Releases · SlicerDMRI/whitematteranalysis

WMA v0.4.1: bugfix release

Tested against Python versions 3.8, 3.9, 3.10 and 3.11.

Summary of changes:

Fix issues after f-strings transition.

What's Changed

BUG: Import joblib modules in cluster outlier removal script by @jhlegarreta in #226
BUG: Remove spare f in an f-string by @jennydaman in #225
ENH: Fix artifact upload naming conflict by @jhlegarreta in #229
STYLE: Fix filename and dirname creation floating point formatting by @jhlegarreta in #232
ENH: Fix workflow actions warnings linked to Node.js by @jhlegarreta in #233
ENH: Bump version to 0.4.1 by @jhlegarreta in #234

New Contributors

@jennydaman made their first contribution in #225

Full Changelog: v0.4.0...v0.4.1

WMA v0.4.0: release all recent enhancements and bug fixes.

Tested against Python versions 3.8, 3.9, 3.10 and 3.11.

Summary of changes:

Fix transform hardening for 3D Slicer so that the appropriate
orientation (RAS vs LPS) is used for fiber bundles.
Avoid random sampling at registration to enable reproducible results
across runs.
Fix packaging issues for compliance with PyPI and improve packaging.
List the dependencies in a dedicated requirements file.
Allow the atlas version to be specified at download.
Build the bundle list dynamically depending on the atlas version.
Add documentation infrastructure.
Miscellaneous enhancements and fixes.

Likely the last release before transitioning to pyproject.toml as the
configuration file for packaging and compatibility with Python 3.12.

What's Changed

QC multi views by @zhangfanmark in #37
EHN: relative path of individual html by @zhangfanmark in #38
Parallel measure extraction by @zhangfanmark in #39
Load measurements by @zhangfanmark in #41
wm quality control after clustering by @zhangfanmark in #42
EHN: WM quality control after clustering 2 by @zhangfanmark in #44
EHN: histogram x-axis labels by @zhangfanmark in #45
Wm harden transform with slicer by @zhangfanmark in #46
ENH: histogram x-axis label fix by @zhangfanmark in #47
Append multiple clusters into one vtp file by @zhangfanmark in #48
Endpoint Analysis NA-MIC project week by @zhangfanmark in #52
Add a new script to decide a cluster belonging to hemispheric or commissural by @zhangfanmark in #54
Slight clean-up of README.md by @ihnorton in #56
Masking all clusters in one loop to reduce running time by @zhangfanmark in #57
Adds shebang for python removes extra Update by @blezek in #58
Update wm_separate_clusters_by_hemisphere.py to perform hemisphere separation when cluster location is known by @zhangfanmark in #64
Add a new script for downloading pre-provided atlases by @zhangfanmark in #70
Add requirements.txt by @ihnorton in #69
Fix another VTK issue, and minor test_pipeline tweak by @ihnorton in #71
Update wm_append_cluster.py to append vtk files in a mrml or in a folder by @zhangfanmark in #72
Fix windows build issues by @ihnorton in #73
More build fixes for clean environment by @ihnorton in #75
Update installation instructions by @ihnorton in #76
Add HemisphereLocation in fiber cluster vtk file by @zhangfanmark in #82
Add compute cluster measures (eg FA) from a volumetric map by @zhangfanmark in #83
Merge tutorial to master by @zhangfanmark in #85
2to3 by @ScLill in #90
Python2to3 by @zhangfanmark in #91
Parallelize outlier removal script by @zhangfanmark in #101
Slicer module by @tashrifbillah in #103
Fix apostrophe in O'Donnell by @tashrifbillah in #107
fix nonrigid registeration by @tengfeixue-victor in #114
fix "fibers_per_subject" as int type by @tengfeixue-victor in #117
STYLE: Upgrade python syntax to 3.6 and newer by @jamesobutler in #118
BUG: fix transform hardening for Slicer by @pieper in #119
DOC: Fix miscellaneous typos and grammar across files by @jhlegarreta in #136
DOC: Add bundle name list by @jhlegarreta in #123
ENH: Add GitHub actions build, test workflow file for CI by @jhlegarreta in #134
ENH: Fix pandas version to 2.0.3 by @jhlegarreta in #145
DOC: Fix typo in subject-specific tractography parcellation doc file by @jhlegarreta in #144
ENH: Use a requirements.txt file to list the external dependencies by @jhlegarreta in #146
ENH: Make tractogram downsampling results reproducible by default by @jhlegarreta in #147
BUG: Fix WM diffusion measurement Python script call for Linux by @jhlegarreta in #156
ENH: Add a command line option to apply a transformation by @jhlegarreta in #143
DOC: Specify call to diffusion measurement module in Linux by @jhlegarreta in #127
DOC: Sync the license file with the current Slicer license file content by @jhlegarreta in #139
DOC: Increase consistency in SlicerDMRI citation message by @jhlegarreta in #140
STYLE: Miscellaneous clean-up by @jhlegarreta in #149
ENH: Add script availability testing by @jhlegarreta in #154
ENH: Remove unnecessary Cython package dependendency by @jhlegarreta in #160
STYLE: Prefer using lowercase to name package by @jhlegarreta in #162
DOC: Remove non-meaningful comment by @jhlegarreta in #163
DOC: Improve Markdown syntax in README file by @jhlegarreta in #165
ENH: Discover scripts automatically by @jhlegarreta in #169
ENH: Define python source encondings by @jhlegarreta in #170
DOC: Remove inaccurate comment by @jhlegarreta in #171
ENH: Define main methods to contain computation logic across scripts by @jhlegarreta in #167
ENH: Add all released Python version above 3.8 until 3.11 to CI by @jhlegarreta in #153
STYLE: Do not use try/except in non-optional package imports by @jhlegarreta in #172
ENH: Ignore further patterns in git by @jhlegarreta in #166
STYLE: Refactor argparsing to own methods in scripts by @jhlegarreta in #174
DOC: Add readthedocs documentation site infrastructure by @jhlegarreta in #155
ENH: Bump checkout GHA to v4 in workflows by @jhlegarreta in #177
ENH: Remove unused pkg_resources module import by @jhlegarreta in #179
STYLE: Fix typo in hemisphere location array name by @jhlegarreta in #131
ENH: Allow specifying the atlas version at download by @jhlegarreta in #132
BUG: Remove non-existing version keyword parameter in script argparser by @jhlegarreta in #173
ENH: Relax the Python package version requirements by @jhlegarreta in #157
ENH: Relocate contents in test_run.py to tests by @jhlegarreta in #176
BUG: Miscellaneous cleanup for compliance PyPI by @jhlegarreta in #178
ENH: Add bundle feature population math script by @jhlegarreta in #138
ENH: Keep the input file format in preprocessing script by @jhlegarreta in #148
BUG: Fix script names in tests by @jhlegarreta in https://github.com/SlicerDMRI/whitematte...