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STAMP v0.12.0 release - #63
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- Modified utils/log.py to add two utility functions for logging startup messages and configuration values.
- Modified cli/pick.py, cli/decoy.py, cli/classify.py, cli/identify.py, cli/refine.py, commands/classify.py to add startup log message.
- Modified commands/pick.py to add messages for vesicle summary, adapter/dispatch branching and resolved voxel size.
- Modified commands/classify.py to add messages for subvolume extraction, feature extraction and dispatch, and for configurations, resolved voxel size, and strict/combined branching.
- Modified commands/identify.py to add messages for report writing and decoy control branching.
- Modified commands/refine.py to add messages for FSC, backend branching and resolved voxel size.
- Modified run/orchestrate.py to add message debug for inferred synthetic shape. - Modified schemas/config.py to add message for run config after loading.
Merge pull request #61 from holsam/logging-improvements
- Modified classify/extract.py to only change MRC file data type to float32 if it isn't already float32, preventing double memory usage for no gain.
- Modified classify/extract.py to add a dataclass for membrane subtraction jobs for splitting membrane subtraction from subtomogram extraction.
- Modified classify/extract.py to add function for subtracting membranes as a process pool worker process.
- Modified classify/extract.py to update subvolume extraction worker to decouple membrane subtraction.
- Modified classify/extract.py to update extraction logic to decouple membrane subtraction and subvolume extraction.
- Modified classify/extract.py to add missing import and logging line for number of membrane-subtracted/raw density extractions. - Modified commands/classify.py to remove log line for kept & skipped subvolumes (now reported directly). - Modified tests/unit/test_classify.py to add unit test for fallback to raw tomogram if segmentation shape doesn't match.
- Added utils/checkpoint.py to define utility functions for getting file signatures and syncing checkpoints. - Modified tests/unit/test_utils.py to add unit tests covering checkpoint utilities.
- Modified commands/classify.py to create a command fingerprint (containing all analysis options) and check for checkpoint with matching signature.
- Modified classify/extract.py to resume extraction from disk when files present.
- Modified utils/checkpoint.py to add additional checkpointing utilities.
- Modified classify/align.py to resume from checkpoint where possible. - Modified classify/features.py to resume from checkpoint where possible. - Modified commands/classify.py to pass cache/checkpoint directories through to feature extraction/alignment functions.
- Modified tests/integration/test_classify_command.py to add tests for resuming from checkpointed run. - Modified tests/unit/test_classify.py to add unit tests for resuming different modules from checkpoints.
Merge pull request #62 from holsam/classify-improvements
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Changelog
classify.classifycommand memory usage and checkpointing #62classify: Improveclassifycommand memory usage and checkpointing #62