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## Description
Set gpt-5-mini back to default LLM as issues with it have been resolved
## Type of Change
<!-- Please check the relevant option -->
- [ ] Bug fix (non-breaking change that fixes an issue)
- [ ] New feature (non-breaking change that adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to change)
- [ ] Documentation update
- [ ] Code refactoring
- [ ] Performance improvement
- [ ] Other (please specify):
## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [ ] **I have tested my changes thoroughly before submitting this PR**
- [ ] **This PR contains minimal changes necessary to address the
issue/feature**
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guidelines
- [ ] I have added tests that prove my fix is effective or that my
feature works
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- [ ] All new and existing tests pass
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submitted already
- [ ] I have linked any relevant issues in the description
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## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.
<!-- .github/pull_request_template.md -->
## Description
Resolve Gemini Adapter issues:
1. resolve embedding batch issue,
2. Resolve slowness because gemini tokenizer was sending word per word
to Googles API to count tokens (using OpenAI's local tokenizer to count
tokens for Gemini now)
3. Update deprecated library and move to instructor
## Type of Change
<!-- Please check the relevant option -->
- [x] Bug fix (non-breaking change that fixes an issue)
- [ ] New feature (non-breaking change that adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to change)
- [ ] Documentation update
- [ ] Code refactoring
- [ ] Performance improvement
- [ ] Other (please specify):
## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [ ] **I have tested my changes thoroughly before submitting this PR**
- [ ] **This PR contains minimal changes necessary to address the
issue/feature**
- [ ] My code follows the project's coding standards and style
guidelines
- [ ] I have added tests that prove my fix is effective or that my
feature works
- [ ] I have added necessary documentation (if applicable)
- [ ] All new and existing tests pass
- [ ] I have searched existing PRs to ensure this change hasn't been
submitted already
- [ ] I have linked any relevant issues in the description
- [ ] My commits have clear and descriptive messages
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.
<!-- .github/pull_request_template.md -->
## Description
PR from contributor MSR97
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.
<!-- .github/pull_request_template.md -->
## Description
<!--
Please provide a clear, human-generated description of the changes in
this PR.
DO NOT use AI-generated descriptions. We want to understand your thought
process and reasoning.
-->
Update default tutorial:
1. Use tutorial from [notebook_tutorial
branch](https://github.com/topoteretes/cognee/blob/notebook_tutorial/notebooks/tutorial.ipynb),
specifically - it's .zip version with all necessary data files
2. Use Jupyter Notebook `Notebook` abstractions to read, and map `ipynb`
into our Notebook model
3. Dynamically update starter notebook code blocks that reference
starter data files, and swap them with local paths to downloaded copies
4. Test coverage
| Before | After (storage backend = local) | After (s3) |
|--------|---------------------------------|------------|
| <img width="613" height="546" alt="Screenshot 2025-09-17 at 01 00 58"
src="https://github.com/user-attachments/assets/20b59021-96c1-4a83-977f-e064324bd758"
/> | <img width="1480" height="262" alt="Screenshot 2025-09-18 at 13 01
57"
src="https://github.com/user-attachments/assets/bd56ea78-7c6a-42e3-ae3f-4157da231b2d"
/> | <img width="1485" height="307" alt="Screenshot 2025-09-18 at 12 56
08"
src="https://github.com/user-attachments/assets/248ae720-4c78-445a-ba8b-8a2991ed3f80"
/> |
## File Replacements
### S3 Demo
https://github.com/user-attachments/assets/bd46eec9-ef77-4f69-9ef0-e7d1612ff9b3
---
### Local FS Demo
https://github.com/user-attachments/assets/8251cea0-81b3-4cac-a968-9576c358f334
## Type of Change
<!-- Please check the relevant option -->
- [ ] Bug fix (non-breaking change that fixes an issue)
- [x] New feature (non-breaking change that adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to change)
- [ ] Documentation update
- [ ] Code refactoring
- [ ] Performance improvement
- [ ] Other (please specify):
## Changes Made
<!-- List the specific changes made in this PR -->
-
-
-
## Testing
<!-- Describe how you tested your changes -->
## Screenshots/Videos (if applicable)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [ ] **I have tested my changes thoroughly before submitting this PR**
- [ ] **This PR contains minimal changes necessary to address the
issue/feature**
- [ ] My code follows the project's coding standards and style
guidelines
- [ ] I have added tests that prove my fix is effective or that my
feature works
- [ ] I have added necessary documentation (if applicable)
- [ ] All new and existing tests pass
- [ ] I have searched existing PRs to ensure this change hasn't been
submitted already
- [ ] I have linked any relevant issues in the description
- [ ] My commits have clear and descriptive messages
## Related Issues
<!-- Link any related issues using "Fixes #issue_number" or "Relates to
#issue_number" -->
## Additional Notes
<!-- Add any additional notes, concerns, or context for reviewers -->
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.
