<!-- .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
<!--
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
Resolve issue with getting role objects for user
## 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):
## 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.
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: Daulet Amirkhanov <damirkhanov01@gmail.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: Igor Ilic <igorilic03@gmail.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: Boris Arzentar <borisarzentar@gmail.com>
Co-authored-by: Boris <boris@topoteretes.com>
Adds base node label to Neo4j Adapter
## 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: Diego B Theuerkauf <diego.theuerkauf@tuebingen.mpg.de>
Co-authored-by: Boris <boris@topoteretes.com>
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: Dmitrii Galkin <36552323+dm1tryG@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: lxobr <122801072+lxobr@users.noreply.github.com>
Co-authored-by: github-actions[bot] <github-actions@users.noreply.github.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: Daniel Molnar <soobrosa@gmail.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: Igor Ilic <30923996+dexters1@users.noreply.github.com>
<!-- .github/pull_request_template.md -->
## Description
Simplify Cognee pipeline usage for 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
<!-- .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
Introducing scructlog.
## 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
Cognee backend fixes
## 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**
- Improved handling of `tenant_id` in JWT payload for enhanced type
safety.
- Unique identifier generation for datasets now considers the owner ID,
allowing for multiple users to share the same dataset name.
- **Bug Fixes**
- Disabled user role permissions in the permission check logic
temporarily during a rework.
- **Refactor**
- Simplified dependencies by removing unnecessary model imports.
- Updated parameter name from `tenant` to `tenant_id` for clarity in JWT
creation.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!-- .github/pull_request_template.md -->
## Description
Added user authorization through JWT header, reworked user and relevant
RBAC models to accompany future User Permission system.
## 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 an automated workflow to validate server startup.
- Added secure JWT token generation for improved session handling.
- Enabled a new structure for permission management with role and
tenant-based controls, including endpoints for creating roles, tenants,
and assigning permissions.
- Added methods for assigning default permissions to roles, tenants, and
users.
- Introduced new classes for managing default permissions for roles,
tenants, and users.
- **Refactor**
- Streamlined authentication and user management flows with enhanced
error handling.
- **Tests**
- Upgraded integration tests with improved database initialization and
data pruning for a more stable environment.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---------
Co-authored-by: Vasilije <8619304+Vasilije1990@users.noreply.github.com>
<!-- .github/pull_request_template.md -->
## Description
<!-- Provide a clear description of the changes in this PR -->
God mode turned on by default for the default user creation.
is_superuser=True in create_default_user.py
## 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**
- The default user is now created with elevated (superuser) privileges,
which may affect access control and permissions.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
* Revert "fix: Add metadata reflection fix to sqlite as well"
This reverts commit 394a0b2dfb.
* COG-810 Implement a top-down dependency graph builder tool (#268)
* feat: parse repo to call graph
* Update/repo_processor/top_down_repo_parse.py task
* fix: minor improvements
* feat: file parsing jedi script optimisation
---------
* Add type to DataPoint metadata (#364)
* Add missing index_fields
* Use DataPoint UUID type in pgvector create_data_points
* Make _metadata mandatory everywhere
