Commit History

3 days ago

  1. merge: fix/chembl-slow-window β€” drugs_for_targets' ChEMBL mechanism lookups share one 150 s window (Annie: A, 2026-11-05) and are retried round-robin instead of 30 s each; unanswered lookups get ONE chembl source_unavailable entry, OT rows always stand; every call's deadline capped by the endpoint budget (240 s holds exactly), 30 s per call unchanged; cause: ChEMBL slow just after 00/06/12/18 UTC from HF, query 1.3 KB < 1 s; 8 cassette tests, suite 327, scan green; not pushed Running

    avoigt1121
    4522ccd
  2. fix(drugs): one ChEMBL window for the mechanism lookups, retried round-robin⁠

    avoigt1121 +1: Claude Opus 5.5
    01b3ee5

5 days ago

  1. merge: fix/graphql-core-3.3.1 β€” graphql-core 3.3.0 -> 3.3.1 (CVE-2026-119286, unbounded memory on aborted validate(), fixed 3.3.1); floor graphql-core>=3.3.1,<3.4 in security floors; lock diff graphql-core alone; via rcsb-api + tooluniverse, not reachable (GraphQL client only; TU validate_query has no caller, no RCSB tool allow-listed); suite 319 passed, scan green incl. the 39 pillow acceptances; not pushed (knowledge smoke week runs to 2026-11-05 21:47 UTC)

    avoigt1121
    d8d8c57
  2. fix(deps): graphql-core 3.3.0 -> 3.3.1 (CVE-2026-119286)⁠

    avoigt1121 +1: Claude Opus 5.5
    e6c023e
  3. merge: fix/pillow-accept-1218 β€” the 39 pillow 12.3.0 acceptances extended 2026-11-20 -> 2026-12-18 (the project lead, 2026-11-03), date only, no id added; addendum + host-table test follow the date; exposure nil, unchanged; gradio 6.31.0 still requires pillow<13 (gradio main allows <14 since 2026-11-02, unreleased); pip-audit: no pillow finding, but RED on unrelated graphql-core 3.3.0 CVE-2026-119286 (fix 3.3.1), already on dev, left for its own decision; not pushed

    avoigt1121
    b677359
  4. security: extend the pillow 12.3.0 acceptances to 2026-12-18⁠

    avoigt1121 +1: Claude Opus 5.5
    abc4da6

10 days ago

  1. merge: docs/phase3-s3-job-created β€” plan s3 DONE (Job 6ae3c084… in the org namespace; triggered run 6/6, record fetched), s4 OPEN from 2026-11-05; docs only, not pushed

    avoigt1121
    9462c78
  2. docs(plans): Phase 3 s3 done β€” the smoke Job exists and its first run came back 6/6⁠

    avoigt1121 +1: Claude Opus 5.5
    7f95498
  3. merge: fix/pillow-batch-8 β€” pillow 12.3.0 PYSEC-2026-4332 (JPEG draft/thumbnail; not reachable: no PIL import, no image or file input) accepted until 2026-11-20 under the project lead's 2026-10-28 decision; 39 accepted, addendum 38 -> 39; scan clean; 319 passed

    avoigt1121
    08ba8fa
  4. security: accept pillow 12.3.0 batch 8 (PYSEC-2026-4332)⁠

    avoigt1121 +1: Claude Opus 5.5
    943ab70
  5. merge: feat/phase3-review-hardening-s3 β€” Plan 4 Phase 3 s3: scripts/smoke_job.py (HF Scheduled Job, cpu-basic, org namespace anne-voigt-co so lit-agent's one-job count holds; every 3 h, self-ending after 7 days; no secret; records printed to the Job logs via smoke_live --print-record and read back by fetch) + tests/test_smoke_job.py; addendum sentence on scheduled runs (C8); plan D1-D4 DECIDED 2026-10-29 (the project lead). 319 passed; not pushed

    avoigt1121
    39d4cd3
  6. feat(smoke): the scheduled smoke Job, and the plan's decisions⁠

    avoigt1121 +1: Claude Opus 5.5
    814e741
  7. merge: feat/phase3-review-hardening-s1 β€” Plan 4 Phase 3 s1: scripts/smoke_live.py (six probes over all six sources, in-process with the cache off or --target space; every failure classed, counts-only records, --report verdict >= 95% and no unstructured failure; no model call) + tests/test_smoke_live.py (probes replayed on their cassettes) + make smoke/smoke-report + docs/plans/PLAN-phase3-review-hardening.md (D1-D4 open). One hand run 2026-10-29: in-process 6/6, Space path 6/6; $0 model credit; not pushed

