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Update cognee version and lock files
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## Description
Remove custom text file resolution, it sometimes wrongly marks other
file types as txt
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## Description
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Fixes https://github.com/topoteretes/cognee/issues/1681
We do not support AWS out of the box in MCP right now.
This PR enables users to select what extras they want to start their
`cognee-mcp` with, so users can extend MCP if need be.
## Testing
1. Added `AWS_REGION`, `AWS_ACCESS_KEY_ID`, and `AWS_SECRET_ACCESS_KEY`
into `.env`
2. Uploaded completely [generated
story](https://github.com/topoteretes/cognee-community/blob/main/packages/hybrid/duckdb/examples/simple_document_example/data/generated_story.txt)
into S3
3. Started mcp, using MCP inspector called `cognify` with s3 path to the
generated story
<img width="780" height="703" alt="Screenshot 2025-10-29 at 17 08 10"
src="https://github.com/user-attachments/assets/47157591-7243-4e87-befb-fb7ca6f3cf61"
/>
4. Called "search" tool with story-specific question
<img width="776" height="717" alt="Screenshot 2025-10-29 at 17 08 34"
src="https://github.com/user-attachments/assets/64ab25f4-80d6-4f8a-a982-17c2191c6503"
/>
### Logs
<details>
```
daulet@Mac cognee-claude % docker run \
-e TRANSPORT_MODE=sse \
-e EXTRAS=aws,postgres,neo4j \
--env-file ./.env \
-p 8121:8000 \
--rm -it cognee/cognee-mcp:custom-deps
Debug mode:
Environment:
Installing optional dependencies: aws,postgres,neo4j
Current cognee version: 0.3.7
Installing cognee with extras: aws,postgres,neo4j
Running: uv pip install 'cognee[aws,postgres,neo4j]==0.3.7'
Resolved 137 packages in 679ms
Prepared 7 packages in 484ms
Installed 7 packages in 86ms
+ aiobotocore==2.25.1
+ aioitertools==0.12.0
+ boto3==1.40.61
+ botocore==1.40.61
+ jmespath==1.0.1
+ s3fs==2025.3.2
+ s3transfer==0.14.0
✓ Optional dependencies installation completed
Transport mode: sse
Debug port: 5678
HTTP port: 8000
Direct mode: Using local cognee instance
Running database migrations...
2025-10-29T16:56:01.562650 [info ] Logging initialized [cognee.shared.logging_utils] cognee_version=0.3.7 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=3.12.12 relational_config=cognee_db structlog_version=25.4.0 vector_config=lancedb
2025-10-29T16:56:01.562816 [info ] Database storage: /app/.venv/lib/python3.12/site-packages/cognee/.cognee_system/databases [cognee.shared.logging_utils]
2025-10-29T16:56:01.782204 [warning ] Failed to import protego, make sure to install using pip install protego>=0.1 [cognee.shared.logging_utils]
2025-10-29T16:56:01.782403 [warning ] Failed to import playwright, make sure to install using pip install playwright>=1.9.0 [cognee.shared.logging_utils]
Database migrations done.
Starting Cognee MCP Server with transport mode: sse
2025-10-29T16:56:06.184893 [info ] Logging initialized [cognee.shared.logging_utils] cognee_version=0.3.7 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=3.12.12 relational_config=cognee_db structlog_version=25.4.0 vector_config=lancedb
2025-10-29T16:56:06.185069 [info ] Database storage: /app/.venv/lib/python3.12/site-packages/cognee/.cognee_system/databases [cognee.shared.logging_utils]
2025-10-29T16:56:06.245181 [warning ] Failed to import protego, make sure to install using pip install protego>=0.1 [cognee.shared.logging_utils]
2025-10-29T16:56:06.245327 [warning ] Failed to import playwright, make sure to install using pip install playwright>=1.9.0 [cognee.shared.logging_utils]
2025-10-29T16:56:06.582115 [info ] Cognee client initialized in direct mode [cognee.shared.logging_utils]
2025-10-29T16:56:06.582268 [info ] Starting MCP server with transport: sse [cognee.shared.logging_utils]
2025-10-29T16:56:06.582618 [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)
INFO: 192.168.65.1:54572 - "GET /sse HTTP/1.1" 200 OK
INFO: 192.168.65.1:57034 - "GET /sse HTTP/1.1" 200 OK
INFO: 192.168.65.1:57104 - "GET /sse HTTP/1.1" 200 OK
INFO: 192.168.65.1:55411 - "POST /messages/?session_id=33fc2c041d184f3ab62597c69259d036 HTTP/1.1" 202 Accepted
INFO: 192.168.65.1:55411 - "POST /messages/?session_id=33fc2c041d184f3ab62597c69259d036 HTTP/1.1" 202 Accepted
INFO: 192.168.65.1:22986 - "POST /messages/?session_id=33fc2c041d184f3ab62597c69259d036 HTTP/1.1" 202 Accepted
Processing request of type CallToolRequest
2025-10-29T16:57:52.864665 [info ] Cognify process starting. [cognee.shared.logging_utils]
2025-10-29T16:57:58.159329 [info ] Pipeline run started: `469d4729-328a-542d-aac1-3ea4167d9b83` [run_tasks_with_telemetry()]
2025-10-29T16:57:58.332811 [info ] Coroutine task started: `resolve_data_directories` [run_tasks_base]
2025-10-29T16:57:58.604008 [info ] Coroutine task started: `ingest_data` [run_tasks_base]
2025-10-29T16:57:58.899181 [info ] Registered loader: pypdf_loader [cognee.infrastructure.loaders.LoaderEngine]
2025-10-29T16:57:58.899637 [info ] Registered loader: text_loader [cognee.infrastructure.loaders.LoaderEngine]
