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[pull] develop from dermatologist:develop#56

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pull[bot] merged 12 commits intomederrata:developfrom
dermatologist:develop
Dec 24, 2025
Merged

[pull] develop from dermatologist:develop#56
pull[bot] merged 12 commits intomederrata:developfrom
dermatologist:develop

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@pull pull bot commented Dec 24, 2025

See Commits and Changes for more details.


Created by pull[bot] (v2.0.0-alpha.4)

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Copilot AI and others added 12 commits December 24, 2025 07:16
…#253)

* Initial plan

* Fix llm_query.py and improve examples with comprehensive documentation

Co-authored-by: dermatologist <6259644+dermatologist@users.noreply.github.com>

* Add .gitignore for sqlite files, improve llm_engine.py comments, add README_LLM.md

Co-authored-by: dermatologist <6259644+dermatologist@users.noreply.github.com>

* Switch to llama-index HuggingFace embeddings, support both string and instance params

Co-authored-by: dermatologist <6259644+dermatologist@users.noreply.github.com>

* Add comprehensive CHANGES_SUMMARY.md documenting all improvements

Co-authored-by: dermatologist <6259644+dermatologist@users.noreply.github.com>

* Update example documentation and database references to use 'cdm.sqlite'

* Add .env to .gitignore to exclude environment variable files

* Refactor code structure for improved readability and maintainability

* Update README to reflect switch from langchain to llama-index for LLM-based queries

* Refactor code structure for improved readability and maintainability

* Remove redundant main function definition and streamline execution flow in LLM example

* Comment out SQL execution verification code in LLM example for clarity

* Update LLM example documentation for clarity and consistency

* Enhance LLM example documentation and remove obsolete file; update query engine configuration for improved clarity and functionality

* Update LLM example usage note to indicate deprecation of create_sql_agent support and introduce MCP server implementation

* Update LLM example documentation to recommend MCP server and adjust LLM initialization for improved functionality

* Enhance LLM example documentation and update query engine to recommend MCP server; add dynamic prompt tool for improved query generation

* Refactor LLM initialization to use OpenAI model; update dependencies and improve dynamic prompt documentation

* Update LLM example and query utilities: increase API call delay, rename dynamic prompt tool, and improve error handling

* Refactor code structure for improved readability and maintainability

* refactor: Replace custom test mocks with `unittest.mock` and configure `nest_asyncio` for async test compatibility.

* refactor: Update LLM example model and enhance query tool documentation; remove unnecessary rate limit delays

* docs: Update README to reference new LLM example notebook and script

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: dermatologist <6259644+dermatologist@users.noreply.github.com>
Co-authored-by: Bell Eapen <github@gulfdoctor.net>
Co-authored-by: Bell Eapen <github_public@gulfdoctor.net>
* refactor: reorganize imports and improve engine initialization in README and engine_factory

* fix: enhance SQLite engine configuration and improve test cleanup

* Update tests/test_d_vector.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Update tests/test_d_vector.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Update t_install.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* refactor: remove unused pytest import from test files

---------

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
@pull pull bot locked and limited conversation to collaborators Dec 24, 2025
@pull pull bot added the ⤵️ pull label Dec 24, 2025
@pull pull bot merged commit 599add7 into mederrata:develop Dec 24, 2025
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