* feat: Add search by dataset for cognee
Added ability to search by datasets for cognee users
Feature COG-912
* feat: outsources chunking parameters to extract chunk from documents … (#289)
* feat: outsources chunking parameters to extract chunk from documents task
* fix: Remove backend lock from UI
Removed lock that prevented using multiple datasets in cognify
Fix COG-912
* COG 870 Remove duplicate edges from the code graph (#293)
* feat: turn summarize_code into generator
* feat: extract run_code_graph_pipeline, update the pipeline
* feat: minimal code graph example
* refactor: update argument
* refactor: move run_code_graph_pipeline to cognify/code_graph_pipeline
* refactor: indentation and whitespace nits
* refactor: add deprecated use comments and warnings
---------
Co-authored-by: Vasilije <8619304+Vasilije1990@users.noreply.github.com>
Co-authored-by: Igor Ilic <30923996+dexters1@users.noreply.github.com>
Co-authored-by: Boris <boris@topoteretes.com>
* test: Added test for getting of documents for search
Added test to verify getting documents related to datasets intended for search
Test COG-912
* Structured code summarization (#375)
* feat: turn summarize_code into generator
* feat: extract run_code_graph_pipeline, update the pipeline
* feat: minimal code graph example
* refactor: update argument
* refactor: move run_code_graph_pipeline to cognify/code_graph_pipeline
* refactor: indentation and whitespace nits
* refactor: add deprecated use comments and warnings
* Structured code summarization
* add missing prompt file
* Remove summarization_model argument from summarize_code and fix typehinting
* minor refactors
---------
Co-authored-by: lxobr <122801072+lxobr@users.noreply.github.com>
Co-authored-by: Vasilije <8619304+Vasilije1990@users.noreply.github.com>
Co-authored-by: Igor Ilic <30923996+dexters1@users.noreply.github.com>
Co-authored-by: Boris <boris@topoteretes.com>
* fix: Resolve issue with cognify router graph model default value
Resolve issue with default value for graph model in cognify endpoint
Fix
* chore: Resolve typo in getting documents code
Resolve typo in code
chore COG-912
* Update .github/workflows/dockerhub.yml
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
* Update .github/workflows/dockerhub.yml
* Update .github/workflows/dockerhub.yml
* Update .github/workflows/dockerhub.yml
* Update get_cognify_router.py
* fix: Resolve syntax issue with cognify router
Resolve syntax issue with cognify router
Fix
* feat: Add ruff pre-commit hook for linting and formatting
Added formatting and linting on pre-commit hook
Feature COG-650
* chore: Update ruff lint options in pyproject file
Update ruff lint options in pyproject file
Chore
* test: Add ruff linter github action
Added linting check with ruff in github actions
Test COG-650
* feat: deletes executor limit from get_repo_file_dependencies
* feat: implements mock feature in LiteLLM engine
* refactor: Remove changes to cognify router
Remove changes to cognify router
Refactor COG-650
* fix: fixing boolean env for github actions
* test: Add test for ruff format for cognee code
Test if code is formatted for cognee
Test COG-650
* refactor: Rename ruff gh actions
Rename ruff gh actions to be more understandable
Refactor COG-650
* chore: Remove checking of ruff lint and format on push
Remove checking of ruff lint and format on push
Chore COG-650
* feat: Add deletion of local files when deleting data
Delete local files when deleting data from cognee
Feature COG-475
* fix: changes back the max workers to 12
* feat: Adds mock summary for codegraph pipeline
* refacotr: Add current development status
Save current development status
Refactor
* Fix langfuse
* Fix langfuse
* Fix langfuse
* Add evaluation notebook
* Rename eval notebook
* chore: Add temporary state of development
Add temp development state to branch
Chore
* fix: Add poetry.lock file, make langfuse mandatory
Added langfuse as mandatory dependency, added poetry.lock file
Fix
* Fix: fixes langfuse config settings
* feat: Add deletion of local files made by cognee through data endpoint
Delete local files made by cognee when deleting data from database through endpoint
Feature COG-475
