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## Description
Merge main to dev
## Type of Change
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- [ ] 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)
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- [ ] Performance improvement
- [ ] Other (please specify):
## Screenshots/Videos (if applicable)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
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- [ ] **I have tested my changes thoroughly before submitting this PR**
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issue/feature**
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guidelines
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feature works
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- [ ] All new and existing tests pass
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submitted already
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- [ ] 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.
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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**
- [ ] 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.
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## Description
Fix latest pydantic version issues
## 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):
## Screenshots/Videos (if applicable)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
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- [ ] **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.
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## Description
Unified dataset resolution mechanisms across cognee
## 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
- [x] 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.
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## 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.
-->
`cognee-cli -ui` has accidentally added - when opening frontend
subprocess - an output decoding into text.
## What happens exactly
On the surface - frontend ui will be stuck loading.
Frontend process hangs as it's output is not being processed (we're
expecting bytes).
## This change
This change removes the `text=True` added to frontend subprocess
## 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):
## 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
## 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
Github Actions job:
https://github.com/topoteretes/cognee/actions/runs/18199627173/job/51815009426?pr=1493
<!--
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.
-->
## 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):
## 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
## 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.
## Description
This pull request introduces a preview step to the `cognee delete`
command, fulfilling the requirements of issue #1366
When a user runs the delete command, it now first queries the database
to calculate the scope of the deletion and presents a summary (number of
datasets, data entries, users) before asking for final confirmation.
This improves the safety and usability of the command, preventing
accidental data loss.
This PR also adds the `--force` flag to bypass the preview, which is
useful for scripting and automation.
## Type of Change
- [x] New feature (non-breaking change that adds functionality)
- [ ] Bug fix (non-breaking change that fixes an issue)
## Changes Made
- **`cognee/cli/commands/delete_command.py`**: Modified to include the
preview logic. It now calls the counting function, displays the results,
and proceeds with deletion only after confirmation.
- **`cognee/modules/data/methods/get_deletion_counts.py`**: Added this
new file to contain the logic for querying the database and calculating
the deletion counts for datasets, data entries, and users.
## Testing
I have tested the changes through **Manual CLI Testing**: I ran the
`cognee delete` command with the `--dataset-name`, `--user-id`, and
`--all` flags to manually verify that the preview output is correct.
### Terminal Output
Here are screenshots of the command working with the all possible flags:
<img width="1898" height="1087" alt="cognee1"
src="https://github.com/user-attachments/assets/939aa4d0-748c-45e4-a2a6-f5e7982c1fc0"
/>
<img width="1788" height="748" alt="cognee2"
src="https://github.com/user-attachments/assets/213884be-cce1-4007-90f9-5e6d3a302ced"
/>
## Pre-submission Checklist
- [x] **I have tested my changes thoroughly before submitting this PR**
- [x] **This PR contains minimal changes necessary to address the
issue/feature**
- [x] My code follows the project's coding standards and style
guidelines
- [x] I have added tests that prove my feature works
- [ ] I have not added or changed documentation (as it was not required
for this CLI change)
- [x] I have searched existing PRs to ensure this change has been
submitted already
- [x] I have linked the relevant issue in the description
## Related Issues
Fixes#1366
## 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 commit introduces the preview functionality for the command. The preview displays a summary of what will be deleted before asking for user confirmation.
The feature is fully functional for the following flags:
- / : Correctly counts the number of data entries within the specified dataset.
- : Correctly counts the total number of datasets, data entries, and users in the system.
The logic for the flag is a work in progress. The current implementation uses a placeholder and needs a method to query a user directly by their ID to be completed.
<!-- .github/pull_request_template.md -->
## Description
Remove MacOS13 support and CI/CD tests
## 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): Remove MacOS13 support
## 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.
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## Description
ruff formatting
## 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):
## Screenshots/Videos (if applicable)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
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- [ ] **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.
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## 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.
-->
I've just added a new PDF parser, AdvancedPdfLoader. It uses the
unstructured library and does a much better job of handling PDFs,
especially with its layout-aware parsing, table preservation, and image
handling.
I also built in a safeguard: if unstructured isn't installed or throws
an error, it'll automatically fall back to the old PyPdfLoader so it
won't just crash. All the related unit tests and project dependencies
are taken care of, too.
https://github.com/topoteretes/cognee/issues/1342
## 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
- [x] Performance improvement
- [ ] Other (please specify):
## Changes Made
<!-- List the specific changes made in this PR -->
- Added AdvancedPdfLoader class for enhanced PDF processing using the
unstructured library.
