fix: Removed automatic config of structlog on import, fixes 855

[jspv]

Description

Per 855

• Changed the automatic setup of structlog (and consequential changing of all existing log handlers) to a standalone routine setup_logging that can be called if desired rather than on import
• Removed the thread locking that stopped multiple setups from occurring at the same time, no longer needed as each module will not try and install it automatically
• Modified existing code with clear entry points (with __main__ fence) to call setup_logging for some backward compatibility.

Net effect: import cognee will no longer change the importing application's log setup.

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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• [ ] I have tested these changes locally.
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• [ ] I have removed unnecessary code and debug statements.
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"""

Walkthrough

This change refactors logging initialization across multiple modules by replacing direct logger retrieval with explicit calls to setup_logging() at runtime. The logging utility module is simplified by removing threading locks and internal lazy initialization, relying instead on a single configuration flag. Example and server scripts are updated to initialize logging at startup.

Changes

File(s)	Change Summary
cognee/shared/logging_utils.py	Refactored logging state management: removed threading, made LoggerInterface a Protocol, updated setup and retrieval logic, clarified docstrings.
cognee-mcp/src/server.py	Replaced global log file variable with dynamic retrieval; switched to setup_logging() for logger initialization.
cognee/api/client.py cognee/api/v1/cognify/code_graph_pipeline.py cognee/api/v1/visualize/visualize.py	Updated to call setup_logging() at runtime for logging initialization.
cognee/modules/retrieval/utils/description_to_codepart_search.py	Updated to initialize logging with setup_logging() in main block.
examples/python/code_graph_example.py examples/python/dynamic_steps_example.py examples/python/graphiti_example.py examples/python/multimedia_example.py examples/python/ontology_demo_example.py examples/python/ontology_demo_example_2.py examples/python/simple_example.py examples/python/simple_node_set_example.py	Changed logger initialization from get_logger to setup_logging() in example scripts.

Sequence Diagram(s)

sequenceDiagram
    participant Script
    participant LoggingUtils

    Script->>LoggingUtils: setup_logging(log_level)
    LoggingUtils-->>Script: Configures logging, sets flag

    Script->>LoggingUtils: get_logger(name, level)
    alt If logging configured
        LoggingUtils-->>Script: Returns structlog logger
    else
        LoggingUtils-->>Script: Returns standard logger
    end

Possibly related PRs

• topoteretes/cognee#434: Both PRs modify the logging setup process, specifically setup_logging, focusing on restructuring and improving robustness.
• topoteretes/cognee#674: Both PRs adjust how logging and log file locations are handled in cognee-mcp/src/server.py, with overlapping changes.
• topoteretes/cognee#658: Both PRs modify logging usage, with this PR introducing explicit runtime setup and dynamic log file handling.

Suggested labels

run-checks

Poem

In the warren, logs now shine bright,
No more tangled threads at night.
With setup_logging called anew,
The rabbits hop with clearer view.
Simpler logs, less bunny stress—
Now every script can log with finesse!
🐇✨ """

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[dexters1]

@jspv Thanks a lot for your contribution! I've made a new branch from your branch (jspv-structlog-auto-config-fix) to run CI/CD on our side and add some changes. This new branch has been merged (https://github.com/topoteretes/cognee/pull/907)

Your commits are all stored there so you'll be part of our contributors 😃

It's currently merged to our dev branch, it will be a part of our next Cognee release