published_at": "2020-11-06T16:59:48Z"
},
{
"tag": "v0.0.5",
"kind": "patch",
"published_at": "2018-09-16T14:17:14Z"
},
{
"tag": "v0.0.4",
"kind": "patch",
"published_at": "2018-06-10T16:58:00Z"
},
{
"tag": "v0.0.3",
"kind": "patch",
"published_at": "2018-04-05T16:56:55Z"
},
{
"tag": "v0.0.2",
"kind": "patch",
"published_at": "2018-02-22T22:29:55Z"
},
{
"tag": "v0.0.1",
"kind": "patch",
"published_at": "2017-09-03T13:29:15Z"
}
],
"recent_commits": [
{
"oid": "14c83457c6cfca8156aabe0615067447a2169791",
"body": "fixed a3m import/sequence parsing",
"is_bot": false,
"headline": "Merge pull request #336 from debbiemarkslab/file_imports",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2026-04-20T13:02:44Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "819547b9c9f2514f58539ba905fffebc6b44d326",
"body": null,
"is_bot": false,
"headline": "fixed a3m import/sequence parsing",
"author_name": "Ethan Eschbach-ete456",
"author_login": null,
"committed_at": "2026-04-20T12:48:42Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "522b0d185411fab8e166ba4d8abc38a3e0556880",
"body": "only lowercase columns if at least one column affected, fixes #327",
"is_bot": false,
"headline": "Merge pull request #332 from debbiemarkslab/filtering-bug",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2025-10-23T14:59:25Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e550a6a347df9169a0f6f72c83118b7d6bed1d8a",
"body": null,
"is_bot": false,
"headline": "only lowercase columns if at least one column affected, fixes #327",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2025-10-23T14:54:30Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "92c5d6faa94630f54e2fad11844c7fd68ff0fd46",
"body": "Fix regressions related to structure loading",
"is_bot": false,
"headline": "Merge pull request #331 from debbiemarkslab/pdb-loading-fixes",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2025-10-23T10:27:20Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "f80222a5593212fa3915c66c2efdd7cedd9cb3ad",
"body": null,
"is_bot": false,
"headline": "fix residue 3 to 1 mapping to cover nonstandard AAs too",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2025-10-22T11:05:30Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "f7b5bf0c35d0a9228b7d378e44772a261967ad49",
"body": null,
"is_bot": false,
"headline": "remap jackhmmer oom to termination",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2025-10-22T09:47:59Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d1d3d588119173bc94883e8a0e606b0fb93e617a",
"body": null,
"is_bot": false,
"headline": "enable skipping of missing structures for more robustness",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2025-10-22T09:24:14Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "30e7903b920eae051debdf0330f76e3f120554f1",
"body": null,
"is_bot": false,
"headline": "remove version from alphafolddb literal",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2025-10-22T08:49:53Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "c4ac882351efdcb6227252947b71ce48304b81c3",
"body": null,
"is_bot": false,
"headline": "switch PDB.from_id from bCIF to mmCIF",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2025-10-04T14:30:02Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b19baffe255a4ba031aa87d366464076466828ce",
"body": "fix models() crash when no structures found",
"is_bot": false,
"headline": "Merge pull request #325 from debbiemarkslab/af_fix",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2025-10-03T15:07:50Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "8f221e4ae79b7267b4e820e4ab7e9d8167e32347",
"body": null,
"is_bot": false,
"headline": "fix models() crash when no structures found",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2025-03-02T13:52:02Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "75bfc9677fc9412ddb7089a9f26c7a01f65bfa12",
"body": "Better weights",
"is_bot": false,
"headline": "Merge pull request #321 from debbiemarkslab/better_weights",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2024-12-03T13:17:24Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7aa49ea977c412e3cf220e5b066e3c7efc054708",
"body": null,
"is_bot": false,
"headline": "adjust plmc log parsing regex",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-12-03T12:34:58Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "4a57dff2dc815235685bee18a3b61a4f3ecf532c",
"body": null,
"is_bot": false,
"headline": "fix wrong file handle",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-12-02T16:57:42Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "84ffb1698f99acf0cf045636454b641011d62ad5",
"body": null,
"is_bot": false,
"headline": "fix weight param handling issues",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-12-02T16:33:32Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "08d3cf385b8ae3fade6f77aaefd3a86cfabd52d3",
"body": null,
"is_bot": false,
"headline": "integrate better sequence weighting into alignment protocols",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-28T13:53:39Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "5499c509f9e111c25a65267fc3eeaf7a1eb9f612",
"body": null,
"is_bot": false,
"headline": "change weight file key",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-28T13:03:30Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7eb7859e65763ece12000caf51e3239c22e6b565",
"body": null,
"is_bot": false,
"headline": "add sequence weight saving/loading",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-28T11:44:30Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "551f66e51c679c660f2fd6e1cbf70b7920513dac",
"body": null,
"is_bot": false,
"headline": "more plmc logging output",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-28T11:44:06Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "be334591cbf293a66a6b41382872407e0393d6a9",
"body": null,
"is_bot": false,
"headline": "allow to call plmc with weights file",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-28T10:58:31Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "f65c425e583d25ad5c6fbef4a88e4d1664d35227",
"body": null,
"is_bot": false,
"headline": "update weight calculation wrapper on alignment class",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-27T16:10:53Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "4c7a369eb2b9e6973120b8191a1c25a558c332cf",
"body": null,
"is_bot": false,
"headline": "update identities wrapper on Alignment class",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-27T15:36:03Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "4d794c079f2fd59c1482094487808534e35f2aa2",
"body": null,
"is_bot": false,
"headline": "update corresponding single-seq id calculation",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-27T14:53:37Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "814c2795bb326a53c7729f3a54856a900c5fd443",
"body": null,
"is_bot": false,
"headline": "simplify exclude_value handling",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-27T14:31:52Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "6afeeb3e161f88f53f4e81d931b92961c197e85d",
"body": null,
"is_bot": false,
"headline": "add better sequence weights function (h/t Lood and Aaron)",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-27T14:29:23Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "86d55a7c63a936eef21f1d179f1e1a18aa5c7ff7",
"body": "Compare predicted 3D models",
"is_bot": false,
