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STAMP v0.13.0 release - #66
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- Modified utils/checkpoint.py to add fingerprint normalisation and signature utilities. - Modified tests/unit/test_utils.py to add unit tests for added utility functions.
- Modified commands/classify.py to use shared checkpointing utilities.
- Modified utils/io.py to cache using atomic writings, and to log warnings if cache file is invalid JSON. - Modified tests/unit/test_utils.py to add unit tests checking pick cache writing and loading.
- Modified commands/pick.py to fingerprint picker inputs and parameters and gate raw with sync_checkpoint. - Modified adapters/native.py to skip tomograms if pick cache already exists. - Modified tests/integration/test_pick_command.py to add interruption-resume and parameter-change tests.
- Modified commands/decoy.py to fingerprint decoy inputs and parameters and gate raw with sync_checkpoint. - Modified decoy/generate.py to reuse finished synthetic-noise volumes and picks from the checkpoint, checkpoint per-tomogram surface scores, checkpoint per-tomogram extracted surfaces, and skip extracting finished tomograms. - Modified tests/integration/test_decoy_command.py to add a synthetic-noise reuse test, and resume tests for rejected-surface and shifted surface.
- Modified commands/identify.py to checkpoint fit scores. - Modified tests/integration/test_identify_command.py to add an interruption-resume test.
- Modified commands/refine.py to fingerprint class inputs and to reuse half-maps finished by an earlier run. - Modified tests/integration/test_refine_command.py to add interruption-resume and parameter-change tests.
- Modified docs/cli.md to add a section on resuming interrupted commands. - Modified docs/architecture.md to add a section on checkpointing with per-command checkpoints given.
Merge pull request #64 from holsam/checkpointing
- Modified classify/cluster.py to fix issue with hdbscan raising warning due to implicit behaviour.
- Modified classify/features.py to add additional logging for resuming features. - Modified commands/classify.py to update log level of feature extraction completion message.
- Modified classify/cluster.py to split PCA from clustering as a separate function.
- Modified classify/cluster.py to fully separate PCA from clustering by calling new PCA function within each clustering function. - Modified tests/unit/test_classify.py to redirect tests for dimension reduction to new PCA function.
- Modified classify/cluster.py to use fast_hdbscan library instead of the original scikit learn implementation.
- Modified commands/classify.py to export numba thread count environment variable.
Merge pull request #65 from holsam/clustering-improvements
- Modified docs/cli.md to update documentation on CLI options.
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