- Integrated fallback mechanism to PyPdfLoader in case of unstructured
library import failure or exceptions.
- Updated supported loaders to include AdvancedPdfLoader.
- Added unit tests for AdvancedPdfLoader to ensure functionality and
error handling.
- Updated poetry.lock and pyproject.toml to include new dependencies and
versions.
## Testing
<!-- Describe how you tested your changes -->
pytest -v ./cognee/tests/test_advanced_pdf_loader.py
## 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 -->
- [x] **I have tested my changes thoroughly before submitting this PR**
- [x] **This PR contains minimal changes necessary to address the
issue/feature**
- [x] My code follows the project's coding standards and style
guidelines
- [x] I have added tests that prove my fix is effective or that my
feature works
- [x] I have added necessary documentation (if applicable)
- [x] All new and existing tests pass
- [x] I have searched existing PRs to ensure this change hasn't been
submitted already
- [x] I have linked any relevant issues in the description
- [x] 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.
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## Description
Use JSON_SCHEMA mode only for GPT-5 series models, it's a new mode from
OpenAI for structured output processing that they didn't properly handle
for older models
## 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.
# **Pull Request: Windows Compatibility and Error Handling
Improvements**
## Description
This PR addresses multiple Windows compatibility issues and improves
error handling across the cognee CLI and frontend, making the
application fully functional on Windows systems. The changes include:
- **Windows Process Termination**: Fixed crashes when terminating
spawned processes by using `taskkill` instead of Unix-specific `killpg`
functions
- **npm Detection**: Resolved npm command failures on Windows by adding
`shell=True` for PowerShell script execution
- **Frontend SSR**: Fixed "window is not defined" errors by implementing
dynamic imports for the graph visualization component
- **Cloud API**: Improved error handling for local installations by
returning graceful responses instead of raising exceptions
- **Connection Retry**: Added retry mechanism for frontend health checks
with better error messages
- **String Formatting**: Fixed mixed f-string formatting that caused
placeholder issues
- **CLI Entry Point**: Added `cognee` command alongside `cognee-cli` for
better user experience
These changes ensure cognee works seamlessly on Windows while
maintaining backward compatibility and improving overall robustness.
## Type of Change
- [x] 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):
## Screenshots/Videos (if applicable)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
- [x] **I have tested my changes thoroughly before submitting this PR**
- [x] **This PR contains minimal changes necessary to address the
issue/feature**
- [x] My code follows the project's coding standards and style
guidelines
- [x] I have added tests that prove my fix is effective or that my
feature works
- [x] I have added necessary documentation (if applicable)
- [x] All new and existing tests pass
- [x] I have searched existing PRs to ensure this change hasn't been
submitted already
- [x] I have linked any relevant issues in the description
- [x] 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.
---
## 🔧 **Technical Details**
### **Files Modified:**
- ✅ **Windows Process Termination**: `cognee/cli/_cognee.py`,
`cognee/tests/test_cognee_server_start.py`
- ✅ **npm Detection**: `cognee/api/v1/ui/ui.py`
- ✅ **Frontend SSR**:
`cognee-frontend/src/app/(graph)/GraphVisualization.tsx`
- ✅ **Cloud API**: `cognee/api/v1/cloud/routers/get_checks_router.py`
- ✅ **Connection Retry**: `cognee-frontend/src/utils/fetch.ts`
- ✅ **String Formatting**:
`cognee/infrastructure/llm/prompts/read_query_prompt.py`
- ✅ **CLI Entry Point**: `pyproject.toml`
### **Key Changes:**
1. **Process Termination**: Added Windows-compatible `taskkill` commands
alongside Unix `killpg`
2. **npm Commands**: Added `shell=True` for Windows PowerShell script
execution
3. **Dynamic Imports**: Implemented `ssr: false` for graph visualization
component
4. **Graceful Errors**: Return JSON responses instead of raising
exceptions for local mode
5. **Retry Logic**: Added 5-retry mechanism with 1-second delays for
health checks
6. **String Formatting**: Fixed mixed f-string and old-style formatting
issues
7. **CLI Commands**: Added `cognee` entry point alongside `cognee-cli`
### **Testing Results:**
- ✅ All existing tests pass
- ✅ Windows process termination works correctly
- ✅ npm detection and commands work on Windows
- ✅ Frontend loads without SSR errors
- ✅ Cloud API returns graceful responses for local mode
- ✅ Frontend connection retries work properly
- ✅ Code formatting and linting checks pass
This PR makes cognee fully functional on Windows while improving error
handling and user experience across all platforms.