"headline": "Merge pull request #320 from debbiemarkslab/compare_af",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2024-11-13T16:45:39Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "745d180a62628579d59928df2a002e7808c10bb2",
"body": null,
"is_bot": false,
"headline": "version bump",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-13T16:34:06Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "95e56fb553a958b06fd7c9c94014a52a1a233340",
"body": null,
"is_bot": false,
"headline": "comment out model comparison settings by default",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-11T15:26:29Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "ff159142834b32f5ba3fabfbbea1880cba613c1c",
"body": null,
"is_bot": false,
"headline": "allow to specify model comparison settings via config",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-11T15:20:43Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "3a14a63f528e1a027a576d0c3d6981645ebcfc32",
"body": null,
"is_bot": false,
"headline": "fix file names and no plotting if no structures",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-10T14:42:40Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0df4bf8c865b9a33e6aac7eef29efff702d0e7c8",
"body": null,
"is_bot": false,
"headline": "first complete draft of models protocol",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-10T14:36:09Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0c9e3baa02bf08f05636f8cc8d2cbdfdf34507e1",
"body": null,
"is_bot": false,
"headline": "add regular CIF parsing to PDB class",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-10T13:05:38Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d78920631c3d84b06836cb5770d8aa8f02ea676a",
"body": null,
"is_bot": false,
"headline": "model comparison skeleton added",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-09T15:27:00Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "1e4a9b1ce02fe8e1a00de50b3225946af6ada82d",
"body": null,
"is_bot": false,
"headline": "Structure identification for models",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-09T10:36:17Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "fd0572e37f1eb3b9fb14acaa3465d29e285976d4",
"body": "Pdb and setup fixes",
"is_bot": false,
"headline": "Merge pull request #317 from debbiemarkslab/pdb_and_setup_fixes",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2024-11-05T11:22:40Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "f2729392badde530c60c108341b5d3d3fd3bd6b8",
"body": null,
"is_bot": false,
"headline": "Update build_test_and_push.yml",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2024-11-05T11:11:30Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "eeffea16d9779a920d8d52879d7c4580bc623c08",
"body": null,
"is_bot": false,
"headline": "Add hatch to publishing action",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2024-11-05T10:44:21Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "009011f987207326c3293fa23fe68730bc7c716e",
"body": null,
"is_bot": false,
"headline": "Add hatch to testing action",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2024-11-05T10:36:49Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "6efe781f63d091e23b3bbdad2902370b014f1f50",
"body": null,
"is_bot": false,
"headline": "retire setup.py for pyproject.toml",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-05T10:17:30Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "3bde767bb37d124c0da282a08fd8d236a0ce8468",
"body": null,
"is_bot": false,
"headline": "fix secondary structure extraction",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-11-05T09:37:17Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "756874916838b90bd14a020e3431fb76d1a2b980",
"body": null,
"is_bot": false,
"headline": "limit to single python version",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2024-09-27T16:24:01Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7c5cc94411c9be5801c8555317fe47eb4f9f6e7b",
"body": null,
"is_bot": false,
"headline": "correct to semantic version number",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2024-09-27T16:23:12Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "1a85dc5618f0c7affc847fd7addf8d23f9e2194c",
"body": "revert update, remove bdist_wheel",
"is_bot": false,
"headline": "Update build_test_and_push.yml",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2024-09-27T16:21:22Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "4edc6e6ed3ef87425961ff7b07b53b7be72b6f73",
"body": null,
"is_bot": false,
"headline": "Merge branch 'master' into develop",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2024-09-26T17:41:31Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "5026d77e54c3450e4dedfbefff8748a4b7e30747",
"body": null,
"is_bot": false,
"headline": "Update build_test_and_push.yml",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2024-09-26T17:39:38Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "88978eeefd9520c7c48fecb15d5a5879704d1d58",
"body": "v0.2",
"is_bot": false,
"headline": "Merge pull request #311 from debbiemarkslab/develop",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2024-09-26T16:13:04Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "188db86e610efa612bd810273df875e649954e35",
"body": "ensure chain IDs are always str",
"is_bot": false,
"headline": "Merge pull request #312 from debbiemarkslab/fix_auth_id_type",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2024-09-26T15:32:10Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "522903baabfc57985e9ed43f53907b2128e2c7d4",
"body": null,
"is_bot": false,
"headline": "ensure chain IDs are always str",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-09-26T15:27:28Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "595472a5e0591e294c3964ad28dcc6ad755cd61e",
"body": null,
"is_bot": false,
"headline": "Merge branch 'master' into develop",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2024-09-26T15:21:01Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "35d93d03f6ac63f9ce2df79f46744c12e855a101",
"body": null,
"is_bot": false,
"headline": "fix atom_id overwrite by coord_id",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-08-27T09:13:54Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b7abe35e1b74372ecbeadaeacb2ecbdec6b50f5b",
"body": "fix KeyError due to absence of secondary structure sections",
"is_bot": false,
"headline": "Merge pull request #308 from debbiemarkslab/fix_mmcif_parser",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2024-07-23T15:09:09Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "f32491f00bd3d702812ce2916add248728ad019e",
"body": null,
"is_bot": false,
"headline": "fix KeyError due to absence of secondary structure sections",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-07-23T15:05:35Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "374d4c56a172a4940f34dd25268bc01b3ebf375b",
"body": "V0.2\r\n\r\nMost notable fixes:\r\n\r\n* MMTF phaseout by RCSB, now loading bCIF structures instead\r\n* Many small regressions that have accumulated over the years. Should now install cleanly with up-to-date versions of numpy and pandas. Packages that depend on specific versions are pinned in setup.py",
"is_bot": false,
"headline": "Merge pull request #293 from debbiemarkslab/v0.2",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2024-07-08T11:35:55Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "476700b43bb087e73dc2f6a7b6c4230f2542541d",
