Fix the UniProt prompt, two typos, and a Quick Start that does not work - #176
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The UniProt system prompt told the model "For Reactome always format citations", a copy-paste from the Reactome prompt. Reported by @GovindhKishore in #121. The rest of that PR is prompt tuning -- preferring retrieved data, citing stable identifiers -- which is a judgement call rather than a fix, and one of those changes would tend to lengthen answers, which is the opposite of what is wanted right now. Not taken. Two spelling fixes found by sweeping every prompt: "final asnwer" in the UniProt prompt, and "LLM generated reponse" in the web-search state. The Quick Start did not work as written, which is why #122, #124 and #158 all try to patch it: - step 5 ran `./bin/embeddings_manager`, whose `#!/usr/bin/env python` shebang fails outright on a system that provides only `python3`, and which needs the project's dependencies either way. Both bin scripts now say `python3`, and the documented commands use `poetry run`. - `PYTHONPATH` was to be "verified" rather than set. Nothing sets it, so verifying it tells a new contributor only that it is wrong. - OPENAI_API_KEY was never mentioned, so the final step could not work. The packaging change will delete most of this by making `poetry install` sufficient, but three people have now filed PRs against these instructions and the fix should not wait on a refactor. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
The Quick Start said to copy env_template, which sets POSTGRES_*. chat-chainlit then builds a connection to host postgres:5432 -- real in Docker Compose, absent on a developer's machine -- and the failure surfaces only on the first message, not at startup. So the fix I made to that section reproduced the class of problem it was fixing: instructions that look right and fail later. It now writes a one-line .env with just the API key, and says why env_template is for the Docker setup instead. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
This was referenced Sep 4, 2026
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Low-risk fixes harvested from three PRs, each verified against current
main.The UniProt prompt describes Reactome citations
In
src/retrievers/uniprot/prompt.py— a copy-paste from the Reactome prompt. Reported by @GovindhKishore in #121.The rest of #121 is prompt tuning rather than a fix: preferring retrieved data over background knowledge, and citing stable identifiers. Both are judgement calls, and the identifier one would tend to make answers longer, which is the opposite of what is currently wanted (see #172). Not taken.
Two spelling fixes
Found by sweeping every prompt string in
src/against a misspelling list:Those were the only hits for that list. It is a fixed set of ~30 common misspellings, not a dictionary check, so it is a floor rather than a guarantee.
The Quick Start did not work
Which is why #122, #124 and #158 all try to patch these instructions. Three separate people hitting the same wall is a signal the docs are wrong, not that the readers are.
Verified failures:
#!/usr/bin/env python, which fails outright on a system providing onlypython3, and the script needs the project dependencies either way. Bothbin/scripts now usepython3, and the documented commands usepoetry run.PYTHONPATHwas to be "verified" rather than set. Nothing sets it, so verifying only tells a new contributor that it is wrong.OPENAI_API_KEYwas never mentioned in the Quick Start, so the final step could not work even if everything before it did.The packaging change (src-layout) will delete most of this by making
poetry installsufficient. But three people have filed PRs against these instructions, and the fix should not wait on a refactor.Closes #121 partially. Addresses the substance of #122, #124 and #158.
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