Chore/code modernization - #21

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chore/code-modernization

Feb 11, 2026

Commits on Jan 26, 2026

refactor: switch from Conda to uv for environment management
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af0e1ec
refactor: use click and pathlib.Path for CLI
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8d730ef
fix: update LangChain imports to restore compatibility
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81194b0
refactor: move prompt to txt file in markdown format for clarity
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c4b528b
feat: add prompt_path option to CLI to query the chatbot
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492c57b
refactor: streamline document processing when creating the database.
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a74c62d

Commits on Jan 27, 2026

chore: add pre-commit configuration and dev dependency for prek
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ec52352
chore: remove unnecessary scripts
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1b73bf9
feat: extend header renumbering to support level 5 headers in Markdown processing
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1e9590b
doc(parse_clean_markdown): add comments and improve docstrings
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0af9c61
feat: enhance `create_database` script to support model and provider options for embeddings + add logs
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e1e5a12
feat: add logger module with configurable logging to file and stdout
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2628212
feat: improve logging with an example of chunk metadata for each markdown file.
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a43861b
refactor: remove useless constants
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538a039
docs: fix logs
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c43ff00
chore: update pre-commit
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d575452
docs: update log
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bb76583
chore: uodate dependencies
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79ac42a
docs: update logs
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809c54d
docs: improve documentation formatting with ruff
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f1505c6

Commits on Feb 2, 2026

chore: adding dependency
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7203587
feat: adding pydantic model settings to configure CLI of BioPyAssistant App
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93b2087
refactor: fix the add of file_name in chunk metadata
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27702ce
chore: fix some docstrings and misspelling
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0a7fa9b
[WIP] - feat: adding the new version of streamlit IU
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eee5c7b

Commits on Feb 6, 2026

Commits on Feb 9, 2026

feat: create YAML file listing all Python chapters and levels
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83e5eaa
refactor(parse_clean_markdown): load chapters and output paths from YAML instead of CLI directories
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cb0b263
docs: change log level to success for chapter loading message
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6a04d81
refactor(create_database): update argument structure to use YAML for course data + improve logging
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ff1bdf0
feat(create_database): add chapter IDs and separate file_path and file_name to chunks metadata
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71de1da
chore: remove unuseful files
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be07be0
chore: remove unused gradio dependency
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2f1ca08
chore(app): remove model config settings (not part of this PR)
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d25335b
chore(pre-commit): update ruff version and format configuration
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dd4f61a
feat(create_database): enable embeddings with all OpenRouter models and persist in Chroma
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abdbb0b
feat(query_chatbot): add level-filtered retrieval, vector DB and LLM provider selection, refactor and improve logging
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adc182d
chore(prompts): rename prompt directory to prompts
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01db3e7
fix(parse_clean_markdown): validate processed_file_path before creating Path
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508e123
chore(chapters_and_levels): update chapter IDs to string format
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87397f9

Commits on Feb 10, 2026

chore(readme): update setup instructions to use uv for environment management and clarify API key requirements
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ebc0872
docs: update scripts to use 'uv' for execution
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1b64888
chore: revert Streamlit app to previous version for history
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6c33371
chore: remove deprecated config_app.toml file
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55ba0fb
chore: update logging messages and argument names
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a4c7d37

Commits on Feb 11, 2026

fixes(query_chatbot): rename ai_api_key to api_key for ChatOpenAI initialization
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1787b52
refactor(prompts): rename prompt folder and files for consistency
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7200618
refactor(yml file): add quotes to values, replace source_file_path and processed_file_path with file_name, and use base_path to avoid redundancy
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1838eb9
chore(gitignore): ignore raw and processed course data paths
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d8c2ef8
refactor(parse_and_clean_markdown): build chapter source and destination paths from yml file
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f19eb97
refactor(yml): update prompt_file to prompt_path for consistency
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2b33578
feat(query_chatbot): answer to the user question even though it is not relevant to the user level + improve logging
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b66f18c
Refactor(create_database): update retrieval to use processed_file_path
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8c39644
refactor(query_chatbot): log answer sentence by sentence for clarity
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f838700
chore: added .gitkeep files to ensure data directories are tracked
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3fd7939
chore: update readme
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418cb3e
refactor: add checks to avoid AttributeError/UnboundLocalError
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340ce00
refactor(create_database): remove short-form options (-c, -s...) on CLI
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9bd746b
refactor(prompt): translate the title in french and remove useless `<<<`
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911c274
refactor(create_database): rename arguments for consistency
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5f1fe1c