"body": null,
"is_bot": false,
"headline": "fix yet another pandas deprecation",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-07-08T11:19:08Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "9bfa113e0db8aa611e130ee56e7d7e21447261b8",
"body": null,
"is_bot": false,
"headline": "fix alt_loc",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-07-08T11:13:48Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "58aa2c07277dee5eb660eacfee06dfc9a3eaeead",
"body": null,
"is_bot": false,
"headline": "fix charge handling pt2",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-07-08T11:02:55Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7e2c0bbb364ec78c3acf08fa51c30e1794e34f92",
"body": null,
"is_bot": false,
"headline": "fix charge handling",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-07-08T10:57:31Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "656725137ed404b1afda1095f47a356d288dd2a5",
"body": null,
"is_bot": false,
"headline": "better backward compatibility for chain extraction",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-07-08T10:33:42Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "05c642334c980077b2add420f5c58f6108d8fb5a",
"body": null,
"is_bot": false,
"headline": "fix scikit-learn warning, cf. #306",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-07-07T08:59:31Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "cccc1ca746fc2e47c5c9cdeb452ae4b47afa5941",
"body": null,
"is_bot": false,
"headline": "fix numpy warning (#306)",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-07-07T08:51:46Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "4778267e736832bb70d4b7adc6e5371598c4311a",
"body": null,
"is_bot": false,
"headline": "fix overlapping secondary structure elements",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-07-07T08:46:28Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "2872d3dcc1814e29bda9fae806e7ffa57a809f65",
"body": null,
"is_bot": false,
"headline": "Replace pd.append with pd.concat",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-07-06T12:23:30Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "cde87ae6e7463a0ab76d485234f9b449ac03c8a1",
"body": null,
"is_bot": false,
"headline": "Make model handling consistent to previous class",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-07-06T08:06:50Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "c2a766d1df45919115330f715179a91466feeb95",
"body": null,
"is_bot": false,
"headline": "Replace MMTF with bCIF",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-07-05T14:58:02Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "8fbf92dce083d0c6a42da13beac60800df2bb333",
"body": "V0.2 patch",
"is_bot": false,
"headline": "Merge pull request #301 from zachcp/v0.2-patch",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2024-01-24T15:55:12Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b4eb674c1ba1332daf954c35644902015d1aac2d",
"body": null,
"is_bot": false,
"headline": "Fix PDB chain retrieval regression by pandas/numpy updates",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2024-01-24T15:45:28Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "686ca3c15ffb9f46272bd8aa9a9ae510ed2785a4",
"body": null,
"is_bot": false,
"headline": "add build",
"author_name": "Zachary Charlop-Powers",
"author_login": null,
"committed_at": "2023-11-26T16:51:05Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "5a50ab9367c531e1d03f298ea8058991f274d99d",
"body": null,
"is_bot": false,
"headline": "build",
"author_name": "Zachary Charlop-Powers",
"author_login": null,
"committed_at": "2023-11-26T16:47:42Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "55ccdf5af7eadd0d085f17d3c5e20a0bb00900a8",
"body": null,
"is_bot": false,
"headline": "add yml files",
"author_name": "Zachary Charlop-Powers",
"author_login": null,
"committed_at": "2023-11-24T20:22:35Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b9951e4765ba741446dde22646e2f6f66408bca1",
"body": "bump to python3.11\nupdate GH actions",
"is_bot": false,
"headline": "bump to python3.10",
"author_name": "Zachary Charlop-Powers",
"author_login": null,
"committed_at": "2023-11-24T19:55:54Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "5b3b3f08a1f9d1a6fbae3130de4b3bbdd9d61b39",
"body": null,
"is_bot": false,
"headline": "Numpy deprecation fix, closes #248",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2023-05-12T17:00:40Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "9d34d5ef38265692275d0f042853434154d1d319",
"body": null,
"is_bot": false,
"headline": "better handler around occasional plmc segfaults, fixes #292",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2023-05-11T12:11:53Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "2324ed63cb6fc70da8fc2d52fb7ab96609d9a321",
"body": null,
"is_bot": false,
"headline": "Correct wrong exception raise, fixes #199",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2023-05-11T11:00:41Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "5cd4033913e5ae20519fa6bc58412928ad9072ed",
"body": null,
"is_bot": false,
"headline": "Fix alignment identifier memory usage, add header splitting, fixes #289",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2023-05-11T09:53:55Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a880fea35340e22d880d928d4b23af6f3b90d926",
"body": null,
"is_bot": false,
"headline": "pin yaml due to upcoming API change",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2023-05-11T08:49:41Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7eab82c28db2d74d3a5797680ef3eff664886cf3",
"body": "Support a3m format in existing alignment protocol",
"is_bot": false,
"headline": "Merge pull request #286 from aaronkollasch/a3m-support",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2023-05-10T16:45:45Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "78633124b2c4ed3b6ba3f47aac4969979aad77e2",
"body": null,
"is_bot": false,
"headline": "fix deprecation in pandas df equality checking in tests",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2023-05-10T16:24:27Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e1362407a0b65d63ca07df55f44cb17b0a3722b7",
"body": null,
"is_bot": false,
"headline": "Fix numpy dtype deprecation, fixes #291",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2023-05-10T13:47:04Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b4fc441f18efb770a53aeb4e183be2fd7595b756",
"body": null,
"is_bot": false,
"headline": "Keep as is due to github security restrictions",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2023-05-10T13:37:24Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7192161ceca6c64f8d11aba16765178f97d50711",
"body": null,
"is_bot": false,
"headline": "Prepare tests for new version, update readme and setup",
"author_name": "Thomas Hopf",
"author_login": "thomashopf",
"committed_at": "2023-05-10T13:34:35Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d472e4b3e38cb9124a8ee4678f271cb6ec92a396",
"body": null,
"is_bot": false,
"headline": "Support a3m format in existing alignment protocol",
"author_name": "Aaron Kollasch",
"author_login": "aaronkollasch",
"committed_at": "2023-03-16T15:04:58Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "af27842c5fc72c291831261c9a19849a3e313efd",
"body": null,
"is_bot": false,
