Update aiofiles version constraint in pyproject.toml

[siillee]

Update aiofiles version constraint from <24.0.0 to <25.1.0 to resolve conflict with Microsoft agent-framework which requires aiofiles >=24.0.1.

Fixes #1829

Description

Type of Change

• 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)

Pre-submission Checklist

• 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-checklist]

Please make sure all the checkboxes are checked:

• I have tested these changes locally.
• I have reviewed the code changes.
• I have added end-to-end and unit tests (if applicable).
• I have updated the documentation and README.md file (if necessary).
• I have removed unnecessary code and debug statements.
• PR title is clear and follows the convention.
• I have tagged reviewers or team members for feedback.

[coderabbitai]

Walkthrough

This PR updates documentation across two README files with restructured sections, expanded quickstart guidance, and new feature listings. It also modifies OllamaEmbeddingEngine to handle alternative response JSON shapes by adding fallback logic to support multiple endpoint response formats.

Changes

Cohort / File(s)	Summary
README Documentation Restructuring README.md	Extensive rewrite reorganizing content into new sections (About Cognee, Basic Usage & Feature Guide, Quickstart, Demos & Examples). Added step-by-step installation and configuration guidance with code blocks. Expanded usage examples to cover both Python workflow and CLI. Updated deployment sections (Open Source vs Cloud). Revised branding, headers, and links. Updated BibTeX citation entry.
MCP Tools Documentation cognee-mcp/README.md	Added new MCP tools to documentation (cognee_add_developer_rules, delete, get_developer_rules, save_interaction). Extended search tool capabilities to include SUMMARIES, CYPHER, and FEELING_LUCKY search modes.
Ollama Embedding Response Handling cognee/infrastructure/databases/vector/embeddings/OllamaEmbeddingEngine.py	Modified _get_embedding() to support alternative response shapes. Added fallback logic: if response contains "embeddings" key, returns first embedding; otherwise falls back to data["data"][0]["embedding"] structure.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

• OllamaEmbeddingEngine.py: Verify fallback response handling correctly prioritizes the "embeddings" key and that the fallback path properly handles the alternative response structure. Ensure both response formats are tested.
• README.md: Extensive content reorganization is largely editorial, but verify all links, code examples, and cross-references are accurate and point to correct destinations.
• cognee-mcp/README.md: Confirm new tools and search modes are accurately described and correspond to actual implementation.

Possibly related PRs

• Handle multiple response formats in OllamaEmbeddingEngine #1735: Modifies OllamaEmbeddingEngine._get_embedding to handle multiple response JSON shapes with similar "embeddings" vs alternative structure logic.
• docs: Fix Readme Instructions #1706: Overlapping README content and branding updates with similar section rewording and link restructuring.
• docs(mcp): update available tools documentation #1740: Directly related; modifies cognee-mcp/README.md to add the same new MCP tools and expanded search options.

Suggested labels

run-checks

Suggested reviewers

• borisarzentar
• dexters1
• Vasilije1990

Poem

🐰 A README blooms with structure anew,
Three formats dance where responses once flew,
Quickstarts and guides now light the way,
While Ollama learns to speak both its ways today! 🌟

Pre-merge checks

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Out of Scope Changes check	⚠️ Warning	The PR summary shows changes to README files and OllamaEmbeddingEngine.py that are unrelated to the aiofiles version constraint update in pyproject.toml.	Remove unrelated changes (README updates and OllamaEmbeddingEngine modifications) from this PR or create separate PRs for each distinct scope.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The PR title directly and specifically summarizes the main change: updating the aiofiles version constraint in pyproject.toml.
Description check	✅ Passed	The PR description explains the purpose (resolve dependency conflict with Microsoft agent-framework) and references issue #1829, though the template checklist boxes remain unchecked.
Linked Issues check	✅ Passed	The PR fulfills issue #1829 by updating aiofiles constraint from <24.0.0 to <25.1.0, resolving the conflict with Microsoft agent-framework that requires >=24.0.1.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

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[coderabbitai]

Actionable comments posted: 0

🧹 Nitpick comments (1)

cognee/infrastructure/databases/vector/embeddings/OllamaEmbeddingEngine.py (1)

120-130: Make embedding extraction more defensive and explicit on unexpected response shapes

The new branch covers both "embeddings" and "data"[0]["embedding"] formats, but it will still raise KeyError/IndexError with little context if the API ever returns an unexpected shape (or an empty list). It would be safer to validate the structure and raise a clear error (and/or log) when neither format matches.

For example:

-                data = await response.json()
-                if "embeddings" in data:
-                    return data["embeddings"][0]
-                else:
-                    return data["data"][0]["embedding"]
+                data = await response.json()
+
+                if "embeddings" in data and isinstance(data["embeddings"], list):
+                    return data["embeddings"][0]
+
+                if (
+                    "data" in data
+                    and isinstance(data["data"], list)
+                    and data["data"]
+                    and "embedding" in data["data"][0]
+                ):
+                    return data["data"][0]["embedding"]
+
+                logger.error("Unexpected embedding response format from Ollama: %s", data)
+                raise ValueError("Unexpected embedding response format from Ollama")

This keeps the intended behavior while failing fast with a useful message if the API contract changes.