<!-- .github/pull_request_template.md -->
## Description
Add update method end endpoint for Cognee
## 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):
## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [x] **I have tested my changes thoroughly before submitting this PR**
- [x] **This PR contains minimal changes necessary to address the
issue/feature**
- [x] 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
- [x] 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.
<!-- CURSOR_SUMMARY -->
---
> [!NOTE]
> <sup>[Cursor Bugbot](https://cursor.com/dashboard?tab=bugbot) is
generating a summary for commit
9524109029. Configure
[here](https://cursor.com/dashboard?tab=bugbot).</sup>
<!-- /CURSOR_SUMMARY -->
<!-- .github/pull_request_template.md -->
## Description
Add return value of creating role and tenant, add detailed permissions
example to Cognee
## 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):
## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [x] **I have tested my changes thoroughly before submitting this PR**
- [x] **This PR contains minimal changes necessary to address the
issue/feature**
- [x] My code follows the project's coding standards and style
guidelines
- [x] I have added tests that prove my fix is effective or that my
feature works
- [x] I have added necessary documentation (if applicable)
- [x] All new and existing tests pass
- [x] I have searched existing PRs to ensure this change hasn't been
submitted already
- [x] I have linked any relevant issues in the description
- [x] 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.
---------
Co-authored-by: Boris <boris@topoteretes.com>
Co-authored-by: Hande <159312713+hande-k@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>
<!-- .github/pull_request_template.md -->
## Description
Resolve issues with gpt 5 models for structured outputs by forcing JSON
mode in 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):
## 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 -->
- [x] **I have tested my changes thoroughly before submitting this PR**
- [x] **This PR contains minimal changes necessary to address the
issue/feature**
- [x] My code follows the project's coding standards and style
guidelines
- [x] I have added tests that prove my fix is effective or that my
feature works
- [x] I have added necessary documentation (if applicable)
- [x] All new and existing tests pass
- [x] I have searched existing PRs to ensure this change hasn't been
submitted already
- [x] I have linked any relevant issues in the description
- [x] 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
Fix Neo4j issue with migrating DB schema
## 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 -->
- [x] **I have tested my changes thoroughly before submitting this PR**
- [x] **This PR contains minimal changes necessary to address the
issue/feature**
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guidelines
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feature works
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submitted already
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## DCO Affirmation
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## Description
<!--
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this PR.
DO NOT use AI-generated descriptions. We want to understand your thought
process and reasoning.
-->
Alice in wonderland expensive to process, plus Azure OpenAI flags it as
inappropriate content. Changed this to a smaller file about quantum
computers.
## 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
- [x] Code refactoring
- [ ] Performance improvement
- [ ] Other (please specify):
## Screenshots/Videos (if applicable)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
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- [ ] **I have tested my changes thoroughly before submitting this PR**
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issue/feature**
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guidelines
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feature works
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submitted already
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## DCO Affirmation
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<!-- CURSOR_SUMMARY -->
---
> [!NOTE]
> Update vector search limit-none tests to use local quantum/NLP files
and add `test_data/Quantum_computers.txt`, adjusting queries
accordingly.
>
> - **Tests**:
> - **Vector engine limit-none coverage**
(`test_vector_engine_search_none_limit`):
> - Replace `examples/data/alice_in_wonderland.txt` with
`tests/test_data/Quantum_computers.txt` and
`tests/test_data/Natural_language_processing.txt` across
`cognee/tests/test_chromadb.py`, `cognee/tests/test_lancedb.py`, and
`cognee/tests/test_pgvector.py`.
> - Update query to "Tell me about Quantum computers" and keep assertion
verifying no implicit `limit` (ensure `len(result) > 15`).
> - **Test data**:
> - Add `cognee/tests/test_data/Quantum_computers.txt`.
>
> <sup>Written by [Cursor
Bugbot](https://cursor.com/dashboard?tab=bugbot) for commit
af1603c8f9. This will update automatically
on new commits. Configure
[here](https://cursor.com/dashboard?tab=bugbot).</sup>
<!-- /CURSOR_SUMMARY -->
<!-- .github/pull_request_template.md -->
## Description
Merge main to dev branch
## 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):
## Screenshots/Videos (if applicable)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
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- [ ] **I have tested my changes thoroughly before submitting this PR**
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issue/feature**
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guidelines
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feature works
- [ ] I have added necessary documentation (if applicable)
- [ ] All new and existing tests pass
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submitted already
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## DCO Affirmation
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<!-- CURSOR_SUMMARY -->
---
> [!NOTE]
> Standardizes vector search to accept `limit=None` (fetch all/count),
updates adapters/interface and retrievers, and adds tests plus minor
logging/doc assets.