* test: Revert changes on test_pgvector
Revert changes on test_pgvector which were made to test deletion of local files
Test COG-475
* chore: deletes the old test for the codegraph pipeline
* test: Add test to verify deletion of local files
Added test that checks local files created by cognee will be deleted and those not created by cognee won't
Test COG-475
* chore: deletes unused old version of the codegraph
* chore: deletes unused imports from code_graph_pipeline
* Ingest non-code files
* Fixing review findings
* Ingest non-code files (#395)
* Ingest non-code files
* Fixing review findings
* test: Update test regarding message
Update assertion message, add veryfing of file existence
* Handle retryerrors in code summary (#396)
* Handle retryerrors in code summary
* Log instead of print
* fix: updates the acreate_structured_output
* chore: Add logging to sentry when file which should exist can't be found
Log to sentry that a file which should exist can't be found
Chore COG-475
* Fix diagram
* fix: refactor mcp
* Add Smithery CLI installation instructions and badge
* Move readme
* Update README.md
* Update README.md
* Cog 813 source code chunks (#383)
* fix: pass the list of all CodeFiles to enrichment task
* feat: introduce SourceCodeChunk, update metadata
* feat: get_source_code_chunks code graph pipeline task
* feat: integrate get_source_code_chunks task, comment out summarize_code
* Fix code summarization (#387)
* feat: update data models
* feat: naive parse long strings in source code
* fix: get_non_py_files instead of get_non_code_files
* fix: limit recursion, add comment
* handle embedding empty input error (#398)
* feat: robustly handle CodeFile source code
* refactor: sort imports
* todo: add support for other embedding models
* feat: add custom logger
* feat: add robustness to get_source_code_chunks
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
* feat: improve embedding exceptions
* refactor: format indents, rename module
---------
Co-authored-by: alekszievr <44192193+alekszievr@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
* Fix diagram
* Fix diagram
* Fix instructions
* Fix instructions
* adding and fixing files
* Update README.md
* ruff format
* Fix linter issues
* Fix linter issues
* Fix linter issues
* Fix linter issues
* Fix linter issues
* Fix linter issues
* Fix linter issues
* Fix linter issues
* Fix linter issues
* Fix linter issues
* Implement PR review
* Comment out profiling
* Comment out profiling
* Comment out profiling
* fix: add allowed extensions
* fix: adhere UnstructuredDocument.read() to Document
* feat: time code graph run and add mock support
* Fix ollama, work on visualization
* fix: Fixes faulty logging format and sets up error logging in dynamic steps example
* Overcome ContextWindowExceededError by checking token count while chunking (#413)
* fix: Fixes duplicated edges in cognify by limiting the recursion depth in add datapoints
* Adjust AudioDocument and handle None token limit
* Handle azure models as well
* Fix visualization
* Fix visualization
* Fix visualization
* Add clean logging to code graph example
* Remove setting envvars from arg
* fix: fixes create_cognee_style_network_with_logo unit test
* fix: removes accidental remained print
* Fix visualization
* Fix visualization
* Fix visualization
* Get embedding engine instead of passing it. Get it from vector engine instead of direct getter.
* Fix visualization
* Fix visualization
* Fix poetry issues
* Get embedding engine instead of passing it in code chunking.
* Fix poetry issues
* Fix poetry issues
* Fix poetry issues
* Fix poetry issues
* Fix poetry issues
* Fix poetry issues
* Fix poetry issues
* Fix poetry issues
* chore: Update version of poetry install action
* chore: Update action to trigger on pull request for any branch
* chore: Remove if in github action to allow triggering on push
* chore: Remove if condition to allow gh actions to trigger on push to PR
* chore: Update poetry version in github actions
* chore: Set fixed ubuntu version to 22.04
* chore: Update py lint to use ubuntu 22.04
* chore: update ubuntu version to 22.04
* feat: implements the first version of graph based completion in search