    avoigt1121
    25f80cb
  8. docs(plans): Phase 3 review and hardening β€” plan, D1-D4 open⁠

    avoigt1121 +1: Claude Opus 5.5
    cbcabf5
  9. feat(smoke): a smoke harness against the live sources, and the week's report⁠

    avoigt1121 +1: Claude Opus 5.5
    84f7513

11 days ago

  1. merge: confirm UniProt, ClinicalTrials.gov and DGIdb licences in sources.yaml

    avoigt1121
    8150d74
  2. docs(sources): confirm UniProt, ClinicalTrials.gov and DGIdb licences⁠

    avoigt1121 +1: Claude Opus 5.5
    8f6c965
  3. merge: fix/pillow-batch-7 β€” pillow 12.3.0 PYSEC-2026-4327 accepted until 2026-11-20 (the project lead, 2026-10-27; not reachable: no PIL import), 38 accepted, addendum count 37 -> 38; scan clean; 267 passed

    avoigt1121
    57f149c
  4. security: accept pillow 12.3.0 batch 7 (PYSEC-2026-4327)⁠

    avoigt1121 +1: Claude Opus 5.5
    2d3c377
  5. merge: fix/ui-oauth-profile β€” UI run handlers get gr.OAuthProfile again (explicit __signature__ from ENDPOINTS + positional profile; special_args stopped at *args, so every signed-in UI run was denied since the Spaces went live 2026-10-21); tests/test_ui_oauth_injection.py drives demo.fns through special_args, 10/21 fail on the old wrapper; 267 passed

    avoigt1121
    f8902cf
  6. fix(ui): every run button denied signed-in users β€” give the run handler a positional profile⁠

    avoigt1121 +1: Claude Opus 5.5
    2a2dd35

13 days ago

  1. merge: fix/cve-2026-10-26 β€” brotli 1.2.0 -> 1.2.1 (PYSEC-2026-4322 / GHSA-9v8h-qqgm-4m35; new security-floors block, one-package floor, lock diff brotli alone); pillow 12.3.0 batch 6 (CVE-2026-114501, CVE-2026-112398; not reachable: no PILLOW_ALIGNMENT, no Arrow export, no olefile) accepted until 2026-11-20 (the project lead, 2026-10-26), 37 accepted, addendum count updated; 246 passed; scan clean

    avoigt1121
    ec7ef9c
  2. security: accept pillow 12.3.0 batch 6 (CVE-2026-114501, CVE-2026-112398)⁠

    avoigt1121 +1: Claude Opus 5.5
    1ed7f10
  3. fix(deps): brotli 1.2.0 -> 1.2.1 (PYSEC-2026-4322 / CVE-2026-111497)⁠

    avoigt1121 +1: Claude Opus 5.5
    b7aac07
  4. merge: docs/notes-drift-1026 β€” Phase 1 s5 marked on orchestrator prod 46f8006; docs only

    avoigt1121
    332c397
  5. docs(plan): s5 is on orchestrator prod (46f8006, 2026-10-23)⁠

    avoigt1121 +1: Claude Opus 5.5
    1eefa35

17 days ago

  1. merge: docs/addendum-file-now β€” record the 2026-10-22 decision: file the security-review addendum now; the project lead files it (docs only, not pushed)

    avoigt1121
    5458b0c
  2. docs: the security-review addendum is to be filed now (decided 2026-10-22, the project lead)⁠

    avoigt1121 +1: Claude Opus 5.5
    aa10ca2
  3. merge: fix/pillow-cve-2026-10-22-batch5 β€” accept 1 more pillow 12.3.0 advisory (GHSA-78g4-xqwv-q3g8, JPEG 2000 via bundled libopenjp2; not reachable here) until 2026-11-20, by id (the project lead, 2026-10-22); the addendum says 35 and test_host_table counts every accepted id type; security files only; pillow clean, 35 accepted

    avoigt1121
    c34c267
  4. security: accept 1 more pillow 12.3.0 advisory until 2026-11-20 (batch 5)⁠