"headline": "Update build_test_and_push.yml",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2023-03-16T15:02:13Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "721875a17150a394abd65cc0b75c95a95577d514",
"body": null,
"is_bot": false,
"headline": "Update build_and_test.yml",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2023-03-16T15:01:59Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "2590f9ee54cbd59bd7ff0bd59875d5a5aac0860b",
"body": "change name inputs to bokeh",
"is_bot": false,
"headline": "Merge pull request #281 from zachcp/20221111-bokeh",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2022-11-14T09:57:47Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d299279fc92ae30938b8f3d7090fe7343bef8451",
"body": null,
"is_bot": false,
"headline": "change name inputs to bokeh",
"author_name": "Zachary Charlop-Powers",
"author_login": null,
"committed_at": "2022-11-11T15:34:40Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7e0076de24426ef62aa13ec7154f1b8661f0e950",
"body": "Fix/uniprot api",
"is_bot": false,
"headline": "Merge pull request #280 from debbiemarkslab/fix/uniprot-api",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2022-08-05T09:24:47Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "90a429675fe4b9522b30146acead881e4d45362d",
"body": null,
"is_bot": false,
"headline": "[FIX] safeguard insertion code checking",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2022-08-05T09:03:15Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "22761e58a91c4c510c090ee8f049fc5335b52f15",
"body": null,
"is_bot": false,
"headline": "[FIX] pandas deprecation and warning",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2022-08-05T08:44:58Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "1f85d74ebdb918dbf82a0cf941fccd72fb2dfe02",
"body": null,
"is_bot": false,
"headline": "Version bump",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2022-08-05T07:58:19Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "792150e6c71e5edc284423ffedc37adf40d5744b",
"body": "… to latest Uniprot API version",
"is_bot": false,
"headline": "[FIX] Upgrade fetch_uniprot_mapping and SIFTS sequence table creation…",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2022-08-05T07:58:04Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "2495dc764f04ebdeacfdce030936ef24d3b5483c",
"body": "…irements",
"is_bot": false,
"headline": "[FIX] Apply sklearn->scikit-learn update also in setup, not just requ…",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2022-08-04T12:09:33Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a50bd0f00914076c7027a471d496d73cb582a24b",
"body": null,
"is_bot": false,
"headline": "[FIX] Update single sequence retrieval Uniprot API endpoint",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2022-08-04T12:02:37Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "791c5faf3725c1eab88aa36ec51e086ed3a01271",
"body": null,
"is_bot": false,
"headline": "[FIX] import Iterable/Mapping from collections.abc, closes #275",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2022-08-04T11:55:23Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "5de7bab3b5202848ace2e16ff2b1cda5c8edfda6",
"body": "sklearn is an alias for scikit-learn",
"is_bot": false,
"headline": "Update requirements.txt",
"author_name": "Aaron Kollasch",
"author_login": "aaronkollasch",
"committed_at": "2022-05-23T20:23:05Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "594b45a9ecd7d429f27c7d576559134c3e9c3bcc",
"body": "ecs = pairs.add_mixture_proability -> ecs = pairs.add_mixture_probability(",
"is_bot": false,
"headline": "Fix typo in complex_probability()",
"author_name": "kpgbrock",
"author_login": "kpgbrock",
"committed_at": "2021-09-30T17:12:47Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "f3b733a9da714f8e77f80c7357aa30ec59bca88e",
"body": null,
"is_bot": false,
"headline": "Update README.md",
"author_name": "Anna Green",
"author_login": "aggreen",
"committed_at": "2021-05-11T15:26:36Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "22be03582e93e3583c2dc8305c1451129054b1be",
"body": "Fix/alignment protocols",
"is_bot": false,
"headline": "Merge pull request #260 from debbiemarkslab/fix/alignment_protocols",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2021-03-19T16:34:12Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "380752e0c1d1bc25c2f3860c018a316bf6600bba",
"body": "…ser choice",
"is_bot": false,
"headline": "[FEATURE] local submitter can now run jobs in parallel depending on u…",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2021-03-13T13:36:50Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d6627a29960167df5535450ddf4b4d1a5037cdf4",
"body": null,
"is_bot": false,
"headline": "[FIX] lowercase columns in frequency stable still led to crash",
"author_name": "thomashopf",
"author_login": "thomashopf",
"committed_at": "2021-03-13T12:43:29Z",
"body_truncated": false,
"is_coding_agent": false
}
],
"releases_count": 7,
"commits_last_year": 11,
"latest_release_at": "2024-11-05T11:16:06Z",
"latest_release_tag": "v0.2.1",
"releases_from_tags": false,
"days_since_last_push": 96,
"active_weeks_last_year": 3,
"days_since_latest_release": 627,
"mean_days_between_releases": 436.7
},
"community": {
"has_readme": true,
"has_license": true,
"has_description": true,
"has_contributing": false,
"health_percentage": 37,
"has_issue_template": false,
"has_code_of_conduct": false,
"has_pull_request_template": false
},
"ecosystem": {
"packages": [
{
"name": "evcouplings",
"exists": true,
"license": null,
"keywords": [
"analysis",
"couplings",
"evolutionary",
"Development Status :: 4 - Beta",
"Intended Audience :: Developers",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Topic :: Scientific/Engineering :: Bio-Informatics"
],
"ecosystem": "pypi",
"matches_repo": true,
"registry_url": "https://pypi.org/project/evcouplings/",
"is_deprecated": false,
"latest_version": "0.2.1",
"repository_url": "https://github.com/debbiemarkslab/EVcouplings",
"versions_count": 7,
"total_downloads": null,
"dependents_count": null,
"deprecation_note": null,
"maintainers_count": null,
"monthly_downloads": null,
"first_published_at": "2017-09-03T13:23:31.661458Z",
"latest_published_at": "2024-11-05T11:18:47.281245Z",
"latest_version_yanked": null,
"days_since_latest_publish": 627
}
]
},
"popularity": {
"forks": 83,
"stars": 313,
"watchers": 25,
"fork_history": {
"days": [
{
"date": "2017-09-19",
"count": 1
},
{
"date": "2017-09-25",
"count": 1
},
{
"date": "2017-09-26",
"count": 1
},
{
"date": "2017-10-23",
"count": 1
},
{
"date": "2018-02-08",
"count": 1
},
{
"date": "2018-02-11",
"count": 1
},
{
"date": "2018-02-12",
"count": 1
},
{
"date": "2018-03-30",
"count": 1
},
{
"date": "2018-05-13",
"count": 1
},
{
"date": "2018-05-25",
"count": 1
},
{
"date": "2018-08-30",
"count": 1
},
{
"date": "2018-09-22",
"count": 1
},
{
"date": "2018-10-15",
"count": 1
},
{
"date": "2018-11-06",
"count": 1
},
{
"date": "2018-11-25",
"count": 1
},
{
"date": "2018-12-14",
"count": 1
},
{
"date": "2019-01-08",
"count": 1
},
{
"date": "2019-03-22",
"count": 1
},
{
"date": "2019-04-23",
"count": 1
},
{
"date": "2019-05-01",
"count": 1
},
{
"date": "2019-06-20",
"count": 1
},
{
"date": "2019-07-17",
"count": 1
},
{
"date": "2019-11-15",
"count": 1
},
{
"date": "2019-12-27",
"count": 1
},
{
"date": "2020-03-05",
"count": 1
},
{
"date": "2020-03-11",
"count": 1
},
{
"date": "2020-05-15",
"count": 1
},
{
"date": "2020-05-21",
"count": 1
},
{
"date": "2020-07-14",