* chore: Update python 3.9 gh action to use 3.12 instead
* chore: Update formatting of utils.py
* Fix poetry issues
* Fix poetry issues
* Fix poetry issues
* Fix poetry issues
* Fix poetry issues
* Fix poetry issues
* Fix poetry issues
* Adjust integration tests
* fix: Fixes ruff formatting
* Handle circular import
* fix: Resolve profiler issue with partial and recursive logger imports
Resolve issue for profiler with partial and recursive logger imports
* fix: Remove logger from __init__.py file
* test: Test profiling on HEAD branch
* test: Return profiler to base branch
* Set max_tokens in config
* Adjust SWE-bench script to code graph pipeline call
* Adjust SWE-bench script to code graph pipeline call
* fix: Add fix for accessing dictionary elements that don't exits
Using get for the text key instead of direct access to handle situation if the text key doesn't exist
* feat: Add ability to change graph database configuration through cognee
* feat: adds pydantic types to graph layer models
* test: Test ubuntu 24.04
* test: change all actions to ubuntu-latest
* feat: adds basic retriever for swe bench
* Match Ruff version in config to the one in github actions
* feat: implements code retreiver
* Fix: fixes unit test for codepart search
* Format with Ruff 0.9.0
* Fix: deleting incorrect repo path
* docs: Add LlamaIndex Cognee integration notebook
Added LlamaIndex Cognee integration notebook
* test: Add github action for testing llama index cognee integration notebook
* fix: resolve issue with langfuse dependency installation when integrating cognee in different packages
* version: Increase version to 0.1.21
* fix: update dependencies of the mcp server
* Update README.md
* Fix: Fixes logging setup
* feat: deletes on the fly embeddings as uses edge collections
* fix: Change nbformat on llama index integration notebook
* fix: Resolve api key issue with llama index integration notebook
* fix: Attempt to resolve issue with Ubuntu 24.04 segmentation fault
* version: Increase version to 0.1.22
---------
Co-authored-by: vasilije <vas.markovic@gmail.com>
Co-authored-by: Igor Ilic <igorilic03@gmail.com>
Co-authored-by: Igor Ilic <30923996+dexters1@users.noreply.github.com>
Co-authored-by: lxobr <122801072+lxobr@users.noreply.github.com>
Co-authored-by: alekszievr <44192193+alekszievr@users.noreply.github.com>
Co-authored-by: hajdul88 <52442977+hajdul88@users.noreply.github.com>
Co-authored-by: Vasilije <8619304+Vasilije1990@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: Rita Aleksziev <alekszievr@gmail.com>
Co-authored-by: Henry Mao <1828968+calclavia@users.noreply.github.com>
* feat: Add error handling in case user is already part of database and permission already given to group
Added error handling in case permission is already given to group and user is already part of group
Feature COG-656
* feat: Add user verification for accessing data
Verify user has access to data before returning it
Feature COG-656
* feat: Add compute search to cognee
Add compute search to cognee which makes searches human readable
Feature COG-656
* feat: Add simple instruction for system prompt
Add simple instruction for system prompt
Feature COG-656
* pass pydantic model tocognify
* feat: Add unauth access error to getting data
Raise unauth access error when trying to read data without access
Feature COG-656
* refactor: Rename query compute to query completion
Rename searching type from compute to completion
Refactor COG-656
* chore: Update typo in code
Update typo in string in code
Chore COG-656
* Add mcp to cognee
* Add simple README
* Update cognee-mcp/mcpcognee/__main__.py
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
* Create dockerhub.yml
* Update get_cognify_router.py
* fix: Resolve reflection issue when running cognee a second time after pruning data
When running cognee a second time after pruning data some metadata doesn't get pruned.
This makes cognee believe some tables exist that have been deleted
Fix
* fix: Add metadata reflection fix to sqlite as well
Added fix when reflecting metadata to sqlite as well
Fix
* update
* Revert "fix: Add metadata reflection fix to sqlite as well"
This reverts commit 394a0b2dfb.