>
> - **Vector search API**:
> - Change `limit` to `Optional[int]` in `vector_db_interface` and
adapters (`ChromaDBAdapter`, `LanceDBAdapter`, `PGVectorAdapter`,
`NeptuneAnalyticsAdapter`).
> - Behavior: `limit=None` fetches all/collection count; early-return on
`limit<=0`; minor logging copy/level tweaks; `PGVector` counts via
`func.count`.
> - **Retrievers**:
> - Switch internal calls to `limit=None` (`CogneeGraph`,
`temporal_retriever`, brute-force triplet search).
> - **Tests**:
> - Add `limit=None` coverage for ChromaDB, LanceDB (new suite), and
PGVector; assert results exceed default caps.
> - **Examples/Docs**:
> - Demo script prunes before run; add tutorial notebook and data
assets; remove one markdown article.
> - **Misc**: LLM utils demote a log line to `debug`.
>
> <sup>Written by [Cursor
Bugbot](https://cursor.com/dashboard?tab=bugbot) for commit
7403e31738. This will update automatically
on new commits. Configure
[here](https://cursor.com/dashboard?tab=bugbot).</sup>
<!-- /CURSOR_SUMMARY -->
<!-- .github/pull_request_template.md -->
## Description
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this PR.
DO NOT use AI-generated descriptions. We want to understand your thought
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Falkordb adapter didn't work on main repo, but we have it working on
community. Decision was to remove it from main repo, so it is removed.
## 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
- [x] 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
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guidelines
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feature works
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submitted already
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## Related Issues
<!-- Link any related issues using "Fixes #issue_number" or "Relates to
#issue_number" -->
## Additional Notes
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## Description
PR from contributor MSR97
## DCO Affirmation
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the terms of the Topoteretes Developer Certificate of Origin.
<!-- .github/pull_request_template.md -->
## Description
Running cognee-mcp as a docker container currently fails when using
latest main version:
```
(cognee-mcp) daulet@Mac cognee-claude % docker run -e TRANSPORT_MODE=sse -p 8001:8000 cognee/cognee-mcp:main
Debug mode:
Environment:
Transport mode: sse
Debug port: 5678
HTTP port: 8000
Running database migrations...
2025-09-25T21:15:17.065171 [info ] Logging initialized [cognee.shared.logging_utils] cognee_version=0.3.2 database_path=/app/.venv/lib/python3.12/site-packages/cognee/.cognee_system/databases graph_database_name= os_info='Linux 6.12.5-linuxkit (#1 SMP Tue Jan 21 10:23:32 UTC 2025)' python_version=3.12.11 relational_config=cognee_db structlog_version=25.4.0 vector_config=lancedb
2025-09-25T21:15:17.065330 [info ] Database storage: /app/.venv/lib/python3.12/site-packages/cognee/.cognee_system/databases [cognee.shared.logging_utils]
generated new fontManager
Database migrations done.
Starting Cognee MCP Server with transport mode: sse
2025-09-25T21:15:24.204708 [info ] Logging initialized [cognee.shared.logging_utils] cognee_version=0.3.2 database_path=/app/.venv/lib/python3.12/site-packages/cognee/.cognee_system/databases graph_database_name= os_info='Linux 6.12.5-linuxkit (#1 SMP Tue Jan 21 10:23:32 UTC 2025)' python_version=3.12.11 relational_config=cognee_db structlog_version=25.4.0 vector_config=lancedb
2025-09-25T21:15:24.204863 [info ] Database storage: /app/.venv/lib/python3.12/site-packages/cognee/.cognee_system/databases [cognee.shared.logging_utils]
Usage: cognee [-h] [--version] [--debug] [-ui]
{add,search,cognify,delete,config} ...
cognee: error: argument command: invalid choice: 'sse' (choose from add, search, cognify, delete, config)
(cognee-mcp) daulet@Mac cognee-claude %
```
This is due to both `cognee-mcp` and `cognee` (v0.3.2) projects defining
their CLI script aliases as `cognee`.
