Rename release from 4.4.1 to 4.4

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: joshfactorial

ChangeLog.md

@@ -1,4 +1,7 @@
-# NEAT v4.4.1
+# NEAT v4.4
+- Official release of NEAT 4.0. Represents major contributions from NCSA and beyond.
+- Added parallel processing support, making NEAT production-ready for large genomes.
+- Includes more options for quality score modeling, a bacterial genome wrapper, additional tests, and performance improvements.
 - Fixed inverted indel gate condition in the sequencing error model: indel errors were never generated due to a `>` vs `<=` logic error.
 - Fixed deletion blacklist bug: the anchor position of a deletion was incorrectly blacklisted, causing the deletion to remove itself during error cleanup.
 - Fixed quality array float promotion: applying a deletion error produced an empty quality slice (`np.array([])`), which defaulted to `float64` and broke quality string encoding.
@@ -10,12 +13,6 @@
 - Replaced debug print sentinels in the mutation model with proper log warnings.
 - Expanded test coverage for the error model, runner, and read simulator.
 
-# NEAT v4.4
-- Official release of NEAT 4.0. Represents major contributions from NCSA and beyond.
-- Added parallel processing support, making NEAT production-ready for large genomes.
-- Includes more options for quality score modeling, a bacterial genome wrapper, additional tests, and performance improvements.
-- Future releases will focus on compatibility, bug fixes, and testing under the 4.4.X versioning scheme.
-
 # NEAT has a new home
 NEAT is now a part of the NCSA github and active development will continue here. Please direct issues, comments, and requests to the NCSA issue tracker. Submit pull requests here insead of the old repo.
 

README.md

@@ -1,10 +1,10 @@
-# The NEAT Project v4.4.1
+# The NEAT Project v4.4
 
-Welcome to the NEAT project, the NExt-generation sequencing Analysis Toolkit, version 4.4.1. NEAT 4.4 is the official release of NEAT 4.0. It represents a lot of hard work from several contributors at NCSA and beyond. With the addition of parallel processing, we feel that the code is ready for production, and future releases will focus on compatibility, bug fixes, and testing. Future releases for the time being will be enumerations of 4.4.X.
+Welcome to the NEAT project, the NExt-generation sequencing Analysis Toolkit, version 4.4. NEAT 4.4 is the official release of NEAT 4.0. It represents a lot of hard work from several contributors at NCSA and beyond. With the addition of parallel processing, we feel that the code is ready for production, and future releases will focus on compatibility, bug fixes, and testing. Future releases for the time being will be enumerations of 4.4.X.
 
-## NEAT v4.4.1
+## NEAT v4.4
 
-NEAT 4.4.1 is a bug-fix release targeting the sequencing error model. Several long-standing bugs in error generation were identified and corrected, resulting in more realistic sequencing error profiles. See the [ChangeLog](ChangeLog.md) for details. 
+NEAT 4.4 is the official release of NEAT 4.0, including parallel processing support and significant bug fixes to the sequencing error model. See the [ChangeLog](ChangeLog.md) for details. 
 
 We have completed major revisions on NEAT since 3.4 and consider NEAT 4.4 to be a stable release, in that we will continue to update and provide bug fixes and support. We will consider new features and pull requests. Please include justification for major changes. See [contribute](CONTRIBUTING.md) for more information. If you'd like to use some of our code in your own, no problem! Just review the [license](LICENSE.md), first.
 
@@ -22,8 +22,8 @@ To cite this work, please use:
 
 ## Table of Contents
 
-* [The NEAT Project v4.4.1](#the-neat-project-v441)
-* [NEAT v4.4.1](#neat-v441)
+* [The NEAT Project v4.4](#the-neat-project-v44)
+* [NEAT v4.4](#neat-v44)
 * [Table of Contents](#table-of-contents)
   * [Prerequisites](#prerequisites)
   * [Installation](#installation)

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "neat-genreads"
-version = "4.4.1"
+version = "4.4"
 description = "NGS Simulation toolkit"
 authors = ["Joshua Allen <jallen17@illinois.edu>"]
 license = "BSD 3-Clause License"