COG 870 Remove duplicate edges from the code graph #293
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WalkthroughThe pull request introduces significant modifications across four files, primarily focusing on the Changes
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (2)
evals/eval_swe_bench.py (2)
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44-49: Consider moving imports inside the function to the top-level scopeThe imports within the
run_code_graph_pipelinefunction can be moved to the top of the module unless there is a specific reason to keep them inside the function (e.g., to avoid circular dependencies). This improves readability and follows Python's best practices.Proposed code change:
-async def run_code_graph_pipeline(repo_path): - import os - import pathlib - import cognee - from cognee.infrastructure.databases.relational import create_db_and_tables +import os +import pathlib +import cognee +from cognee.infrastructure.databases.relational import create_db_and_tables +async def run_code_graph_pipeline(repo_path):
71-71: Remove unused parametersearch_typeThe parameter
search_typein the functiongenerate_patch_with_cogneeis not used in the function body. Consider removing it to clean up the function signature.Proposed code change:
-async def generate_patch_with_cognee(instance, llm_client, search_type=SearchType.CHUNKS): +async def generate_patch_with_cognee(instance, llm_client):
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📒 Files selected for processing (3)
cognee/tasks/summarization/summarize_code.py(1 hunks)evals/eval_swe_bench.py(3 hunks)examples/python/code_graph_example.py(1 hunks)
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Actionable comments posted: 0
♻️ Duplicate comments (2)
cognee/tasks/summarization/summarize_code.py (2)
14-14: 🛠️ Refactor suggestionUpdate return type annotation to reflect generator
The function
summarize_codenow yieldsDataPointobjects instead of returning a list. Update the return type annotation to-> AsyncGenerator[DataPoint, None]to accurately represent its behavior.Apply this diff:
- ) -> list[DataPoint]: + ) -> AsyncGenerator[DataPoint, None]:
3-3: 🛠️ Refactor suggestionImport
AsyncGeneratorfromtypingSince
summarize_codeis now an async generator, importAsyncGeneratorfrom thetypingmodule to properly annotate the return type.Apply this diff:
- from typing import Type + from typing import Type, AsyncGenerator
🧹 Nitpick comments (6)
cognee/api/v1/cognify/code_graph_pipeline.py (5)
113-116: Consider moving imports to the module levelThe imports inside the
run_code_graph_pipelinefunction (lines 113-116) can be moved to the top of the file. This enhances readability and adheres to standard Python conventions.Apply this diff to move the imports:
+ import os + import pathlib + import cognee + from cognee.infrastructure.databases.relational import create_db_and_tables async def run_code_graph_pipeline(repo_path): - import os - import pathlib - import cognee - from cognee.infrastructure.databases.relational import create_db_and_tables
114-114: Remove redundant import ofpathlibThe module
pathlibis already imported at the module level on line 3 (from pathlib import Path). The import on line 114 is redundant and can be removed.Apply this diff to remove the redundant import:
- import pathlib
116-116: Movecreate_db_and_tablesimport to the module levelFor consistency and clarity, consider moving the import of
create_db_and_tablesto the module level with other imports.Apply this diff:
+ from cognee.infrastructure.databases.relational import create_db_and_tables async def run_code_graph_pipeline(repo_path): - from cognee.infrastructure.databases.relational import create_db_and_tables
119-122: Simplify path manipulations usingPathobjectsCurrently, both
os.path.joinandpathlib.Pathare used for path manipulations. For better readability and consistency, consider usingPathobjects throughout.Apply this diff to refactor the path handling:
- data_directory_path = str(pathlib.Path(os.path.join(file_path, ".data_storage/code_graph")).resolve()) - cognee_directory_path = str(pathlib.Path(os.path.join(file_path, ".cognee_system/code_graph")).resolve()) + data_directory_path = (file_path / ".data_storage" / "code_graph").resolve() + cognee_directory_path = (file_path / ".cognee_system" / "code_graph").resolve()
112-136: Add a docstring torun_code_graph_pipelineAdding a docstring to the
run_code_graph_pipelinefunction will improve code readability and maintainability by explaining the purpose and usage of the function.cognee/tasks/summarization/summarize_code.py (1)
18-18: Ensure generator function concludes appropriatelyThe
returnstatement at line 18 exits the generator function without yielding any values ifcode_graph_nodesis empty. This is acceptable, but for clarity, consider usingreturn Noneto explicitly indicate the end of the generator.
