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The progress bar feature added in PR #20 requires tqdm, but it was not added to the dependencies list. This caused the integration tests to fail with an ImportError when importing graphrelax modules. https://claude.ai/code/session_01QUT5Lv9GyV2Qs35A4TbxZg
The logging configuration had two issues: 1. logging.basicConfig() does nothing if handlers already exist on the root logger (e.g., from imported modules) 2. Third-party libraries (ProDy, OpenMM) have their own loggers that weren't being silenced This fix clears existing handlers before configuring and explicitly silences verbose third-party loggers. https://claude.ai/code/session_01QUT5Lv9GyV2Qs35A4TbxZg
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Getting a weird logging bug at runtime that makes this look dumb. Need to investigate further |
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The logging configuration had two issues: 1. logging.basicConfig() does nothing if handlers already exist on the root logger (e.g., from imported modules) 2. Third-party libraries (ProDy, OpenMM) have their own loggers that weren't being silenced This fix clears existing handlers before configuring and explicitly silences verbose third-party loggers. https://claude.ai/code/session_01QUT5Lv9GyV2Qs35A4TbxZg
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…elalamo/GraphRelax into claude/fix-failing-tests-P4Vp0
The "ProDy is configured" message appeared twice because confProDy() was called in both cli.py and data_utils.py. Removed the call from cli.py since data_utils.py already handles it at import time. Also clear any handlers that third-party loggers may have added to ensure they respect our log level settings. https://claude.ai/code/session_01QUT5Lv9GyV2Qs35A4TbxZg
The previous logging changes that removed handlers from root and third-party loggers were causing the application to hang. Reverted to a simpler setup using basicConfig with force=True. The force=True parameter ensures our configuration takes effect even if logging was configured by imported modules. https://claude.ai/code/session_01QUT5Lv9GyV2Qs35A4TbxZg
ProDy's debug messages were appearing because: 1. confProDy(verbosity="none") in data_utils.py runs before our logging configuration 2. ProDy's loggers weren't being silenced Added silence_third_party_loggers() which: - Calls confProDy(verbosity="none") to silence ProDy's internal logging - Sets ProDy-related Python loggers to ERROR level This is called after the heavy imports complete, ensuring the loggers exist and can be properly configured. https://claude.ai/code/session_01QUT5Lv9GyV2Qs35A4TbxZg
- Modified data_utils.py to silence ProDy loggers BEFORE importing prody - This prevents any debug messages from appearing during import - Renamed silence_third_party_loggers() to configure_third_party_loggers() - When --verbose is set, ProDy logging is re-enabled to debug level - When not verbose, ProDy stays completely silent https://claude.ai/code/session_01QUT5Lv9GyV2Qs35A4TbxZg
Using logging.disable(logging.CRITICAL) to completely suppress all logging output during the prody import and confProDy call. This prevents any debug/info messages from getting through regardless of logger configuration. logging.disable(logging.NOTSET) restores normal logging after import. https://claude.ai/code/session_01QUT5Lv9GyV2Qs35A4TbxZg
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The progress bar feature added in PR #20 requires tqdm, but it was not added to the dependencies list. This caused the integration tests to fail with an ImportError when importing graphrelax modules.
https://claude.ai/code/session_01QUT5Lv9GyV2Qs35A4TbxZg