bumped version, updated CHANGELOG

CHANGELOG.md

@@ -2,6 +2,25 @@
 
 ## [Unreleased]
 
+## [0.4.0] - 2020-09-16
+
+### Added
+- Sequences for benchmarking in notebooks dir and a notebook to process the sequence
+- Benchmarking notebooks
+- Notebook to time Basset conv and fc separately 
+- Ability to specify custom mutations
+- For each mutation, models only run on input sequences for which character is different from mutation. As a result, each batch usually has a different size. This is slow for the first few batches as it entails a one-time cost.  
+- Lots of documentation and a logo!
+
+### Changed
+- Models updated:
+  - Activation added to Basset
+  - Num output for Basset and Factorized Basset
+  - For BPNet, only one channel output and one counts instead of two
+
+### Fixed
+- FastISM object would keep intermediate outputs of a batch even after it was used, as a result it would occupy extra memory. Get rid of such objects now through a `cleanup()` function. This has stopped GPU Resource errors that popped up after running a few batches
+
 ## [0.3.0] - 2020-08-24
 
 ### Added
@@ -28,7 +47,8 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 
-[unreleased]: https://github.com/kundajelab/fastISM/compare/v0.3.0...HEAD
+[unreleased]: https://github.com/kundajelab/fastISM/compare/v0.4.0...HEAD
+[0.4.0]: https://github.com/kundajelab/fastISM/compare/v0.3.0...v0.4.0
 [0.3.0]: https://github.com/kundajelab/fastISM/compare/v0.2.0...v0.3.0
 [0.2.0]: https://github.com/kundajelab/fastISM/compare/v0.1.3...v0.2.0
 [0.1.3]: https://github.com/kundajelab/fastISM/releases/tag/v0.1.3

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fastism"
-version = "0.3.0"
+version = "0.4.0"
 description = "Fast In-silico Mutagenesis for Convolution-based Neural Networks"
 authors = ["Surag Nair <surag@stanford.edu>"]
 license = "MIT"