* COG-810 Implement a top-down dependency graph builder tool (#268)
* feat: parse repo to call graph
* Update/repo_processor/top_down_repo_parse.py task
* fix: minor improvements
* feat: file parsing jedi script optimisation
---------
* Add type to DataPoint metadata (#364)
* Add type to DataPoint metadata
* Add missing index_fields
* Use DataPoint UUID type in pgvector create_data_points
* Make _metadata mandatory everywhere
* Fixes
* Fixes to our demo
* feat: Add search by dataset for cognee
Added ability to search by datasets for cognee users
Feature COG-912
* feat: outsources chunking parameters to extract chunk from documents … (#289)
* feat: outsources chunking parameters to extract chunk from documents task
* fix: Remove backend lock from UI
Removed lock that prevented using multiple datasets in cognify
Fix COG-912
* COG 870 Remove duplicate edges from the code graph (#293)
* feat: turn summarize_code into generator
* feat: extract run_code_graph_pipeline, update the pipeline
* feat: minimal code graph example
* refactor: update argument
* refactor: move run_code_graph_pipeline to cognify/code_graph_pipeline
* refactor: indentation and whitespace nits
* refactor: add deprecated use comments and warnings
---------
Co-authored-by: Vasilije <8619304+Vasilije1990@users.noreply.github.com>
Co-authored-by: Igor Ilic <30923996+dexters1@users.noreply.github.com>
Co-authored-by: Boris <boris@topoteretes.com>
* test: Added test for getting of documents for search
Added test to verify getting documents related to datasets intended for search
Test COG-912
* Structured code summarization (#375)
* feat: turn summarize_code into generator
* feat: extract run_code_graph_pipeline, update the pipeline
* feat: minimal code graph example
* refactor: update argument
* refactor: move run_code_graph_pipeline to cognify/code_graph_pipeline
* refactor: indentation and whitespace nits
* refactor: add deprecated use comments and warnings
* Structured code summarization
* add missing prompt file
* Remove summarization_model argument from summarize_code and fix typehinting
* minor refactors
---------
Co-authored-by: lxobr <122801072+lxobr@users.noreply.github.com>
Co-authored-by: Vasilije <8619304+Vasilije1990@users.noreply.github.com>
Co-authored-by: Igor Ilic <30923996+dexters1@users.noreply.github.com>
Co-authored-by: Boris <boris@topoteretes.com>
* fix: Resolve issue with cognify router graph model default value
Resolve issue with default value for graph model in cognify endpoint
Fix
* chore: Resolve typo in getting documents code
Resolve typo in code
chore COG-912
* Update .github/workflows/dockerhub.yml
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
* Update .github/workflows/dockerhub.yml
* Update .github/workflows/dockerhub.yml
* Update .github/workflows/dockerhub.yml
* Update get_cognify_router.py
* fix: Resolve syntax issue with cognify router
Resolve syntax issue with cognify router
Fix
* feat: Add ruff pre-commit hook for linting and formatting
Added formatting and linting on pre-commit hook
Feature COG-650
* chore: Update ruff lint options in pyproject file
Update ruff lint options in pyproject file
Chore
* test: Add ruff linter github action
Added linting check with ruff in github actions
Test COG-650
* feat: deletes executor limit from get_repo_file_dependencies
* feat: implements mock feature in LiteLLM engine
* refactor: Remove changes to cognify router
Remove changes to cognify router
Refactor COG-650
* fix: fixing boolean env for github actions
* test: Add test for ruff format for cognee code
Test if code is formatted for cognee
Test COG-650
* refactor: Rename ruff gh actions
Rename ruff gh actions to be more understandable
Refactor COG-650
* chore: Remove checking of ruff lint and format on push
Remove checking of ruff lint and format on push
Chore COG-650
* feat: Add deletion of local files when deleting data
