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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.
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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)
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- [ ] Performance improvement
- [ ] Other (please specify):
## Changes Made
<!-- List the specific changes made in this PR -->
-
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-
## 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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## Related Issues
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## DCO Affirmation
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## Type of Change
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## Changes Made
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## Summary
The `root_dir.py/ensure_absolute_path` validation in the `GraphConfig`
model currently enforces that all paths start with `/`.
This works for local file system paths but breaks when using S3 storage,
since S3 paths do not begin with `/` and fail validation.
## Fix
This PR updates the `ensure_absolute_path` method to recognize and treat
S3 paths as valid.
## Logs before
```
(.venv) daulet@Mac cognee-claude % cognee-cli -ui
2025-09-18T01:30:39.768877 [info ] Deleted old log file: /Users/daulet/Desktop/dev/cognee-claude/logs/2025-09-18_02-15-14.log [cognee.shared.logging_utils]
2025-09-18T01:30:40.391407 [error ] Exception [cognee.shared.logging_utils] exception_message="1 validation error for GraphConfig\n Value error, Path must be absolute. Got relative path: s3://daulet-personal-dev/cognee/data [type=value_error, input_value={'data_root_directory': '...45daea63bc5392d85746fb'}, input_type=dict]\n For further information visit https://errors.pydantic.dev/2.11/v/value_error" traceback=True
```
## Logs after
```
(.venv) daulet@Mac cognee-claude % cognee-cli -ui
2025-09-18T01:34:34.404642 [info ] Deleted old log file: /Users/daulet/Desktop/dev/cognee-claude/logs/2025-09-18_02-17-55.log [cognee.shared.logging_utils]
2025-09-18T01:34:35.026078 [info ] Logging initialized [cognee.shared.logging_utils] cognee_version=0.3.4.dev1-local database_path=s3://daulet-personal-dev/cognee/system/databases graph_database_name= os_info='Darwin 24.5.0 (Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132)' python_version=3.10.11 relational_config=cognee_db structlog_version=25.4.0 vector_config=lancedb
2025-09-18T01:34:35.026223 [info ] Database storage: s3://daulet-personal-dev/cognee/system/databases [cognee.shared.logging_utils]
Starting cognee UI...
2025-09-18T01:34:36.105617 [info ] Starting cognee UI... [cognee.shared.logging_utils]
2025-09-18T01:34:36.105756 [info ] Starting cognee backend API server... [cognee.shared.logging_utils]
2025-09-18T01:34:37.522194 [info ] Logging initialized [cognee.shared.logging_utils] cognee_version=0.3.4.dev1-local database_path=s3://daulet-personal-dev/cognee/system/databases graph_database_name= os_info='Darwin 24.5.0 (Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132)' python_version=3.10.11 relational_config=cognee_db structlog_version=25.4.0 vector_config=lancedb
2025-09-18T01:34:37.522376 [info ] Database storage: s3://daulet-personal-dev/cognee/system/databases [cognee.shared.logging_utils]
2025-09-18T01:34:38.115247 [info ] ✓ Backend API started at http://localhost:8000 [cognee.shared.logging_utils]
2025-09-18T01:34:38.198637 [info ] Starting frontend server at http://localhost:3000 [cognee.shared.logging_utils]
2025-09-18T01:34:38.198879 [info ] This may take a moment to compile and start... [cognee.shared.logging_utils]
INFO: Started server process [83608]
INFO: Waiting for application startup.
2025-09-18T01:34:39.781430 [warning ] Kuzu S3 storage file not found: s3://daulet-personal-dev/cognee/system/databases/cognee_graph_kuzu [cognee.shared.logging_utils]
2025-09-18T01:34:39.802516 [info ] Loaded JSON extension [cognee.shared.logging_utils]
2025-09-18T01:34:40.197857 [info ] Deleted Kuzu database files at s3://daulet-personal-dev/cognee/system/databases/cognee_graph_kuzu [cognee.shared.logging_utils]
2025-09-18T01:34:41.211523 [info ] ✓ Cognee UI is starting up... [cognee.shared.logging_utils]
2025-09-18T01:34:41.212561 [info ] ✓ Open your browser to: http://localhost:3000 [cognee.shared.logging_utils]
2025-09-18T01:34:41.212814 [info ] ✓ The UI will be available once Next.js finishes compiling [cognee.shared.logging_utils]
Success: UI server started successfully!
