WMA v0.4.0

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 #181
• ENH: Fix requirements by @jhlegarreta in #183
• ENH: Specify statsmodels package version for Python>=3.10 by @jhlegarreta in #184
• ENH: Install package using pip in GHA workflow by @jhlegarreta in #185
• ENH: Test with code coverage in GHA package test workflow by @jhlegarreta in #186
• ENH: Auto-discover packages by @jhlegarreta in #187
• ENH: Set the hemisphere location name to the correct name by @jhlegarreta in #188
• STYLE: Apply isort to package imports by @jhlegarreta in #189
• ENH: Build bundle list dynamically depending on atlas version by @jhlegarreta in #133
• ENH: Check code format on PRs by @jhlegarreta in #190
• STYLE: Fix import formatting by @jhlegarreta in #193
• DOC: Fix typos in printed messages by @jhlegarreta in #197
• STYLE: Remove trailing semicolons by @jhlegarreta in #198
• DOC: Fix typo in cluster module printed message by @jhlegarreta in #202
• ENH: Do not find packages in documentation folder by @jhlegarreta in #207
• DOC: Fix Sphinx documentation by @jhlegarreta in #180
• ENH: Make the bin folder a package by @jhlegarreta in #208
• DOC: Exclude tests from documentation by @jhlegarreta in #210
• ENH: Fix code format check badge in README file by @jhlegarreta in #211
• DOC: Improve documentation index by @jhlegarreta in #212
• DOC: Add Markdown tutorial files to the documentation by @jhlegarreta in #209
• STYLE: Prefer importing nibabel as nib by @jhlegarreta in #199
• ENH: Remove unnecessary/uninformative version optional arg in scripts by @jhlegarreta in #203
• ENH: Make scripts have executable permissions by @jhlegarreta in #205
• STYLE: Prefer importing numpy as np by @jhlegarreta in #200
• ENH: Make documentation batch file have executable permissions by @jhlegarreta in #206
• DOC: Refactor and use logo in documentation by @jhlegarreta in #214
• DOC: Prefer using furo theme for Sphinx documentation by @jhlegarreta in #213
• STYLE: Prefer obtaining the module filenames automatically from Python by @jhlegarreta in #201
• ENH: Remove unused imports contained within try/expect blocks by @jhlegarreta in #191
• ENH: Do not try/except on non-optional imports by @jhlegarreta in #192
• ENH: Improve importing optional packages and modules by @jhlegarreta in #195
• STYLE: Make doc module consistent with Sphinx conventions by @jhlegarreta in #204
• STYLE: Prefer using f-strings by @jhlegarreta in #196
• DOC: Fix broken documentation links in README file by @jhlegarreta in #219
• BUG: Include data files in package installation by @jhlegarreta in #220
• ENH: Bump version number to 0.4.0 by @jhlegarreta in #222

New Contributors

• @ihnorton made their first contribution in #56
• @blezek made their first contribution in #58
• @ScLill made their first contribution in #90
• @tashrifbillah made their first contribution in #103
• @tengfeixue-victor made their first contribution in #114
• @jamesobutler made their first contribution in #118
• @pieper made their first contribution in #119
• @jhlegarreta made their first contribution in #136

Full Changelog: https://github.com/SlicerDMRI/whitematteranalysis/commits/v0.4.0