`entrypoint.sh` uses `cognee` cli, assuming it's `cognee-mcp`, which is
failing (see logs above).
While in later version of cognee we define `cognee-cli` instead of
`cognee`, it's still important to be safer and be more explicit in
`cognee-mcp` cli alias.
## Testing the fix
```
(cognee-mcp) daulet@Mac cognee-claude % docker run -e TRANSPORT_MODE=sse -p 8001:8000 cognee/cognee-mcp:daulet-dev
Debug mode:
Environment:
Transport mode: sse
Debug port: 5678
HTTP port: 8000
Running database migrations...
2025-09-25T21:18:45.855092 [info ] Logging initialized [cognee.shared.logging_utils] cognee_version=0.3.2 database_path=/app/.venv/lib/python3.12/site-packages/cognee/.cognee_system/databases graph_database_name= os_info='Linux 6.12.5-linuxkit (#1 SMP Tue Jan 21 10:23:32 UTC 2025)' python_version=3.12.11 relational_config=cognee_db structlog_version=25.4.0 vector_config=lancedb
2025-09-25T21:18:45.855270 [info ] Database storage: /app/.venv/lib/python3.12/site-packages/cognee/.cognee_system/databases [cognee.shared.logging_utils]
generated new fontManager
Database migrations done.
Starting Cognee MCP Server with transport mode: sse
2025-09-25T21:18:53.188498 [info ] Logging initialized [cognee.shared.logging_utils] cognee_version=0.3.2 database_path=/app/.venv/lib/python3.12/site-packages/cognee/.cognee_system/databases graph_database_name= os_info='Linux 6.12.5-linuxkit (#1 SMP Tue Jan 21 10:23:32 UTC 2025)' python_version=3.12.11 relational_config=cognee_db structlog_version=25.4.0 vector_config=lancedb
2025-09-25T21:18:53.188665 [info ] Database storage: /app/.venv/lib/python3.12/site-packages/cognee/.cognee_system/databases [cognee.shared.logging_utils]
2025-09-25T21:18:54.272533 [info ] Starting MCP server with transport: sse [cognee.shared.logging_utils]
2025-09-25T21:18:54.272661 [info ] Running MCP server with SSE transport on 0.0.0.0:8000 [cognee.shared.logging_utils]
INFO: Started server process [1]
INFO: Waiting for application startup.
INFO: Application startup complete.
INFO: Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)
```
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## Type of Change
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## Description
Enhance search results of relational db data by adding more information
on data type and content
PR also includes schema migration done by contributor ( Geoff-Robin )
from contribute to win competition
## 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
- [x] Performance improvement
- [ ] Other (please specify):
## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [x] **I have tested my changes thoroughly before submitting this PR**
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issue/feature**
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guidelines
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feature works
- [x] I have added necessary documentation (if applicable)
- [x] All new and existing tests pass
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submitted already
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## DCO Affirmation
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## Overall UI
<img width="1908" height="881" alt="Screenshot 2025-09-25 at 22 21 35"
src="https://github.com/user-attachments/assets/a3e26827-8e1a-47d1-8ac6-346387d6407f"
/>
## MCP connection - live
<img width="1519" height="691" alt="Screenshot 2025-09-25 at 22 22 02"
src="https://github.com/user-attachments/assets/2314242f-0998-4401-99e1-cfc745d40728"
/>
## MCP connection - disconnected
<img width="1520" height="698" alt="Screenshot 2025-09-25 at 22 22 11"
src="https://github.com/user-attachments/assets/ef13bb5e-6d50-4248-8d4c-8845becb1582"
/>
## Description
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this PR.
DO NOT use AI-generated descriptions. We want to understand your thought
process and reasoning.
-->
## Type of Change
<!-- Please check the relevant option -->
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- [ ] New feature (non-breaking change that adds functionality)
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functionality to change)
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- [ ] Performance improvement
- [ ] Other (please specify):
## Screenshots/Videos (if applicable)
<!-- Add screenshots or videos to help explain your changes -->
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feature works
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## Description
Updated the README file to include the correct URL to the hosted
solution. Previously it tried to go as param after GitHub URL, instead I
included 'https'.
## Type of Change
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- [ ] Bug fix (non-breaking change that fixes an issue)
- [ ] New feature (non-breaking change that adds functionality)
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functionality to change)
- [x] Documentation update
- [ ] Code refactoring
- [ ] Performance improvement
- [ ] Other (please specify):
## Pre-submission Checklist
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feature works
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submitted already
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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.