The interface is available at: http://localhost:3000
The API backend is available at: http://localhost:8000
Note: Press Ctrl+C to stop the server...
```
## Description
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this PR.
DO NOT use AI-generated descriptions. We want to understand your thought
process and reasoning.
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## Type of Change
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- [ ] New feature (non-breaking change that adds functionality)
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functionality to change)
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- [ ] Other (please specify):
## Changes Made
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## Testing
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## Screenshots/Videos (if applicable)
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## Related Issues
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## Description
Fixes infinite loop introduced in combined search refactor
## Type of Change
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- [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
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## Changes Made
<!-- List the specific changes made in this PR -->
Fixes infinite loop introduced in combined search refactor
## Testing
Manual
## Screenshots/Videos (if applicable)
None
## Pre-submission Checklist
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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
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- [x] My commits have clear and descriptive messages
## Related Issues
https://github.com/topoteretes/cognee/pull/1341
## Additional Notes
None
## DCO Affirmation
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the terms of the Topoteretes Developer Certificate of Origin.
---------
Co-authored-by: Igor Ilic <igorilic03@gmail.com>
Co-authored-by: Igor Ilic <30923996+dexters1@users.noreply.github.com>
Co-authored-by: hajdul88 <52442977+hajdul88@users.noreply.github.com>
Co-authored-by: Gao,Wei <kaovip@gmail.com>
Co-authored-by: Vasilije <8619304+Vasilije1990@users.noreply.github.com>
Co-authored-by: Andrej Milicevic <milicevicandrej@yahoo.com>
Co-authored-by: Daulet Amirkhanov <damirkhanov01@gmail.com>
<!-- .github/pull_request_template.md -->
## Description
<!--
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this PR.
DO NOT use AI-generated descriptions. We want to understand your thought
process and reasoning.
-->
Add more details to README.md on how to install cognee to be able to run
`cognee-cli -ui`
## 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)
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functionality to change)
- [X] Documentation update
- [ ] Code refactoring
- [ ] Performance improvement
- [ ] Other (please specify):
## Changes Made
<!-- List the specific changes made in this PR -->
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-
-
## Testing
<!-- Describe how you tested your changes -->
## Screenshots/Videos (if applicable)
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<!-- .github/pull_request_template.md -->
## Description
Resolves issue with file path handling of some uploaded files in Cognee
## Type of Change
<!-- Please check the relevant option -->
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- [ ] New feature (non-breaking change that adds functionality)
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## Testing
Uploaded file that had issue and was successfully resolved
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## Description
Resolve issue with getting role objects for user
## Type of Change
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## Description
Enable Data object serialization when returning PipelineRunInfo type
objects in backend
## Type of Change
<!-- Please check the relevant option -->
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- [ ] Other (please specify):
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… pipeline in backend
<!-- .github/pull_request_template.md -->
## Description
Resolve issue with cognify backend error message serialization
## Type of Change
<!-- Please check the relevant option -->
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## Testing
Reproduced error it is handled appropriately
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## Description
Make Cypher search optional
## Type of Change
<!-- Please check the relevant option -->
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- [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
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---------
Co-authored-by: Igor Ilic <igorilic03@gmail.com>
Co-authored-by: Igor Ilic <30923996+dexters1@users.noreply.github.com>
Co-authored-by: hajdul88 <52442977+hajdul88@users.noreply.github.com>
Co-authored-by: Gao,Wei <kaovip@gmail.com>
Co-authored-by: Vasilije <8619304+Vasilije1990@users.noreply.github.com>
Co-authored-by: Andrej Milicevic <milicevicandrej@yahoo.com>
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Co-authored-by: Vasilije <8619304+Vasilije1990@users.noreply.github.com>
Co-authored-by: Andrej Milicevic <milicevicandrej@yahoo.com>
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## Description
Fixes temporal graph ci/cd by deleting open ended asserts. Azure llm
handles the time extraction differently, however both of them are
correct
## 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)
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## Changes Made
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Deletes open ended asserts
## Testing
Manual
## Screenshots/Videos (if applicable)
None
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feature works
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- [x] All new and existing tests pass
- [x] I have searched existing PRs to ensure this change hasn't been
submitted already
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## Related Issues
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## Additional Notes
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## Description
Adds default value for last_k in search to avoid unwanted failure when
users don't provide the needed parameter.
