bump version 0.4.0 -> 1.0.0

CHANGELOG.rst

@@ -6,6 +6,14 @@ All notable changes to this project will be documented in this file.
 
 The format is based on `Keep a Changelog <https://keepachangelog.com>`_.
 
+
+0.5.0
+-----
+- This release re-implements the joint model as a using a generalized lasso, and bit-flipping, as described in `#156 https://github.com/matsengrp/multidms/issues/156`_. Please see the issue for more detailed description about how, and why these changes were made. Note that this changes the parameters that one may get from the model including a set of beta's for each experimental condition.
+- It also cleans up various TODO's in the code as checked-off in `# https://github.com/matsengrp/multidms/issues/153`.
+- Fixes a bug, where the phenotype predictions for single mutants did not correctly include the bundle effects.
+- Fixes and cleans various plotting bugs. 
+
 0.4.0
 -----
 - new simulation validation analysis and plotting functions (at the time of re-submission)

CONTRIBUTING.rst

@@ -128,4 +128,4 @@ the package to the **real** PyPI repository.
 .. _twine: https://github.com/pypa/twine
 .. _`numpy style documentation`: https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html
 .. _nbval: https://nbval.readthedocs.io
-.. _bumpver: https://github.com/mbarkhau/bumpver
+.. _bumpver: https://github.com/mbarkhau/bumpver

docs/conf.py

@@ -16,7 +16,7 @@
 project = "multidms"
 copyright = "2023, Jared Galloway, Hugh Haddox"
 author = "Jared Galloway"
-release = "0.4.0"
+release = "1.0.0"
 
 needs_sphinx = "1.0"
 

multidms/__init__.py

@@ -47,7 +47,7 @@ class works to compose, compile, and optimize the model parameters
 
 __author__ = "Jared Galloway"
 __email__ = "[email protected]"
-__version__ = "0.4.0"
+__version__ = "1.0.0"
 __url__ = "https://github.com/matsengrp/multidms"
 
 from binarymap.binarymap import AAS_NOSTOP as AAS  # noqa: F401

pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "multidms"
-version = "0.4.0"
+version = "1.0.0"
 description = "Joint modeling of multiple deep mutational scanning experiments."
 readme = "README.md"
 authors = [
@@ -111,7 +111,7 @@ repository = "https://github.com/matsengrp/multidms"
 packages = ["multidms"]
 
 [tool.bumpver]
-current_version = "0.4.0"
+current_version = "1.0.0"
 version_pattern = "MAJOR.MINOR.PATCH"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true