"count": 1
},
{
"date": "2020-08-14",
"count": 1
},
{
"date": "2020-09-01",
"count": 1
},
{
"date": "2020-09-30",
"count": 1
},
{
"date": "2020-11-09",
"count": 1
},
{
"date": "2020-11-17",
"count": 1
},
{
"date": "2021-01-02",
"count": 1
},
{
"date": "2021-02-08",
"count": 1
},
{
"date": "2021-03-29",
"count": 1
},
{
"date": "2021-05-08",
"count": 1
},
{
"date": "2021-05-24",
"count": 1
},
{
"date": "2021-10-18",
"count": 1
},
{
"date": "2021-11-01",
"count": 1
},
{
"date": "2021-12-12",
"count": 1
},
{
"date": "2022-02-01",
"count": 1
},
{
"date": "2022-03-14",
"count": 1
},
{
"date": "2022-04-04",
"count": 1
},
{
"date": "2022-04-20",
"count": 1
},
{
"date": "2022-07-31",
"count": 1
},
{
"date": "2022-11-11",
"count": 1
},
{
"date": "2022-11-14",
"count": 1
},
{
"date": "2022-12-20",
"count": 1
},
{
"date": "2023-01-09",
"count": 1
},
{
"date": "2023-01-10",
"count": 1
},
{
"date": "2023-01-17",
"count": 1
},
{
"date": "2023-03-03",
"count": 1
},
{
"date": "2023-03-07",
"count": 1
},
{
"date": "2023-03-17",
"count": 1
},
{
"date": "2023-03-26",
"count": 1
},
{
"date": "2023-05-01",
"count": 1
},
{
"date": "2023-07-05",
"count": 1
},
{
"date": "2023-08-01",
"count": 1
},
{
"date": "2024-04-18",
"count": 1
},
{
"date": "2024-05-29",
"count": 1
},
{
"date": "2024-06-07",
"count": 1
},
{
"date": "2024-06-12",
"count": 1
},
{
"date": "2024-07-23",
"count": 1
},
{
"date": "2024-08-20",
"count": 1
},
{
"date": "2024-10-08",
"count": 1
},
{
"date": "2025-01-21",
"count": 1
},
{
"date": "2025-02-16",
"count": 1
},
{
"date": "2025-03-26",
"count": 1
},
{
"date": "2025-05-10",
"count": 1
},
{
"date": "2025-11-14",
"count": 1
},
{
"date": "2025-12-05",
"count": 1
},
{
"date": "2025-12-18",
"count": 1
},
{
"date": "2026-04-08",
"count": 1
},
{
"date": "2026-06-19",
"count": 1
},
{
"date": "2026-07-13",
"count": 1
}
],
"complete": true,
"collected": 77,
"total_forks": 83
},
"star_history": null,
"open_issues_and_prs": 66
},
"ai_readiness": {
"has_nix": false,
"example_dirs": [
"example",
"notebooks"
],
"has_llms_txt": false,
"has_dockerfile": false,
"has_mcp_signal": false,
"bootstrap_files": [
"docs/Makefile"
],
"api_schema_files": [],
"has_devcontainer": false,
"typecheck_configs": [],
"toolchain_manifests": [],
"largest_source_bytes": 263767,
"source_files_sampled": 81,
"oversized_source_files": 2,
"agent_instruction_files": [],
"agent_instruction_max_bytes": null
},
"dependencies": {
"manifests": [
"pyproject.toml"
],
"advisories": {
"error": null,
"scope": "published_package",
"source": "osv",
"findings": [],
"collected": true,
"malicious": [],
"truncated": false,
"by_severity": {},
"advisory_count": 0,
"affected_count": 0,
"assessed_count": 39,
"malicious_count": 0,
"assessed_package": "pypi:evcouplings@0.2.1",
"unassessed_count": 0,
"direct_affected_count": 0
},
"ecosystems": [
"pypi"
],
"dependencies": [
{
"name": "billiard",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "biopython",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=1.84"
},
{
"name": "bokeh",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "click",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "filelock",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "jinja2",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "matplotlib",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "msgpack",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "numba",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "numpy",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "pandas",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "psutil",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "requests",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "ruamel.yaml",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": "<0.18"
},
{
"name": "scikit-learn",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "scipy",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "seaborn",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "setuptools",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=18.2"
}
],
"all_dependencies": {
"error": null,
"source": "github-sbom",
"packages": [
{
"name": "billiard",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "biopython",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "bokeh",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "click",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "filelock",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "jinja2",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "matplotlib",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "msgpack",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "numba",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "numpy",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "pandas",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "psutil",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "requests",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "ruamel-yaml",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "scikit-learn",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "scipy",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "seaborn",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "setuptools",
"direct": true,
"version": null,
"ecosystem": "pypi"
}
],
"collected": true,
"truncated": false,
"total_count": 18,
"direct_count": 18,
"indirect_count": 0
}
},
"maintainership": {
"issues": {
"open_prs": 7,
"merged_prs": 108,
"open_issues": 59,
"closed_ratio": 0.704,
"closed_issues": 140,
"closed_unmerged_prs": 24
},
"bus_factor": 1,
"bot_contributors": 0,
"top_contributors": [
{
"type": "User",
"login": "thomashopf",
"commits": 698,
"avatar_url": "https://avatars.githubusercontent.com/u/7434098?v=4"
},
{
"type": "User",
"login": "aggreen",
"commits": 200,
"avatar_url": "https://avatars.githubusercontent.com/u/7906910?v=4"
},
{
"type": "User",
"login": "b-schubert",
"commits": 110,
"avatar_url": "https://avatars.githubusercontent.com/u/6513079?v=4"
},
{
"type": "User",
"login": "sophiamersmann",
"commits": 29,
"avatar_url": "https://avatars.githubusercontent.com/u/12461810?v=4"
},
{
"type": "User",
"login": "sacdallago",
"commits": 23,
"avatar_url": "https://avatars.githubusercontent.com/u/6240943?v=4"
},
{
"type": "User",
"login": "joemin",
"commits": 20,
"avatar_url": "https://avatars.githubusercontent.com/u/3230165?v=4"
},
{
"type": "User",
"login": "ChannyClaus",
"commits": 17,
"avatar_url": "https://avatars.githubusercontent.com/u/10104080?v=4"
},
{
"type": "User",
"login": "aaronkollasch",
"commits": 2,
"avatar_url": "https://avatars.githubusercontent.com/u/7785912?v=4"
},
{
"type": "User",
"login": "kpgbrock",
"commits": 2,
"avatar_url": "https://avatars.githubusercontent.com/u/19981675?v=4"
}
],
"contributors_sampled": 9,
"top_contributor_share": 0.634
},
"quality_signals": {
"has_ci": true,
"has_tests": true,
"ci_workflows": [
"build_and_test.yml",
"build_test_and_push.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": null,
"reason": "internal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#branch-protection"
},
{
"name": "CI-Tests",
"score": 3,
"reason": "2 out of 6 merged PRs checked by a CI test -- score normalized to 3",
"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": 1,
"reason": "Found 1/6 approved changesets -- score normalized to 1",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#code-review"