## 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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- [x] Code refactoring
- [ ] Performance improvement
- [ ] Other (please specify):
## Changes Made
Add default value to last_k.
## Testing
Manual + tests are already present for the funtionality
## Screenshots/Videos (if applicable)
None
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guidelines
- [x] I have added tests that prove my fix is effective or that my
feature works
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- [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
None
## Additional Notes
None
## DCO Affirmation
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## Description
This PR adds default values and descriptions to the Timestamp pydantic
object used in temporal graph.
## Type of Change
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## Changes Made
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Adds default value and description to Timestamp pydantic object
## Testing
Tested it manually, althought I was unable to reproduce the issue
(therefore is probably a rare event), but based on the ci/cd logs I
fixed the cause.
## Screenshots/Videos (if applicable)
None
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guidelines
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feature works
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- [x] All new and existing tests pass
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submitted already
- [x] I have linked any relevant issues in the description
- [x] My commits have clear and descriptive messages
## Related Issues
None
## Additional Notes
None
## 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.
Compatible private embeddeding model (openai format)
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## Description
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this PR.
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process and reasoning.
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ChromaDB versions earlier than 0.4.13 don't work with pydantic v2. I
made some changes to the adapter to make it work for versions >= 0.6,
and I changed the chromadb version in the `pyproject.toml` file.
## Type of Change
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functionality to change)
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- [ ] Other (please specify):
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- [ ] All new and existing tests pass
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submitted already
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## Description
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this PR.
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Anthropic didn't work as an LLM Provider, and the issue was that our
versions of anthropic and httpx didn't work together. The solutions were
to either downgrade httpx, or upgrade anthropic. Since httpx is used by
various async clients, upgrading anthropic is the better approach.
## Type of Change
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functionality to change)
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feature works
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## Description
The PR fixes issue with CLI unit tests, where some of the tests were
starting UI because of unexpected MagicMock behavior causing infinite
test runs.
## Type of Change
<!-- Please check the relevant option -->
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## Changes Made
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- The PR fixes issue with CLI unit tests, where some of the tests were
starting UI because of unexpected MagicMock behavior causing infinite
test runs.
## Testing
Tested it via CI/CD + manually
## Screenshots/Videos (if applicable)
None
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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
None
## Additional Notes
None
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## Description
Vector URL fix, MCP Fix
## Type of Change
<!-- Please check the relevant option -->
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- [ ] New feature (non-breaking change that adds functionality)
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- [ ] Performance improvement
- [ ] Other (please specify):
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<!-- List the specific changes made in this PR -->
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<!-- Describe how you tested your changes -->
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feature works
- [ ] I have added necessary documentation (if applicable)
- [ ] All new and existing tests pass
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## DCO Affirmation
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---------
Co-authored-by: Boris <boris@topoteretes.com>
Co-authored-by: Boris Arzentar <borisarzentar@gmail.com>
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- [ ] New feature (non-breaking change that adds functionality)
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## Description
Increase default postgres connection pool
## 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
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- [ ] Code refactoring
- [ ] Performance improvement
- [ ] Other (please specify):
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<!-- List the specific changes made in this PR -->
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<!-- Describe how you tested your changes -->
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<!-- Add screenshots or videos to help explain your changes -->
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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.
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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.
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## 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 -->
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## 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
<!--
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 -->
- [ ] 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.
