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Fixing the Installation Guide in README - #158

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Ehsanstp wants to merge 4 commits into
reactome:mainfrom
Ehsanstp:Ehsanstp-README
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Fixing the Installation Guide in README#158
Ehsanstp wants to merge 4 commits into
reactome:mainfrom
Ehsanstp:Ehsanstp-README

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@Ehsanstp

@Ehsanstp Ehsanstp commented Mar 26, 2026

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@GFJHogue, I've updated the installation documentation for issue #88 to include the missing instructions after testing this setup on separate devices. Please let me know if anything else needs to be added or corrected.

Fixes #88 with the following:

  1. Supported OS
  2. Added a warning that Chainlit-based run method is no longer supported.
  3. Document the use of pre-built docker image.
  4. Add a section for troubleshooting common issues

Corrected formatting and punctuation in README.md for clarity.
Updated installation instructions for Windows, including WSL2 requirements and Docker setup. Clarified troubleshooting issues related to Docker builds and access errors.
Updated note to a warning regarding the barebones method.
@adamjohnwright

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Thank you — you were right that these instructions were wrong, and three separate people filing PRs against the same section is the clearest possible signal.

Fixed on main in #176, going further than the docs alone. The Quick Start had three defects, each verified:

  • ./bin/embeddings_manager failed outright with /usr/bin/env: ‘python’: No such file or directory on any system providing only python3. Both bin/ scripts now use python3, and the documented commands use poetry run.
  • PYTHONPATH was to be "verified" rather than set. Nothing sets it, so verifying only tells a new contributor that it is wrong.
  • OPENAI_API_KEY was never mentioned, so the final step could not work even if everything before it did.

The underlying cause is the layout: src/ on PYTHONPATH instead of an installed package. Moving to a standard src-layout will make poetry install sufficient and delete this whole class of problem — but that should not have blocked fixing the instructions, and it did for too long.

Closing as resolved rather than stale.

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Update installation documentation in README

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