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STAMP v0.10.0 release - #56
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- Modified utils/io.py to add utility functions for saving a tomogram's picks to a cache directory, and reading a cache directory back into memory.
- Modified decoy/generate.py to update generation functions to cache each tomogram's picks to a JSON file, then read these back. - Modified commands/decoy.py to pass output directory through to decoy generation command, and add keep raw logic. - Modified cli/decoy.py to add --keep-raw option for disabling raw pick archiving.
- Modified commands/pick.py to use shared pick caching utility. - Modified adapters/native.py to use shared pick caching utility.
- Modified classify/extract.py to cache each tomogram's subvolume stack to a cache directory. - Modified commands/classify.py to pass cache directory through to extraction functions, and add cache directory archiving logic. - Modified schemas/config.py to add keep_raw field to ClassifyStage configuration table. - Modified cli/classify to add a --keep-raw option for disabling archiving of raw subvolumes.
- Modified schemas/config.py to add keep raw option to DecoySettings configuration table. - Modified commands/decoy.py to use above config key when constructing decoy command.
Merge pull request #54 from holsam/output-flushing
- Modified schemas/config.py to allow n_decoys_per_tomogram to be None as well as integer.
- Modified cli/decoy.py to allow --n_decoys_per_tomogram to be None as well as integer, and to default to None.
- Modified decoy/generate.py to add function for calculating the number of target decoys to generate for rejected surface method, and to raise error for synthetic noise error if omitted. - Modified commands/decoy.py to wrap synthetic noise generation in try...except to catch any validation errors.
- Modified tests/unit/test_decoy.py to add unit tests for adaptive targeting, and to split tests into two classes.
Merge pull request #55 from holsam/adaptive-decoy
- Modified schemas/config.py to add threshold to RefineStage configuration table. - Modified cli/refine.py to add --threshold option and pass it through to run_refine. - Modified commands/refine.py to pass threshold through to refinement functions. - Modified refine/fsc.py to use threshold instead of a hard-coded 0.143 when drawing the FSC threshold line.
- Modified commands/decoy.py to fix incorrect options and duplicated output directory resolution. - Modified commands/pick.py to fix incorrect options and duplicated output directory resolution.
- Modified utils/io.py to fix non-None but falsy voxel sizes falling back to resolved_voxel_size which wouldn't be assigned.
- Modified tests/unit/test_utils.py to add unit tests for logging configuration.
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Changelog
decoy: Add adaptive decoy targeting #55--thresholdoption torefineand passing this through to all refinement functions.