    avoigt1121 +1: Claude Opus 5.5
    bd00037
  5. merge: fix/pillow-cve-2026-10-22-batch4 β€” accept 10 more pillow 12.3.0 advisories (CVE-2026-96636..-96644, CVE-2026-96778; none reachable here) until 2026-11-20, by id (the project lead, 2026-10-22); the security-review addendum's count 24 -> 34; security files only; scan clean, 34 accepted

    avoigt1121
    f58958b
  6. security: accept 10 more pillow 12.3.0 advisories until 2026-11-20 (batch 4)⁠

    avoigt1121 +1: Claude Opus 5.5
    8016795
  7. merge: docs/phase1-knowledge-specialist-s5-status β€” plan: s5 on orchestrator dev 62e1e23, C1 next; the institution-name scrub recorded

    avoigt1121
    5eea567
  8. docs(plans): s5 on orchestrator dev 62e1e23 (C10-C12 met; C1 is the project lead's); the name scrub⁠

    avoigt1121 +1: Claude Opus 5.5
    a145232
  9. merge: docs/no-institution-name-in-public-repo β€” the public Space repo names no institution or centre (project lead, 2026-10-22, after the client's Tech Transfer rule); comments/docs only; guard test; 246 passed

    avoigt1121
    d267318
  10. docs: name no institution in the public repo (the client's Tech Transfer rule)⁠

    avoigt1121 +1: Claude Opus 5.5
    081f1c7

18 days ago

  1. merge: docs/phase1-knowledge-specialist-s3-s5-s6-status β€” plan table: s3 ON PROD f1bf43d (public, gate verified), s6 done, s5 merged on orchestrator dev bc9bacc but its dev push is blocked by KNO-006

    avoigt1121
    06e2ac6
  2. docs(plans): s3 on prod f1bf43d, s6 done, s5 merged on orchestrator dev (dev push blocked by KNO-006)⁠

    avoigt1121 +1: Claude Opus 5.5
    92fb816
  3. merge: fix/phase1-knowledge-specialist-s3-surface-check β€” the live surface check lists gradio's own /_ endpoints (hf_oauth's /_check_login_status) rather than failing on them; dev Space ca9fcc8 passed gate, surface and five lookups

    avoigt1121
    f1bf43d
  4. fix(scripts): check_live_surface lists gradio's /_ endpoints instead of comparing them⁠

    avoigt1121 +1: Claude Opus 5.5
    b598cb3
  5. merge: fix/pillow-cve-2026-10-21-batch3 β€” accept CVE-2026-112393/-112396 (pillow 12.3.0 TIFF encoding) until 2026-11-20 (project lead, 2026-10-21); addendum says 24; 245 passed

    avoigt1121
    ca9fcc8
  6. security: accept 2 more pillow 12.3.0 advisories until 2026-11-20 (batch 3)⁠

    avoigt1121 +1: Claude Opus 5.5
    cc8a03e
  7. merge: feat/phase1-knowledge-specialist-s3 β€” both Spaces' initial commits merged (ours, never force-pushed over) so dev and main fast-forward onto hf-dev and origin; scripts/check_live_surface.py checks C9 against the live Space (gate fails closed, view_api == descriptor, one lookup per endpoint); 245 passed

    avoigt1121
    5f838ea
  8. feat(scripts): check_live_surface.py β€” C9 against the live Space⁠

    avoigt1121 +1: Claude Opus 5.5
    6e55d2d
  9. merge: the prod Space's initial commit (8a4edea), keeping this repo's tree β€” never force-push over it⁠

    avoigt1121 +1: Claude Opus 5.5
    57ade3d
  10. merge: the dev Space's initial commit (a0b30e9), keeping this repo's tree β€” never force-push over it⁠

    avoigt1121 +1: Claude Opus 5.5
    ebbb80d
  11. initial commit

    Verified signature
    8a4edea
  12. initial commit

    Verified signature
    a0b30e9
  13. merge: fix/pillow-cve-2026-10-21-batch2 β€” accept 14 more pillow 12.3.0 advisories until 2026-11-20 (project lead, 2026-10-21); addendum now says 22 and its test reads the count from accepted-vulns.txt; 245 passed; scan clean

    avoigt1121
    0c36a30
  14. security: accept 14 more pillow 12.3.0 advisories until 2026-11-20 (batch 2)⁠

    avoigt1121 +1: Claude Opus 5.5
    e436d30