<!-- .github/pull_request_template.md -->
## Description
Make Cypher search optional
## Type of Change
<!-- Please check the relevant option -->
- [ ] Bug fix (non-breaking change that fixes an issue)
- [ ] New feature (non-breaking change that adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to change)
- [ ] Documentation update
- [ ] Code refactoring
- [ ] Performance improvement
- [x] Other (please specify):
Security upgrade
## Changes Made
Made cypher search optional for security reasons
## Testing
Tried running cypher queries with feature turned on and off
## Screenshots/Videos (if applicable)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [ ] **I have tested my changes thoroughly before submitting this PR**
- [ ] **This PR contains minimal changes necessary to address the
issue/feature**
- [ ] My code follows the project's coding standards and style
guidelines
- [ ] I have added tests that prove my fix is effective or that my
feature works
- [ ] I have added necessary documentation (if applicable)
- [ ] All new and existing tests pass
- [ ] I have searched existing PRs to ensure this change hasn't been
submitted already
- [ ] I have linked any relevant issues in the description
- [ ] My commits have clear and descriptive messages
## Related Issues
<!-- Link any related issues using "Fixes #issue_number" or "Relates to
#issue_number" -->
## Additional Notes
<!-- Add any additional notes, concerns, or context for reviewers -->
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.
<!-- .github/pull_request_template.md -->
## Description
<!-- Provide a clear description of the changes in this PR -->
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.
<!-- .github/pull_request_template.md -->
## Description
<!-- Provide a clear description of the changes in this PR -->
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.
---------
Co-authored-by: vasilije <vas.markovic@gmail.com>
<!-- .github/pull_request_template.md -->
## Description
Add multi db support for Neo4j Enterprise users
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.
---------
Signed-off-by: Raj2604 <rajmandhare26@gmail.com>
Co-authored-by: vasilije <vas.markovic@gmail.com>
Co-authored-by: Vasilije <8619304+Vasilije1990@users.noreply.github.com>
Co-authored-by: Daulet Amirkhanov <damirkhanov01@gmail.com>
Co-authored-by: Hande <159312713+hande-k@users.noreply.github.com>
Co-authored-by: Boris <boris@topoteretes.com>
Co-authored-by: Matea Pesic <80577904+matea16@users.noreply.github.com>
Co-authored-by: github-actions[bot] <github-actions@users.noreply.github.com>
Co-authored-by: hajdul88 <52442977+hajdul88@users.noreply.github.com>
Co-authored-by: Boris Arzentar <borisarzentar@gmail.com>
Co-authored-by: Raj Mandhare <96978537+Raj2604@users.noreply.github.com>
Co-authored-by: Pedro Thompson <thompsonp17@hotmail.com>
Co-authored-by: Pedro Henrique Thompson Furtado <pedrothompson@petrobras.com.br>
<!-- .github/pull_request_template.md -->
## Description
<!-- Provide a clear description of the changes in this PR -->
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.
