Chore/code modernization

[Essmaw]

No description provided.

[Essmaw]

Thanks @Essmaw

I managed to create the vector database, but I encountered an error while running the command:

$ uv run python src/query_chatbot.py --query "What is the difference between list and set ?" \
                  --level "intermediaire" \
                  --model gpt-4o \
                  --prompt_path "prompts/zero_shot.txt" \
                  --include-metadata
2026-02-11 14:46:36 | INFO     | Starting the command line interface for querying the chatbot...
2026-02-11 14:46:36 | INFO     | Loading the vector database...
2026-02-11 14:46:36 | INFO     | Chunks in the database: 1317
2026-02-11 14:46:36 | SUCCESS  | Vector database prepared successfully.
2026-02-11 14:46:36 | INFO     | Getting the list of chapter IDs relevant to the user level...
2026-02-11 14:46:36 | SUCCESS  | Chapter IDs for level 'intermediaire': ['01', '02', '03', '04', '05', '06', '07', '08', '09', '10', '11', '12', '13', '14', '15', '16', 'B']
2026-02-11 14:46:36 | INFO     | Searching for relevant documents in the database...
2026-02-11 14:46:37 | SUCCESS  | Retrieval completed with 3 relevant chunks found.
/home/pierre/workp/teaching/AO/2023_AAP_Idex_innov_péda_LLM-UPCité/2024_stage_M1_Essmay_Touami/Essmay_Touami/biopyassistant.git/.venv/lib/python3.13/site-packages/click/core.py:824: UserWarning: WARNING! ai_api_key is not default parameter.
                ai_api_key was transferred to model_kwargs.
                Please confirm that ai_api_key is what you intended.

[...]
  File "/home/pierre/workp/teaching/AO/2023_AAP_Idex_innov_péda_LLM-UPCité/2024_stage_M1_Essmay_Touami/Essmay_Touami/biopyassistant.git/.venv/lib/python3.13/site-packages/openai/_utils/_utils.py", line 286, in wrapper
    return func(*args, **kwargs)
TypeError: Completions.create() got an unexpected keyword argument 'ai_api_key'

Thanks @pierrepo! Fixed this — it was a wrong ChatOpenAI initialization.
And to get a response from the chatbot, the question must be asked in French. Example command:

uv run python src/query_chatbot.py --query "C'est quoi la différence entre une liste et un set ?" \
    --level "avance" \
    --model gpt-4o \
    --prompt_path "prompts/zero_shot.txt" \
    --include-metadata

[Copilot]

Pull request overview

Copilot reviewed 16 out of 20 changed files in this pull request and generated 6 comments.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[pierrepo]

For some reason I don't understand, the streamlit app cannot run.

Here is the error message I got:

File "/home/pierre/workp/teaching/AO/2023_AAP_Idex_innov_péda_LLM-UPCité/2024_stage_M1_Essmay_Touami/Essmay_Touami/biopyassistant.git/src/streamlit_app.py", line 26, in <module>
    from query_chatbot import load_database, search_similarity_in_database, get_metadata, format_chat_history, contextualize_question,  generate_answer, add_metadata_to_answer, MSGS_QUERY_NOT_RELATED, OPENAI_MODEL_NAME, CHROMA_PATH

[Essmaw]

For some reason I don't understand, the streamlit app cannot run.

Here is the error message I got:

File "/home/pierre/workp/teaching/AO/2023_AAP_Idex_innov_péda_LLM-UPCité/2024_stage_M1_Essmay_Touami/Essmay_Touami/biopyassistant.git/src/streamlit_app.py", line 26, in <module>
    from query_chatbot import load_database, search_similarity_in_database, get_metadata, format_chat_history, contextualize_question,  generate_answer, add_metadata_to_answer, MSGS_QUERY_NOT_RELATED, OPENAI_MODEL_NAME, CHROMA_PATH

The error is expected because this is the old script that was working before the changes in this PR. I’ve created a separate PR for the new Streamlit interface (#24), but I’m waiting to merge this PR first so everything fits together correctly!

[pierrepo]

Good for me. Thanks @Essmaw