Repository navigation

Tooling, quality gates, and integration of upgrade-langchain / plantreactome / userguide-qa - #167

Merged

adamjohnwright merged 34 commits into

mainfrom

integrate/tooling-and-branch-merges

Sep 4, 2026

Commits on Apr 29, 2026
- upgrade langchain-core
  GFJHogue
  committed
  94c35e9
- adjust chunk size for embeddings generation
  GFJHogue
  committed
  bb9c102
- docker build/push for pushes to release/* branches
  GFJHogue
  committed
  f7a5e5c
Commits on Apr 30, 2026
- Revert "docker build/push for pushes to release/* branches"
  GFJHogue
  committed
  30b72ee
- fix mac-intel runner
  GFJHogue
  committed
  503e330
Commits on Jun 25, 2026
- Add Reactome user guide Q&A with intent-based routing.
  heliamoh
  committed
  ab63139
- fix lint and formatting
  heliamoh
  committed
  e285e0c
- URL dedup, DOM perf, safe routing fallback, requests dep.
  heliamoh
  committed
  d8a704c
- resolve mypy error
  heliamoh
  committed
  f99b816
Commits on Aug 19, 2026
- Stop tracking poetry.lock
  elserj
  committed
  cd06433
- Secure postgres port to only be on loopback
  elserj
  committed
  494a49e
- Lock down open redirect/trailing slash fix
  elserj
  committed
  8638e6e
- Fix guest metadata per-session isolation
  elserj
  committed
  3d835a3
- Initial commit of adding PlantReactome profile
  elserj
  committed
  a8aa04c
- Change readme help text to Plant Reactome from Reactome
  elserj
  committed
  5fdcb4d
Commits on Aug 20, 2026
- Change example pathways and disclaimer URL
  elserj
  committed
  ed6b67b
- Security fix didn't actually work for logins. This version should now.
  elserj
  committed
  73e7c99
- Remove accidental /util stub directory
  elserj
  committed
  4b945fd
Commits on Aug 21, 2026
- Add ORCiD as OAuth provider
  elserj
  committed
  fb23675
Commits on Sep 2, 2026
- Add ruff/mypy/pytest config, CI gates, and first test suite
  
  adamjohnwright
  and
  claude
  committed
  7ff12ee
- Add the beta.reactome.org/chat deployment recipe
  
  adamjohnwright
  and
  claude
  committed
  a0643a2
- Fix the config bugs the characterization tests pinned
  
  adamjohnwright
  and
  claude
  committed
  a09f988
Commits on Sep 3, 2026
- Cache CI dependencies, drop a third-party action, tighten permissions
  
  adamjohnwright
  and
  claude
  committed
  65ebc0e
- Merge branch 'upgrade-langchain'
  adamjohnwright
  committed
  a69cf03
- Merge branch 'plantreactome'
  
  adamjohnwright
  and
  claude
  committed
  4b3b437
Commits on Sep 4, 2026
- Merge branch 'feature/userguide-qa'
  
  adamjohnwright
  and
  claude
  committed
  5673d28
- Add the evaluation toolkits from the analysis branch
  
  adamjohnwright
  and
  claude
  committed
  f64436f
- Raise lint and type checking to one standard across the whole repo
  
  adamjohnwright
  and
  claude
  committed
  95a613b
- Verify against the real dependency set, and fix what that exposed
  
  adamjohnwright
  and
  claude
  committed
  04e25ac
- Install Poetry with pip, not pipx, so it uses the Python we set up
  
  adamjohnwright
  and
  claude
  committed
  8f4b810
- Add a retrieval baseline harness
  
  adamjohnwright
  and
  claude
  committed
  0fb9d79
- Fix three problems found reviewing this work
  
  adamjohnwright
  and
  claude
  committed
  3c1362a
- Fuse BM25 and vector separately, and de-duplicate per Reactome entity
  
  adamjohnwright
  and
  claude
  committed
  2c98316
- Cap the fused documents each collection contributes
  
  adamjohnwright
  and
  claude
  committed
  f0383e7

Commits

Commits on Apr 29, 2026

Commits on Apr 30, 2026

Commits on Jun 25, 2026

Commits on Aug 19, 2026

Commits on Aug 20, 2026

Commits on Aug 21, 2026

Commits on Sep 2, 2026

Commits on Sep 3, 2026

Commits on Sep 4, 2026