v0.3.0

jmschrei · Sep 6, 2024 · 4c74dd7 · 4c74dd7
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diff --git a/docs/whats_new.rst b/docs/whats_new.rst
@@ -5,9 +5,37 @@
 Release History
 ===============
 
-Version 0.2.4
+Version 0.3.0
 ==============
 
+Highlights
+----------
+
+	- Added in a new TOMTOM implementation and a revamped FIMO implementation
+	- TOMTOM and FIMO both have command-line tools in `tangermeme`
+
+
+FIMO
+----
+
+	- The PyTorch implementation has been exchanged for a numba based one.
+	- The new signature is a single function called `fimo`
+	- A command-line tool can be used with the signature `tangermeme fimo ...`
+
+
+TOMTOM
+------
+
+	- A numba-based implementation has been added in the function `tomtom`
+	- A command-line tool can be used with the signature `tangermeme tomtom ...`
+
+
+utils
+-----
+
+	- `chunk` and `unchunk` have been added in to chunk long sequences into blocks that can be operated on by methods with fixed-window inputs, such as machine learning models, and for converting the predictions from these approaches back into a contiguous format.
+
+
 match
 -----
 

diff --git a/setup.py b/setup.py
@@ -2,7 +2,7 @@
 
 setup(
     name='tangermeme',
-    version='0.2.3',
+    version='0.3.0',
     author='Jacob Schreiber',
     author_email='jmschreiber91@gmail.com',
     packages=['tangermeme', 'tangermeme/tools'],

diff --git a/tangermeme/__init__.py b/tangermeme/__init__.py
@@ -1,4 +1,4 @@
 # tangermeme: biological sequence analysis for the modern age
 # Author: Jacob Schreiber
 
-__version__ = '0.2.3'
+__version__ = '0.3.0'