2025-10-29T16:57:58.899817 [info ] Registered loader: image_loader [cognee.infrastructure.loaders.LoaderEngine]
2025-10-29T16:57:58.899964 [info ] Registered loader: audio_loader [cognee.infrastructure.loaders.LoaderEngine]
2025-10-29T16:57:58.900103 [info ] Registered loader: unstructured_loader [cognee.infrastructure.loaders.LoaderEngine]
2025-10-29T16:57:58.900197 [info ] Registered loader: advanced_pdf_loader [cognee.infrastructure.loaders.LoaderEngine]
2025-10-29T16:57:58.900321 [info ] Registered loader: beautiful_soup_loader [cognee.infrastructure.loaders.LoaderEngine]
2025-10-29T16:57:59.022385 [info ] Coroutine task completed: `ingest_data` [run_tasks_base]
2025-10-29T16:57:59.183862 [info ] Coroutine task completed: `resolve_data_directories` [run_tasks_base]
2025-10-29T16:57:59.347932 [info ] Pipeline run completed: `469d4729-328a-542d-aac1-3ea4167d9b83` [run_tasks_with_telemetry()]
2025-10-29T16:57:59.600721 [info ] Loaded JSON extension [cognee.shared.logging_utils]
2025-10-29T16:57:59.616370 [info ] Ontology file 'None' not found. No owl ontology will be attached to the graph. [OntologyAdapter]
2025-10-29T16:57:59.633495 [info ] Pipeline run started: `21372a56-1d44-5e19-a024-209d03a99218` [run_tasks_with_telemetry()]
2025-10-29T16:57:59.784198 [info ] Coroutine task started: `classify_documents` [run_tasks_base]
2025-10-29T16:57:59.933817 [info ] Coroutine task started: `check_permissions_on_dataset` [run_tasks_base]
2025-10-29T16:58:00.147315 [info ] Async Generator task started: `extract_chunks_from_documents` [run_tasks_base]
2025-10-29T16:58:00.366572 [info ] Coroutine task started: `extract_graph_from_data` [run_tasks_base]
2025-10-29T16:58:51.639973 [info ] No close match found for 'person' in category 'classes' [OntologyAdapter]
2025-10-29T16:58:51.642293 [info ] No close match found for 'khaélith orun' in category 'individuals' [OntologyAdapter]
2025-10-29T16:58:51.642456 [info ] No close match found for 'location' in category 'classes' [OntologyAdapter]
2025-10-29T16:58:51.642551 [info ] No close match found for 'vorrxundra' in category 'individuals' [OntologyAdapter]
2025-10-29T16:58:51.642632 [info ] No close match found for 'creature' in category 'classes' [OntologyAdapter]
2025-10-29T16:58:51.642739 [info ] No close match found for 'thirvalque' in category 'individuals' [OntologyAdapter]
2025-10-29T16:58:51.642823 [info ] No close match found for 'ossaryn' in category 'individuals' [OntologyAdapter]
2025-10-29T16:58:51.642928 [info ] No close match found for 'fyrneloch' in category 'individuals' [OntologyAdapter]
2025-10-29T16:58:51.643126 [info ] No close match found for 'mirror-river' in category 'individuals' [OntologyAdapter]
2025-10-29T16:58:51.643237 [info ] No close match found for 'zyrrhalin' in category 'individuals' [OntologyAdapter]
2025-10-29T16:58:51.643325 [info ] No close match found for 'artifact' in category 'classes' [OntologyAdapter]
2025-10-29T16:58:51.643410 [info ] No close match found for 'crystal plates' in category 'individuals' [OntologyAdapter]
2025-10-29T16:58:51.643468 [info ] No close match found for 'concept' in category 'classes' [OntologyAdapter]
2025-10-29T16:58:51.643551 [info ] No close match found for 'forgotten futures' in category 'individuals' [OntologyAdapter]
2025-10-29T16:58:52.968522 [info ] Coroutine task started: `summarize_text` [run_tasks_base]
2025-10-29T16:59:03.982055 [info ] Coroutine task started: `add_data_points` [run_tasks_base]
2025-10-29T16:59:04.884215 [info ] Coroutine task completed: `add_data_points` [run_tasks_base]
2025-10-29T16:59:05.038833 [info ] Coroutine task completed: `summarize_text` [run_tasks_base]
2025-10-29T16:59:05.200412 [info ] Coroutine task completed: `extract_graph_from_data` [run_tasks_base]
2025-10-29T16:59:05.361403 [info ] Async Generator task completed: `extract_chunks_from_documents` [run_tasks_base]
2025-10-29T16:59:05.529879 [info ] Coroutine task completed: `check_permissions_on_dataset` [run_tasks_base]
2025-10-29T16:59:05.694801 [info ] Coroutine task completed: `classify_documents` [run_tasks_base]
2025-10-29T16:59:05.852353 [info ] Pipeline run completed: `21372a56-1d44-5e19-a024-209d03a99218` [run_tasks_with_telemetry()]
2025-10-29T16:59:06.042754 [info ] Cognify process finished. [cognee.shared.logging_utils]
INFO: 192.168.65.1:25778 - "POST /messages/?session_id=33fc2c041d184f3ab62597c69259d036 HTTP/1.1" 202 Accepted
Processing request of type CallToolRequest
2025-10-29T17:01:03.372413 [info ] Graph projection completed: 17 nodes, 33 edges in 0.01s [CogneeGraph]
2025-10-29T17:01:03.790022 [info ] Vector collection retrieval completed: Retrieved distances from 6 collections in 0.07s [cognee.shared.logging_utils]
```
</details>
## 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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- [ ] Code refactoring
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## 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**
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issue/feature**
- [ ] My code follows the project's coding standards and style