📜 Review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 508165e and f7e072f.

⛔ Files ignored due to path filters (5)

• .github/release-drafter.yml is excluded by !**/*.yml
• .mergify.yml is excluded by !**/*.yml
• poetry.lock is excluded by !**/*.lock, !**/*.lock
• pyproject.toml is excluded by !**/*.toml
• uv.lock is excluded by !**/*.lock, !**/*.lock

📒 Files selected for processing (3)

• README.md (5 hunks)
• cognee-mcp/README.md (1 hunks)
• cognee/infrastructure/databases/vector/embeddings/OllamaEmbeddingEngine.py (1 hunks)

🧰 Additional context used

📓 Path-based instructions (3)

**/*.py

📄 CodeRabbit inference engine (AGENTS.md)

**/*.py: Use 4-space indentation in Python code
Use snake_case for Python module and function names
Use PascalCase for Python class names
Use ruff format before committing Python code
Use ruff check for import hygiene and style enforcement with line-length 100 configured in pyproject.toml
Prefer explicit, structured error handling in Python code

Files:

• cognee/infrastructure/databases/vector/embeddings/OllamaEmbeddingEngine.py

cognee/**/*.py

📄 CodeRabbit inference engine (AGENTS.md)

Use shared logging utilities from cognee.shared.logging_utils in Python code

Files:

• cognee/infrastructure/databases/vector/embeddings/OllamaEmbeddingEngine.py

cognee/{modules,infrastructure,tasks}/**/*.py

📄 CodeRabbit inference engine (AGENTS.md)

Co-locate feature-specific helpers under their respective package (modules/, infrastructure/, or tasks/)

Files:

• cognee/infrastructure/databases/vector/embeddings/OllamaEmbeddingEngine.py

🧠 Learnings (2)

📚 Learning: 2025-11-24T16:45:09.996Z

Learnt from: CR
Repo: topoteretes/cognee PR: 0
File: AGENTS.md:0-0
Timestamp: 2025-11-24T16:45:09.996Z
Learning: Applies to {cognee-mcp,cognee-frontend}/**/*.{js,ts,tsx} : Follow local README.md and ESLint/TypeScript configuration in cognee-frontend/ for MCP server and Frontend code

Applied to files:

• cognee-mcp/README.md

📚 Learning: 2025-10-11T04:18:24.594Z

Learnt from: Vattikuti-Manideep-Sitaram
Repo: topoteretes/cognee PR: 1529
File: cognee/api/v1/cognify/ontology_graph_pipeline.py:69-74
Timestamp: 2025-10-11T04:18:24.594Z
Learning: The code_graph_pipeline.py and ontology_graph_pipeline.py both follow an established pattern of calling cognee.prune.prune_data() and cognee.prune.prune_system(metadata=True) at the start of pipeline execution. This appears to be intentional behavior for pipeline operations in the cognee codebase.

Applied to files:

• cognee-mcp/README.md

🪛 LanguageTool

README.md

[grammar] ~66-~66: Ensure spelling is correct
Context: ... width="50%" /> ## About Cognee Cognee is an open-source tool and platfo...

(QB_NEW_EN_ORTHOGRAPHY_ERROR_IDS_1)

---

[grammar] ~191-~191: Ensure spelling is correct
Context: ...86b2e-305a-42b0-9c2d-9f4473f15df8) ### Cognee with Ollama [Watch Demo](https://githu...

(QB_NEW_EN_ORTHOGRAPHY_ERROR_IDS_1)

---

[style] ~199-~199: Using many exclamation marks might seem excessive (in this case: 7 exclamation marks for a text that’s 4270 characters long)
Context: ...welcome contributions from the community! Your input helps make Cognee better for...

(EN_EXCESSIVE_EXCLAMATION)

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (22)

• GitHub Check: CLI Tests / CLI Unit Tests
• GitHub Check: End-to-End Tests / Conversation sessions test (FS)
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• GitHub Check: End-to-End Tests / Concurrent Subprocess access test
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🔇 Additional comments (2)

cognee-mcp/README.md (1)

444-463: Tool list updates read clearly and match the surrounding feature descriptions

The new entries for cognee_add_developer_rules, delete, get_developer_rules, save_interaction, and the expanded search description are concise and consistent with the earlier “Developer rules bootstrap”/data‑management narrative. I don’t see any issues here.

README.md (1)

8-219: Expanded README structure and examples look consistent and actionable

The new intro, “About Cognee”, Quickstart, demos, and community sections are well‑structured and the Python/CLI examples are coherent (async usage, LLM_API_KEY, cognee.add/cognify/memify/search, and cognee-cli commands all line up logically). The static grammar/style hints around “platform”/“Ollama” and exclamation usage don’t indicate any real issues here, so I wouldn’t change anything based on them.

[pazone]

@siillee These are many previous commits in the PR. Make sure that the branch is rebased

[siillee]

@siillee These are many previous commits in the PR. Make sure that the branch is rebased

Yeah the problem was main and dev were not synced fully, Igor and I fixed it.

[dexters1]

Already resolved on dev branch