Delete local files when deleting data from cognee
Feature COG-475
* fix: changes back the max workers to 12
* feat: Adds mock summary for codegraph pipeline
* refacotr: Add current development status
Save current development status
Refactor
* Fix langfuse
* Fix langfuse
* Fix langfuse
* Add evaluation notebook
* Rename eval notebook
* chore: Add temporary state of development
Add temp development state to branch
Chore
* fix: Add poetry.lock file, make langfuse mandatory
Added langfuse as mandatory dependency, added poetry.lock file
Fix
* Fix: fixes langfuse config settings
* feat: Add deletion of local files made by cognee through data endpoint
Delete local files made by cognee when deleting data from database through endpoint
Feature COG-475
* test: Revert changes on test_pgvector
Revert changes on test_pgvector which were made to test deletion of local files
Test COG-475
* chore: deletes the old test for the codegraph pipeline
* test: Add test to verify deletion of local files
Added test that checks local files created by cognee will be deleted and those not created by cognee won't
Test COG-475
* chore: deletes unused old version of the codegraph
* chore: deletes unused imports from code_graph_pipeline
* Ingest non-code files
* Fixing review findings
* Ingest non-code files (#395)
* Ingest non-code files
* Fixing review findings
* test: Update test regarding message
Update assertion message, add veryfing of file existence
* Handle retryerrors in code summary (#396)
* Handle retryerrors in code summary
* Log instead of print
* fix: updates the acreate_structured_output
* chore: Add logging to sentry when file which should exist can't be found
Log to sentry that a file which should exist can't be found
Chore COG-475
* Fix diagram
* fix: refactor mcp
* Add Smithery CLI installation instructions and badge
* Move readme
* Update README.md
* Update README.md
* Cog 813 source code chunks (#383)
* fix: pass the list of all CodeFiles to enrichment task
* feat: introduce SourceCodeChunk, update metadata
* feat: get_source_code_chunks code graph pipeline task
* feat: integrate get_source_code_chunks task, comment out summarize_code
* Fix code summarization (#387)
* feat: update data models
* feat: naive parse long strings in source code
* fix: get_non_py_files instead of get_non_code_files
* fix: limit recursion, add comment
* handle embedding empty input error (#398)
* feat: robustly handle CodeFile source code
* refactor: sort imports
* todo: add support for other embedding models
* feat: add custom logger
* feat: add robustness to get_source_code_chunks
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
* feat: improve embedding exceptions
* refactor: format indents, rename module
---------
Co-authored-by: alekszievr <44192193+alekszievr@users.noreply.github.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
* Fix diagram
* Fix instructions
* adding and fixing files
* Update README.md
* ruff format
* Fix linter issues
* Implement PR review
* Comment out profiling
* fix: add allowed extensions
* fix: adhere UnstructuredDocument.read() to Document
* feat: time code graph run and add mock support
* Fix ollama, work on visualization
* fix: Fixes faulty logging format and sets up error logging in dynamic steps example
* Overcome ContextWindowExceededError by checking token count while chunking (#413)
* fix: Fixes duplicated edges in cognify by limiting the recursion depth in add datapoints
* Adjust AudioDocument and handle None token limit
* Handle azure models as well
* Add clean logging to code graph example
* Remove setting envvars from arg
* fix: fixes create_cognee_style_network_with_logo unit test
* fix: removes accidental remained print
* Get embedding engine instead of passing it. Get it from vector engine instead of direct getter.
* Fix visualization
* Get embedding engine instead of passing it in code chunking.