},
{
"name": "Contributors",
"score": 10,
"reason": "project has 10 contributing companies or organizations",
"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": 9,
"reason": "license file detected",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#license"
},
{
"name": "Maintained",
"score": 0,
"reason": "0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0",
"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": "14c83457c6cfca8156aabe0615067447a2169791",
"ran_at": "2026-07-26T07:41:24Z",
"aggregate_score": 3.7,
"scorecard_version": "v5.5.0"
},
"has_codeql_workflow": false,
"has_security_policy": false,
"has_dependabot_config": false
},
"contribution_flow": {
"collected": true,
"ci_last_run_at": "2026-04-20T13:05:18Z",
"oldest_open_prs": [
{
"number": 166,
"created_at": "2018-04-19T15:39:31Z",
"last_comment_at": "2018-12-16T23:58:07Z",
"last_comment_author": "sacdallago"
},
{
"number": 203,
"created_at": "2019-01-27T11:05:50Z",
"last_comment_at": "2019-03-04T11:18:46Z",
"last_comment_author": "sacdallago"
},
{
"number": 223,
"created_at": "2019-07-22T18:52:12Z",
"last_comment_at": "2020-04-28T16:03:34Z",
"last_comment_author": "aggreen"
},
{
"number": 225,
"created_at": "2019-10-08T17:23:35Z",
"last_comment_at": "2020-12-23T19:44:36Z",
"last_comment_author": "aggreen"
},
{
"number": 319,
"created_at": "2024-11-08T12:05:29Z",
"last_comment_at": null,
"last_comment_author": null
},
{
"number": 329,
"created_at": "2025-09-04T15:45:26Z",
"last_comment_at": null,
"last_comment_author": null
},
{
"number": 333,
"created_at": "2025-12-05T16:54:18Z",
"last_comment_at": null,
"last_comment_author": null
}
],
"last_merged_pr_at": "2026-04-20T13:02:44Z",
"ci_last_conclusion": "FAILURE",
"oldest_open_issues": [
{
"number": 10,
"created_at": "2017-04-20T22:19:40Z",
"last_comment_at": null,
"last_comment_author": null
},
{
"number": 13,
"created_at": "2017-04-21T00:26:24Z",
"last_comment_at": null,
"last_comment_author": null
},
{
"number": 18,
"created_at": "2017-04-27T15:03:38Z",
"last_comment_at": "2017-12-08T15:37:54Z",
"last_comment_author": "thomashopf"
},
{
"number": 20,
"created_at": "2017-04-27T15:14:48Z",
"last_comment_at": "2018-01-10T18:30:49Z",
"last_comment_author": "sacdallago"
},
{
"number": 23,
"created_at": "2017-05-02T20:14:03Z",
"last_comment_at": "2017-12-08T21:56:23Z",
"last_comment_author": "sacdallago"
},
{
"number": 28,
"created_at": "2017-05-15T15:33:24Z",
"last_comment_at": "2018-01-09T18:47:02Z",
"last_comment_author": "thomashopf"
},
{
"number": 68,
"created_at": "2017-10-11T14:23:26Z",
"last_comment_at": null,
"last_comment_author": null
},
{
"number": 69,
"created_at": "2017-10-11T14:24:16Z",
"last_comment_at": "2017-10-14T16:53:50Z",
"last_comment_author": "thomashopf"
},
{
"number": 70,
"created_at": "2017-10-11T14:25:27Z",
"last_comment_at": "2017-10-14T17:00:15Z",
"last_comment_author": "thomashopf"
},
{
"number": 72,
"created_at": "2017-10-17T17:24:38Z",
"last_comment_at": "2018-04-06T15:01:56Z",
"last_comment_author": "sacdallago"
},
{
"number": 87,
"created_at": "2017-11-15T20:46:51Z",
"last_comment_at": "2017-12-05T21:13:31Z",
"last_comment_author": "aggreen"
},
{
"number": 93,
"created_at": "2018-01-08T19:40:22Z",
"last_comment_at": null,
"last_comment_author": null
},
{
"number": 116,
"created_at": "2018-01-26T16:29:54Z",
"last_comment_at": "2020-04-21T07:19:40Z",
"last_comment_author": "thomashopf"
},
{
"number": 117,
"created_at": "2018-01-26T19:17:40Z",
"last_comment_at": "2018-01-27T14:53:14Z",
"last_comment_author": "thomashopf"
},
{
"number": 141,
"created_at": "2018-03-05T15:19:33Z",
"last_comment_at": "2018-04-06T14:52:46Z",
"last_comment_author": "sacdallago"
},
{
"number": 168,
"created_at": "2018-05-17T15:51:23Z",
"last_comment_at": null,
"last_comment_author": null
},
{
"number": 172,
"created_at": "2018-06-05T15:25:54Z",
"last_comment_at": null,
"last_comment_author": null
},
{
"number": 177,
"created_at": "2018-06-19T17:53:02Z",
"last_comment_at": "2018-06-19T18:55:51Z",
"last_comment_author": "aggreen"
},
{
"number": 178,
"created_at": "2018-06-19T17:59:08Z",
"last_comment_at": "2018-07-03T17:21:49Z",
"last_comment_author": "thomashopf"
},
{
"number": 182,
"created_at": "2018-07-05T18:36:58Z",
"last_comment_at": "2018-07-07T15:59:20Z",
"last_comment_author": "thomashopf"
}
]
}
},
"config": {
"disabled_metrics": [],
"disabled_categories": [],
"disabled_components": {}
},
"source": {
"url": "https://github.com/debbiemarkslab/EVcouplings",
"host": "github.com",
"name": "EVcouplings",
"owner": "debbiemarkslab"
},
"metrics": {
"overall": {
"key": "overall",
"band": "moderate",
"name": "Overall health",
"note": null,
"notes": [],
"value": 54,
"inputs": {
"security": 50,
"vitality": 31,
"community": 55,
"governance": 61,
"engineering": 72
},
"components": []
},
"categories": [
{
"key": "vitality",
"band": "at_risk",
"name": "Vitality",
"value": 31,
"weight": 0.22,
"metrics": [
{
"key": "development_activity",
"band": "critical",
"name": "Development activity",
"note": null,
"notes": [],
"value": 22,
"inputs": {
"commits_last_year": 11,
"human_commit_share": 1,
"days_since_last_push": 96,
"active_weeks_last_year": 3
},
"components": [
{
"key": "push_recency",
"name": "Push recency",
"detail": "last push 96 days ago",
"points": 9.9,
"status": "partial",
"details": [
{
"code": "push_recency",
"params": {
"days": 96
}
}
],
"max_points": 36
},
{
"key": "commit_cadence",
"name": "Commit cadence",
"detail": "3/52 weeks with commits",
"points": 2.1,
"status": "partial",
"details": [
{
"code": "commit_cadence_weeks",
"params": {
"weeks": 3
}
}
],
"max_points": 36
},
{
"key": "commit_volume",
"name": "Commit volume",
"detail": "11 commits in the last year",
"points": 9.7,
"status": "partial",
"details": [
{
"code": "commits_last_year",
"params": {
"count": 11
}
}
],
"max_points": 18
},
{
"key": "openssf_scorecard_maintained",
"name": "OpenSSF Scorecard: Maintained",
"detail": "0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
}
]
},
{
"key": "release_discipline",
"band": "at_risk",
"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": 44,
"inputs": {
"releases_count": 7,
"latest_release_tag": "v0.2.1",
"releases_from_tags": false,
"days_since_latest_release": 627,
"mean_days_between_releases": 436.7
},
"components": [
{
"key": "ships_releases",
"name": "Ships releases",
"detail": "7 releases published",
"points": 27,
"status": "met",
"details": [
{
"code": "releases_published",
"params": {
"count": 7
}
}
],
"max_points": 27
},
{
"key": "release_recency",
"name": "Release recency",
"detail": "latest release 627 days ago",
"points": 7.2,
"status": "partial",
"details": [
{
"code": "release_recency",
"params": {
"days": 627
}
}
],
"max_points": 36
},
{
"key": "release_cadence",
"name": "Release cadence",
"detail": "a release every ~436.7 days",
"points": 5.4,
"status": "partial",
"details": [
{
"code": "release_cadence",
"params": {
"gap": 436.7
}
}
],
"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": 96,
"days_since_last_human_commit_is_floor": false
},
"components": [
{
"key": "project_is_still_maintained",
"name": "Project is still maintained",
"detail": "last human commit 96 days ago",
"points": 100,
"status": "met",
"details": [
{
"code": "abandonment_maintained",
"params": {
"days": 96
}
}
],
"max_points": 100
}
]
}
],
"description": "Is the project alive — is code being written and are releases shipping?"
