Merge pull request #40 from aertslab/release_1.1.0

release 1.1.0

docs/changelog.md

@@ -1,5 +1,46 @@
 # Release Notes
 
-## Release 1.0.0
+## 1.1.0
+
+### Features
+
+-   enhancer design plotting and calculation functions in the `crested.tl.Crested` object
+-   new module `crested.tl.modisco` with enhancer code analysis functionality
+-   new plots for enhancer code analysis in `crested.pl.patterns`
+-   new plot for sequence prediction in `crested.pl.bar`
+-   hidden utility functions now public in `crested.utils` (such as one hot encoding)
+-   CosineMSELog loss now default in peak_regression configs instead of CosineMSE
+-   tangermeme tomtom option in tfmodisco functions
+-   get_embeddings based on layer name in `crested.tl.Crested`
+-   `crested.utils.EnhancerOptimizer` utility function
+-   `crested.utils.permute_model` utility, useful for using with other toch packages
+-   `crested.utils.extract_bigwig_values_per_bp` utility
+-   improved correlation calculation speed in heatmaps
+
+### Tutorials
+
+-   introductory notebook is updated with new functionality
+-   new enhancer code analysis tutorial
+
+### Bug Fixes
+
+-   transfer Learning function now doesn't expect the dense block anymore
+-   bigwigs importing checks if it can open the file instead of looking for .bw extension
+-   no more ambiguous names in bed importing
+-   version requirement for modiscolite
+-   general pattern matching code bugfixes
+
+### Breaking Changes
+
+-   utility functions and logging moved to `crested.utils`
+-   tfmodisco functionality moved to `crested.tl.modisco`
+
+### Other
+
+-   general documentation fixes
+-   style checks now enforced on push
+-   both tf and torch backend tests on push
+
+## 1.0.0
 
 -   Initial release of CREsted

pyproject.toml

@@ -4,7 +4,7 @@ requires = ["hatchling"]
 
 [project]
 name = "crested"
-version = "1.0.0"
+version = "1.1.0"
 description = "CREsted: Cis-Regulatory Element Sequence Training, Explanation, and Design"
 readme = "README.md"
 requires-python = ">=3.9"