Update docs, add checks for formatting/docs building, and refactor modisco and utils modules #34
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LukasMahieu
commented
Oct 4, 2024
•
LukasMahieu
commented
- update introduction notebook & removed old notebook
- update enhancer analysis notebooks to use renamed functions and add api refs
- crested.pl.bar.prediction_bar renamed to crested.pl.bar.prediction
- crested.pl.patterns.plot_patterns and crested.pl.patterns.plot_pattern_instances renamed to crested.pl.patterns.selected_instances and crested.pl.patterns.class_instances respectively.
- crested.pl.patterns.plot_ ... all renamed to crested.pl.patterns. ... (removed 'plot_' from names since redundant)
- moved all tfmodisco functionality to new module crested.tl.modisco (e.g. crested.tl.modisco.tfmodisco)
- moved all utility functions to crested.utils (e.g; crested.utils.one_hot_encode_sequence)
- moved logging to crested.utils
- added docs for all functions & example images for plots
- fixed incorrect & missing type hints
- removed a bunch of unused arguments (e.g; 'coordinates' in locus_scoring)
- added github action to check for docs building correctly & ruff formatting
- moved tangermeme import into crested modisco tomtom function
… etc to selected & class_indices
LukasMahieu
changed the title
nkempynck
approved these changes
Oct 9, 2024
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