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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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## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
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## Description
Fix issue with logs
## Type of Change
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- [ ] New feature (non-breaking change that adds functionality)
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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
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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
Remove custom PDF handling and let filetype handle PDF documents
## Type of Change
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- [ ] I have added tests that prove my fix is effective or that my
feature works
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- [ ] All new and existing tests pass
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submitted already
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## DCO Affirmation
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the terms of the Topoteretes Developer Certificate of Origin.
<!-- .github/pull_request_template.md -->
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process and reasoning.
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## 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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- [ ] Other (please specify):
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guidelines
- [ ] I have added tests that prove my fix is effective or that my
feature works
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submitted already
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## DCO Affirmation
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the terms of the Topoteretes Developer Certificate of Origin.
<!-- .github/pull_request_template.md -->
## Description
Remove fallback when provided vector adapter is not reckognized to use
LanceDB. When no adapter provider info is provided LanceDB will still be
used.
## 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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feature works
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submitted already
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## DCO Affirmation
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the terms of the Topoteretes Developer Certificate of Origin.
<!-- .github/pull_request_template.md -->
## Description
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## Description
In case of a read-only file system handle the inability to create an
.anon_id file
## Type of Change
<!-- Please check the relevant option -->
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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
Adds the concept of now to the qa for temporal queries
## 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
<!-- 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
Adds multifile ontology support
## 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
- [x] Code refactoring
- [ ] Performance improvement
- [ ] Other (please specify):
## Screenshots/Videos (if applicable)
None
## 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
- [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.
…de ID
<!-- .github/pull_request_template.md -->
## Description
Update description of relational database column to use relational
database ID value instead of graph node ID value
## 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
Enable Cognee to work on read only file systems by avoiding use of file
handler when logging if log file location is read only
## 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):
## 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
Adds new tenant id (if available) to telemetry packages for basic cognee
operations
## 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
<!-- 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.
## Description
Updated the Ollama embedding API endpoint in `.env.template` from
`/api/embeddings` to `/api/embed` to align with Ollama's current API
standards. The `/api/embeddings` endpoint has been deprecated and
superseded by `/api/embed`, which is now the recommended endpoint for
generating vector embeddings.
This change ensures users following the template will configure the
correct endpoint when setting up Ollama integration, preventing
potential API errors and maintaining compatibility with current Ollama
versions.
## Type of Change
- [x] Bug fix (non-breaking change that fixes an issue)
- [x] Documentation update
## Screenshots/Videos (if applicable)
N/A - Configuration file change only
## 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
- [ ] I have added tests that prove my fix is effective or that my
feature works *(N/A for template changes)*
- [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
- [ ] I have linked any relevant issues in the description *(link if
available)*
- [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.