},
{
"key": "community",
"band": "moderate",
"name": "Community & Adoption",
"value": 55,
"weight": 0.18,
"metrics": [
{
"key": "popularity",
"band": "moderate",
"name": "Popularity & adoption",
"note": null,
"notes": [],
"value": 64,
"inputs": {
"forks": 83,
"stars": 313,
"watchers": 25,
"growth_state": "unverified",
"growth_factor_pct": 100,
"growth_unverified_reason": "no_history"
},
"components": [
{
"key": "stars",
"name": "Stars",
"detail": "313 stars",
"points": 40.5,
"status": "partial",
"details": [
{
"code": "stars",
"params": {
"count": 313
}
}
],
"max_points": 60
},
{
"key": "forks",
"name": "Forks",
"detail": "83 forks",
"points": 16,
"status": "partial",
"details": [
{
"code": "forks",
"params": {
"count": 83
}
}
],
"max_points": 25
},
{
"key": "watchers",
"name": "Watchers",
"detail": "25 watchers",
"points": 7.7,
"status": "partial",
"details": [
{
"code": "watchers",
"params": {
"count": 25
}
}
],
"max_points": 15
}
]
},
{
"key": "community_health",
"band": "at_risk",
"name": "Community health",
"note": null,
"notes": [],
"value": 44,
"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": "license file present, not a recognized license",
"points": 16.9,
"status": "partial",
"details": [
{
"code": "license_custom",
"params": {}
}
],
"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": "moderate",
"name": "Sustainability & Governance",
"value": 61,
"weight": 0.24,
"metrics": [
{
"key": "maintainer_resilience",
"band": "at_risk",
"name": "Maintainer resilience (bus factor)",
"note": null,
"notes": [],
"value": 39,
"inputs": {
"bus_factor": 1,
"contributors_sampled": 9,
"top_contributor_share": 0.634
},
"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 63% of commits",
"points": 8.2,
"status": "partial",
"details": [
{
"code": "top_contributor_share",
"params": {
"share": 63
}
}
],
"max_points": 22.5
},
{
"key": "contributor_breadth",
"name": "Contributor breadth",
"detail": "9 contributors",
"points": 12.2,
"status": "partial",
"details": [
{
"code": "contributors_sampled",
"params": {
"count": 9
}
}
],
"max_points": 13.5
},
{
"key": "openssf_scorecard_contributors",
"name": "OpenSSF Scorecard: Contributors",
"detail": "project has 10 contributing companies or organizations",
"points": 10,
"status": "met",
"details": [],
"max_points": 10
}
]
},
{
"key": "responsiveness",
"band": "moderate",
"name": "Issue & PR responsiveness",
"note": null,
"notes": [],
"value": 66,
"inputs": {
"merged_prs": 108,
"open_issues": 59,
"closed_issues": 140,
"issue_closed_ratio": 0.704,
"closed_unmerged_prs": 24
},
"components": [
{
"key": "issue_resolution",
"name": "Issue resolution",
"detail": "70% of issues closed",
"points": 32.9,
"status": "partial",
"details": [
{
"code": "issues_closed_share",
"params": {
"share": 70
}
}
],
"max_points": 46.75
},
{
"key": "pr_acceptance",
"name": "PR acceptance",
"detail": "108/132 decided PRs merged",
"points": 31.3,
"status": "partial",
"details": [
{
"code": "decided_prs_merged",
"params": {
"merged": 108,
"decided": 132
}
}
],
"max_points": 38.25
},
{
"key": "openssf_scorecard_code_review",
"name": "OpenSSF Scorecard: Code-Review",
"detail": "Found 1/6 approved changesets -- score normalized to 1",
"points": 1.5,
"status": "partial",
"details": [],
"max_points": 15
}
]
},
{
"key": "stewardship",
"band": "moderate",
"name": "Ownership & stewardship",
"note": null,
"notes": [],
"value": 68,
"inputs": {
"followers": 135,
"owner_type": "Organization",
"is_verified": null,
"owner_login": "debbiemarkslab",
"public_repos": 33,
"account_age_days": 4316
},
"components": [
{
"key": "ownership_backing",
"name": "Ownership backing",
"detail": "organization-owned",
"points": 30,
"status": "met",
"details": [
{
"code": "owner_organization",
"params": {}
}
],
"max_points": 30
},
{
"key": "verified_domain",
"name": "Verified domain",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 20
},
{
"key": "owner_reach",
"name": "Owner reach",
"detail": "135 followers of debbiemarkslab",
"points": 15.3,
"status": "partial",
"details": [
{
"code": "owner_followers",
"params": {
"count": 135,
"login": "debbiemarkslab"
}
}
],
"max_points": 25
},
{
"key": "track_record",
"name": "Track record",
"detail": "33 public repos, account ~11 yr old",
"points": 23.2,
"status": "partial",
"details": [
{
"code": "public_repos",
"params": {
"count": 33
}
},
{
"code": "account_age_years",
"params": {
"years": 11
}
}
],
"max_points": 25
}
]
},
{
"key": "package_maintenance",
"band": "good",
"name": "Package maintenance",
"note": null,
"notes": [],
"value": 79,
"inputs": {
"packages": [
"evcouplings"
],
"ecosystems": "pypi",
"any_deprecated": false,
"min_days_since_publish": 627
},
"components": [
{
"key": "published_resolvable",
"name": "Published & resolvable",
"detail": "1 package(s) on pypi",
"points": 25,
"status": "met",
"details": [
{
"code": "packages_published",
"params": {
"count": 1,
"ecosystems": "pypi"
}
}
],
"max_points": 25
},
{
"key": "publish_recency",
"name": "Publish recency",
"detail": "latest publish 627 days ago",
"points": 14,
"status": "partial",
"details": [
{
"code": "publish_recency",
"params": {
"days": 627
}
}
],
"max_points": 35
},
{
"key": "version_history",
"name": "Version history",
"detail": "7 published versions",
"points": 20,
"status": "met",
"details": [
{
"code": "published_versions",
"params": {
"count": 7
}
}
],
"max_points": 20
},
{
"key": "not_deprecated",
"name": "Not deprecated",
"detail": "active, not deprecated or yanked",
"points": 20,
"status": "met",
"details": [
{
"code": "package_not_deprecated",
"params": {}
}
],
"max_points": 20
}
]
}
],
"description": "Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?"