---------
Signed-off-by: Raj2604 <rajmandhare26@gmail.com>
Co-authored-by: Daulet Amirkhanov <damirkhanov01@gmail.com>
Co-authored-by: Hande <159312713+hande-k@users.noreply.github.com>
Co-authored-by: Igor Ilic <igorilic03@gmail.com>
Co-authored-by: Igor Ilic <30923996+dexters1@users.noreply.github.com>
Co-authored-by: Boris <boris@topoteretes.com>
Co-authored-by: Matea Pesic <80577904+matea16@users.noreply.github.com>
Co-authored-by: github-actions[bot] <github-actions@users.noreply.github.com>
Co-authored-by: hajdul88 <52442977+hajdul88@users.noreply.github.com>
Co-authored-by: Boris Arzentar <borisarzentar@gmail.com>
Co-authored-by: Raj Mandhare <96978537+Raj2604@users.noreply.github.com>
Co-authored-by: Pedro Thompson <thompsonp17@hotmail.com>
Co-authored-by: Pedro Henrique Thompson Furtado <pedrothompson@petrobras.com.br>
<!-- .github/pull_request_template.md -->
## Description
Modify endpoints to allow better security for different infrastructure
needs and setups
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.
<!-- .github/pull_request_template.md -->
## Description
<!-- Provide a clear description of the changes in this PR -->
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.
<!-- .github/pull_request_template.md -->
## Description
Add how to use postgres with Cognee docker compose
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.
<!-- .github/pull_request_template.md -->
## Description
<!-- Provide a clear description of the changes in this PR -->
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.
---------
Co-authored-by: Boris Arzentar <borisarzentar@gmail.com>
Co-authored-by: Boris <boris@topoteretes.com>
<!-- .github/pull_request_template.md -->
## Description
<!-- Provide a clear description of the changes in this PR -->
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.
---------
Co-authored-by: vasilije <vas.markovic@gmail.com>
Co-authored-by: Igor Ilic <30923996+dexters1@users.noreply.github.com>
Co-authored-by: Vasilije <8619304+Vasilije1990@users.noreply.github.com>
Co-authored-by: Igor Ilic <igorilic03@gmail.com>
Co-authored-by: Hande <159312713+hande-k@users.noreply.github.com>
Co-authored-by: Matea Pesic <80577904+matea16@users.noreply.github.com>
Co-authored-by: hajdul88 <52442977+hajdul88@users.noreply.github.com>
Co-authored-by: Daniel Molnar <soobrosa@gmail.com>
Co-authored-by: Diego Baptista Theuerkauf <34717973+diegoabt@users.noreply.github.com>
Co-authored-by: github-actions[bot] <github-actions@users.noreply.github.com>
## Description
Document that Cognee collects usage data in the readme and add
instructions how users can opt out.
---------
Co-authored-by: i555611 <jan.mueller01@sap.com>
Co-authored-by: Vasilije <8619304+Vasilije1990@users.noreply.github.com>
<!-- .github/pull_request_template.md -->
## Description
LiteLLM adds the debugging lines: LiteLLM:INFO to the output when
running and can flood the output making actual cognee debugging
difficult. This .env config will suppress logging to ERROR level only.
Note there is an open bug with LiteLLM here
[https://github.com/BerriAI/litellm/issues/9815](https://github.com/BerriAI/litellm/issues/9815)
as 'cost calculation' lines will still be shown despite ERROR level
logging
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.
Co-authored-by: rex <rex@epicx.me>
<!-- .github/pull_request_template.md -->
## Description
<!-- Provide a clear description of the changes in this PR -->
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.
---------
Co-authored-by: Boris Arzentar <borisarzentar@gmail.com>
<!-- .github/pull_request_template.md -->
## Description
Add ability to migrate relational database to graph database
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin
<!-- .github/pull_request_template.md -->
## Description
Let's scope it out.
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
- **New Features**
- Introduced support for the Kuzu graph database provider, enhancing
graph operations and data management capabilities.
- Added a comprehensive adapter for Kuzu, facilitating various graph
database operations.
- Expanded the enumeration of graph database types to include Kuzu.
- **Tests**
- Launched comprehensive asynchronous tests to validate the new Kuzu
graph integration’s performance and reliability.
- **Chores**
- Updated dependency settings and continuous integration workflows to
include the Kuzu provider, ensuring smoother deployments and improved
system quality.
- Enhanced configuration documentation to clarify Kuzu database
requirements.
- Modified Dockerfile to include Kuzu in the installation extras.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---------
Co-authored-by: Igor Ilic <30923996+dexters1@users.noreply.github.com>
<!-- .github/pull_request_template.md -->
## Description
<!-- Provide a clear description of the changes in this PR -->
# Add Support for ChromaDB
## Summary
This PR adds support for ChromaDB as a vector database option in the
Cognee application. ChromaDB is a modern, open-source embedding database
designed for AI applications.