* Fix poetry issues
* chore: Update version of poetry install action
* chore: Update action to trigger on pull request for any branch
* chore: Remove if in github action to allow triggering on push
* chore: Remove if condition to allow gh actions to trigger on push to PR
* chore: Update poetry version in github actions
* chore: Set fixed ubuntu version to 22.04
* chore: Update py lint to use ubuntu 22.04
* chore: update ubuntu version to 22.04
* feat: implements the first version of graph based completion in search
* chore: Update python 3.9 gh action to use 3.12 instead
* chore: Update formatting of utils.py
* Fix poetry issues
* Adjust integration tests
* fix: Fixes ruff formatting
* Handle circular import
* fix: Resolve profiler issue with partial and recursive logger imports
Resolve issue for profiler with partial and recursive logger imports
* fix: Remove logger from __init__.py file
* test: Test profiling on HEAD branch
* test: Return profiler to base branch
* Set max_tokens in config
* Adjust SWE-bench script to code graph pipeline call
* Adjust SWE-bench script to code graph pipeline call
* fix: Add fix for accessing dictionary elements that don't exits
Using get for the text key instead of direct access to handle situation if the text key doesn't exist
* feat: Add ability to change graph database configuration through cognee
* feat: adds pydantic types to graph layer models
* feat: adds basic retriever for swe bench
* Match Ruff version in config to the one in github actions
* feat: implements code retreiver
* Fix: fixes unit test for codepart search
* Format with Ruff 0.9.0
* Fix: deleting incorrect repo path
* fix: resolve issue with langfuse dependency installation when integrating cognee in different packages
* version: Increase version to 0.1.21
---------
Co-authored-by: Igor Ilic <igorilic03@gmail.com>
Co-authored-by: Vasilije <8619304+Vasilije1990@users.noreply.github.com>
Co-authored-by: Igor Ilic <30923996+dexters1@users.noreply.github.com>
Co-authored-by: Rita Aleksziev <alekszievr@gmail.com>
Co-authored-by: vasilije <vas.markovic@gmail.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Co-authored-by: lxobr <122801072+lxobr@users.noreply.github.com>
Co-authored-by: alekszievr <44192193+alekszievr@users.noreply.github.com>
Co-authored-by: hajdul88 <52442977+hajdul88@users.noreply.github.com>
Co-authored-by: Henry Mao <1828968+calclavia@users.noreply.github.com>
* feat: log search queries and results
* fix: address coderabbit review comments
* fix: parse UUID when logging search results
* fix: remove custom UUID type and use DB agnostic UUID from sqlalchemy
* Add new cognee_db
---------
Co-authored-by: Leon Luithlen <leon@topoteretes.com>
* feat: Add support for LlamaIndex Document type
Added support for LlamaIndex Document type
Feature #COG-337
* docs: Add Jupyer Notebook for cognee with llama index document type
Added jupyter notebook which demonstrates cognee with LlamaIndex document type usage
Docs #COG-337
* feat: Add metadata migration from LlamaIndex document type
Allow usage of metadata from LlamaIndex documents
Feature #COG-337
* refactor: Change llama index migration function name
Change name of llama index function
Refactor #COG-337
* chore: Add llama index core dependency
Downgrade needed on tenacity and instructor modules to support llama index
Chore #COG-337
* Feature: Add ingest_data_with_metadata task
Added task that will have access to metadata if data is provided from different data ingestion tools
Feature #COG-337
* docs: Add description on why specific type checking is done
Explained why specific type checking is used instead of isinstance, as isinstace returns True for child classes as well
Docs #COG-337
* fix: Add missing parameter to function call
Added missing parameter to function call
Fix #COG-337
* refactor: Move storing of data from async to sync function
Moved data storing from async to sync
Refactor #COG-337
* refactor: Pretend ingest_data was changes instead of having two tasks
Refactor so ingest_data file was modified instead of having two ingest tasks
Refactor #COG-337
* refactor: Use old name for data ingestion with metadata
Merged new and old data ingestion tasks into one
Refactor #COG-337
* refactor: Return ingest_data and save_data_to_storage Tasks
Returned ingest_data and save_data_to_storage tasks
Refactor #COG-337
* refactor: Return previous ingestion Tasks to add function
Returned previous ignestion tasks to add function
Refactor #COG-337
* fix: Remove dict and use string for search query
Remove dictionary and use string for query in notebook and simple example
Fix COG-337
* refactor: Add changes request in pull request
Added the following changes that were requested in pull request:
Added synchronize label,
Made uniform syntax in if statement in workflow,
fixed instructor dependency,
added llama-index to be optional
Refactor COG-337
* fix: Resolve issue with llama-index being mandatory
Resolve issue with llama-index being mandatory to run cognee
Fix COG-337
* fix: Add install of llama-index to notebook
Removed additional references to llama-index from core cognee lib.
Added llama-index-core install from notebook
Fix COG-337
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* 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