},
{
"key": "engineering",
"band": "good",
"name": "Engineering Quality",
"value": 72,
"weight": 0.2,
"metrics": [
{
"key": "engineering_practices",
"band": "moderate",
"name": "Engineering practices",
"note": null,
"notes": [],
"value": 54,
"inputs": {
"has_ci": true,
"has_tests": true,
"has_editorconfig": false,
"has_linter_config": false,
"has_precommit_config": false
},
"components": [
{
"key": "ci_workflows",
"name": "CI workflows",
"detail": "2 workflow(s)",
"points": 24,
"status": "met",
"details": [
{
"code": "ci_workflows",
"params": {
"count": 2
}
}
],
"max_points": 24
},
{
"key": "tests_present",
"name": "Tests present",
"detail": null,
"points": 24,
"status": "met",
"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": "2 out of 6 merged PRs checked by a CI test -- score normalized to 3",
"points": 6,
"status": "partial",
"details": [],
"max_points": 20
}
]
},
{
"key": "documentation",
"band": "excellent",
"name": "Documentation",
"note": null,
"notes": [],
"value": 100,
"inputs": {
"topics": [
"structure-prediction",
"3d-structure",
"protein",
"protein-complexes"
],
"has_wiki": true,
"homepage": "http://evcouplings.org",
"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": "http://evcouplings.org",
"points": 15,
"status": "met",
"details": [],
"max_points": 15
},
{
"key": "repository_description",
"name": "Repository description",
"detail": null,
"points": 10,
"status": "met",
"details": [],
"max_points": 10
},
{
"key": "topics",
"name": "Topics",
"detail": "4 topics",
"points": 10,
"status": "met",
"details": [
{
"code": "topics_count",
"params": {
"count": 4
}
}
],
"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": 50,
"weight": 0.16,
"metrics": [
{
"key": "security_posture",
"band": "at_risk",
"name": "Security posture",
"note": "Excluded from scoring (no data or not applicable): Branch-Protection, Packaging, Signed-Releases. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"branch_protection",
"packaging",
"signed_releases"
]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 37,
"inputs": {
"source": "openssf_scorecard",
"checks_evaluated": 15,
"scorecard_version": "v5.5.0",
"checks_inconclusive": 3,
"scorecard_aggregate": 3.7
},
"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": "internal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 7.5
},
{
"key": "ci_tests",
"name": "CI-Tests",
"detail": "2 out of 6 merged PRs checked by a CI test -- score normalized to 3",
"points": 0.8,
"status": "partial",
"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 1/6 approved changesets -- score normalized to 1",
"points": 0.8,
"status": "partial",
"details": [],
"max_points": 7.5
},
{
"key": "contributors",
"name": "Contributors",
"detail": "project has 10 contributing companies or organizations",
"points": 2.5,
"status": "met",
"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": 2.2,
"status": "partial",
"details": [],
"max_points": 2.5
},
{
"key": "maintained",
"name": "Maintained",
"detail": "0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0",
"points": 0,
"status": "missed",
"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): No advisories left outstanding. Remaining weights renormalized. Matched the pypi:evcouplings@0.2.1 runtime dependency closure — what installing the published package pulls in — 39 packages. Reachability is not analyzed.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"no_advisories_left_outstanding"
]
}
},
{
"code": "weights_renormalized",
"params": {}
},
{
"code": "advisories_scope_published",
"params": {
"package": "pypi:evcouplings@0.2.1",
"assessed": 39
}
},
{
"code": "advisories_reachability",
"params": {}
}
],
"value": 100,
"inputs": {
"source": "osv",
"advisories": 0,
"affected_packages": 0,
"assessed_packages": 39,
"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": "no indirect dependency carries a known advisory",
"points": 25,
"status": "met",
"details": [
{
"code": "no_indirect_advisories",
"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": 39,
"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": 11
},
"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": "at_risk",
"name": "AI Readiness",
"value": 34,
"weight": 0,
"metrics": [
{
"key": "ai_agent_context",
"band": "critical",
"name": "Agent context & guidance",
"note": null,
"notes": [],
"value": 13,
"inputs": {
"has_llms_txt": false,
"legible_history_share": 0.25,
"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": "25 of 100 human commits state their intent (structured subject or explanatory body)",
"points": 13.3,
"status": "partial",
"details": [
{
"code": "legible_history",
"params": {
"legible": 25,
"sampled": 100
}
}
],
"max_points": 40
}
]
},
{
"key": "ai_verify_loop",
"band": "at_risk",
"name": "Verify loop (build / test / typecheck)",
"note": null,
"notes": [],
"value": 40,
"inputs": {
"has_nix": false,
"has_tests": true,
"lockfiles": [],
"has_dockerfile": false,
"typed_language": false,
"bootstrap_files": [
"docs/Makefile"
],
"has_devcontainer": false,
"has_linter_config": false,
"typecheck_configs": [],
"agent_commit_share": 0,
"toolchain_manifests": [],
"dependency_bot_commit_share": 0
},
"components": [
{
"key": "one_command_bootstrap",
"name": "One-command bootstrap",
"detail": "docs/Makefile",
"points": 18,
"status": "met",
"details": [
{
"code": "file_list",
"params": {
"files": "docs/Makefile"
}
}
],
"max_points": 18
},
{
"key": "automated_tests",
"name": "Automated tests",
"detail": null,
"points": 22,
"status": "met",
"details": [],
"max_points": 22
},
{
"key": "lint_format_config",
"name": "Lint / format config",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 11
},
{
"key": "static_type_checking",
"name": "Static type checking",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 11
},
{
"key": "reproducible_environment",
"name": "Reproducible environment",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
},
{
"key": "demonstrated_agent_practice",
"name": "Demonstrated agent practice",
"detail": "no agent-authored commits among the last 100",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_agent_authored_commits",
"params": {
"sampled": 100
}
}
],
"max_points": 10
},
{
"key": "automated_maintenance",
"name": "Automated maintenance",
"detail": "no automated dependency updates observed",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_dependency_automation",
"params": {}
}
],
"max_points": 8
},
{
"key": "openssf_scorecard_pinned_dependencies",
"name": "OpenSSF Scorecard: Pinned-Dependencies",
"detail": "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": 54,
"inputs": {
"primary_language": "Jupyter Notebook",
"largest_source_bytes": 263767,
"source_files_sampled": 81,
"oversized_source_files": 2
},
"components": [
{
"key": "type_checkable_code",
"name": "Type-checkable code",
"detail": "Jupyter Notebook without a type-check config",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_typecheck_config_language",
"params": {
"language": "Jupyter Notebook"
}
}
],
"max_points": 45
},
{
"key": "manageable_file_sizes",
"name": "Manageable file sizes",
"detail": "2/81 source files over 60KB",
"points": 53.6,
"status": "partial",
"details": [
{
"code": "oversized_source_files",
"params": {
"kb": 60,
"sampled": 81,
"oversized": 2
}
}
],
"max_points": 55
}
]
},
{
"key": "ai_interfaces",
"band": "at_risk",
"name": "Machine-readable interfaces",
"note": null,
"notes": [],
"value": 40,
"inputs": {
"example_dirs": [
"example",
"notebooks"
],
"has_mcp_signal": false,
"api_schema_files": []
},
"components": [
{
"key": "api_schema_openapi_graphql_proto",
"name": "API schema (OpenAPI/GraphQL/proto)",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 40
},
{
"key": "mcp_server",
"name": "MCP server",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 20
},
{
"key": "runnable_examples",
"name": "Runnable examples",
"detail": "example, notebooks",
"points": 40,
"status": "met",
"details": [
{
"code": "file_list",
"params": {
"files": "example, notebooks"
}
}
],
"max_points": 40
}
]
}
],
"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": "2026-07-26T07:41:44.719075Z",
"schema_version": "0.27.0",
"badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/d/debbiemarkslab/EVcouplings.svg",
"full_name": "debbiemarkslab/EVcouplings",
"license_state": "custom",
"license_spdx": null
}