## Changes
- Created a new ChromaDBAdapter implementation for vector database
operations
- Added comprehensive test suite for ChromaDB functionality
- Updated docker-compose.yml to include ChromaDB service
- Modified environment configuration to support ChromaDB settings
- Updated vector engine creation logic to support ChromaDB as an option
## Technical Details
- Implemented `ChromaDBAdapter.py` (347 lines) with full CRUD operations
for vector data
- Created test suite (`test_chromadb.py`) with 171 lines of test
coverage
- Updated vector engine creation process to dynamically select ChromaDB
when configured
- Modified settings router to accommodate new database option
- Updated environment template with ChromaDB configuration options
## Docker Changes
- Added ChromaDB service to docker-compose.yml with appropriate
configuration
This PR enhances Cognee's flexibility by providing an alternative vector
database option, allowing users to choose the most appropriate database
for their specific use case.
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin
Tested with UI + tests.
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
- **New Features**
- Expanded vector database integration by adding support for Chromadb,
enabling enhanced data management and search functionalities.
- **Tests**
- Added automated tests to validate the Chromadb integration and related
operations.
- **Chores**
- Updated configuration guidance and dependency management to include
Chromadb.
- Provided an optional container deployment template for Chromadb.
- Added a new entry to ignore the `.chromadb_data/` directory in version
control.
- Introduced a new GitHub Actions workflow for testing Chromadb
integration.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---------
Co-authored-by: hajdul88 <52442977+hajdul88@users.noreply.github.com>
Co-authored-by: Vasilije <8619304+Vasilije1990@users.noreply.github.com>
<!-- .github/pull_request_template.md -->
## Description
Simplest cognee docker setup of SQLite-NetworkX-LanceDB should not
enable postgres configuration in the .env.template by default. I think
leaving postgres details commented is better than removing them
entirely. This keeps simple optionality visible for newcomers.
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
- **Chores**
- Updated configuration template to remove database parameters not used
in the default setup, with clearer guidance to ensure the intended
configuration is maintained.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!-- .github/pull_request_template.md -->
## Description
PR to test Gemini PR from holchan
1. Add Gemini LLM and Gemini Embedding support
2. Fix CodeGraph issue with chunks being bigger than maximum token value
3. Add Tokenizer adapters to CodeGraph
## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
- **New Features**
- Added support for the Gemini LLM provider.
- Expanded LLM configuration options.
- Introduced a new GitHub Actions workflow for multimetric QA
evaluation.
- Added new environment variables for LLM and embedding configurations
across various workflows.
- **Bug Fixes**
- Improved error handling in various components.
- Updated tokenization and embedding processes.
- Removed warning related to missing `dict` method in data items.
- **Refactor**
- Simplified token extraction and decoding methods.
- Updated tokenizer interfaces.
- Removed deprecated dependencies.
- Enhanced retry logic and error handling in embedding processes.
- **Documentation**
- Updated configuration comments and settings.
- **Chores**
- Updated GitHub Actions workflows to accommodate new secrets and
environment variables.
- Modified evaluation parameters.
- Adjusted dependency management for optional libraries.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---------
Co-authored-by: holchan <61059652+holchan@users.noreply.github.com>
Co-authored-by: Boris <boris@topoteretes.com>
* fix: remove groups from UserRead model
* fix: add missing system dependencies for postgres
* fix: change vector db provider environment variable name
* fix: WeaviateAdapter retrieve bug
* fix: correctly return data point objects from retrieve method
* fix: align graph object properties
* feat: add node example
* fix: resolve issue with dlt sqlalchemy usage
Cognee database configuration information was not handled properly by dlt, a new dlt handler
moudle was made to handle database configuration propagation.
* fix: resolve issue with jupyter notebook
cognee add function uses old way of working in the notebook, updated it to
work with the latest state of the cognee add function which doesn't return output.
* fix: Remove empty DB_PATH argument from .env.template
Empty value for DB_PATH in the .env file overrides default value for path intended to be used by cognee.
---------