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📒 Files selected for processing (4)
cognee/api/v1/cognify/code_graph_pipeline.py(3 hunks)cognee/tasks/summarization/summarize_code.py(1 hunks)evals/eval_swe_bench.py(2 hunks)examples/python/code_graph_example.py(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- examples/python/code_graph_example.py
🔇 Additional comments (2)
evals/eval_swe_bench.py (2)
10-10: Refactored run_code_graph_pipeline import improves modularity
Good job moving run_code_graph_pipeline to code_graph_pipeline.py and importing it here. This enhances code organization and reusability.
39-44: Function generate_patch_with_cognee correctly utilizes the pipeline
The updated function properly calls run_code_graph_pipeline and processes the results asynchronously, which aligns with best practices for async operations.
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Actionable comments posted: 2
🧹 Nitpick comments (3)
cognee/api/v1/cognify/code_graph_pipeline.py (3)
1-4: Enhance deprecation notice with timelineThe deprecation notice is clear but could be more helpful by including:
- When these functions will be removed
- Migration guide or link to documentation
# NOTICE: This module contains deprecated functions. # Use only the run_code_graph_pipeline function; all other functions are deprecated. +# These functions will be removed in version X.Y.Z. See migration guide at <link> # Related issue: COG-906
133-139: Make task configurations configurableThe task configurations use hardcoded batch sizes which might not be optimal for all scenarios.
Consider making these configurable:
+ def get_batch_size(task_name: str) -> int: + return cognee.config.get(f"tasks.{task_name}.batch_size", default=50) + tasks = [ Task(get_repo_file_dependencies), - Task(enrich_dependency_graph, task_config={"batch_size": 50}), - Task(expand_dependency_graph, task_config={"batch_size": 50}), - Task(summarize_code, summarization_model=SummarizedContent, task_config={"batch_size": 50}), - Task(add_data_points, task_config={"batch_size": 50}), + Task(enrich_dependency_graph, task_config={"batch_size": get_batch_size("enrich_dependency_graph")}), + Task(expand_dependency_graph, task_config={"batch_size": get_batch_size("expand_dependency_graph")}), + Task(summarize_code, summarization_model=SummarizedContent, task_config={"batch_size": get_batch_size("summarize_code")}), + Task(add_data_points, task_config={"batch_size": get_batch_size("add_data_points")}), ]
124-127: Consider using temporary directories for isolationUsing fixed directory names under the package directory could cause conflicts between different runs or in different environments.
Consider using
tempfile.mkdtemp()to create isolated directories for each run, or make the paths configurable through environment variables.
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📒 Files selected for processing (1)
cognee/api/v1/cognify/code_graph_pipeline.py(4 hunks)
🔇 Additional comments (1)
cognee/api/v1/cognify/code_graph_pipeline.py (1)
62-62: Verify error handling migration
While the deprecation notice is good, ensure that the error handling and telemetry capabilities from run_pipeline are properly migrated to run_code_graph_pipeline.
✅ Verification successful
Error handling and telemetry are properly migrated
The new run_code_graph_pipeline implementation includes comprehensive error handling and telemetry:
- Sends telemetry events at pipeline start, completion, and error states
- Wraps core execution in try-except block
- Updates pipeline status appropriately for both success and error cases
- Maintains consistent error reporting pattern with the deprecated version
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# Search for error handling and telemetry in the new implementation
rg -A 5 "try|except|send_telemetry" cognee/api/v1/cognify/code_graph_pipeline.py
Length of output: 1600
* 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 394a0b2. * 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 <[email protected]> Co-authored-by: Igor Ilic <[email protected]> Co-authored-by: Boris <[email protected]> * 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 <[email protected]> Co-authored-by: Vasilije <[email protected]> Co-authored-by: Igor Ilic <[email protected]> Co-authored-by: Boris <[email protected]> * 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 <[email protected]> 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 <[email protected]> Co-authored-by: Vasilije <[email protected]> Co-authored-by: Igor Ilic <[email protected]> Co-authored-by: Rita Aleksziev <[email protected]> Co-authored-by: vasilije <[email protected]> Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> Co-authored-by: lxobr <[email protected]> Co-authored-by: alekszievr <[email protected]> Co-authored-by: hajdul88 <[email protected]> Co-authored-by: Henry Mao <[email protected]>
Refactored the
summarize_codetask into a generator that does not call theadd_pointsfunction.summarize_codenow:This ensures all data points reach the
add_datapointsfunction.Moved the
add_datapointstask to the end of the pipeline.Extracted
run_code_graph_pipelineinto a standalone function.Added a script example for running the code graph pipeline with the new function.
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New Features
Improvements
Bug Fixes
Deprecation Notices
Documentation