SDC-BIDS-dMRI v10.0.0

SDC-BIDS-dMRI v10.0.0: release all recent enhancements.

Summary of changes:

• Fixes and improvements to episode contents.
• Fixes to show the figures, and how they are sorted.
• Turn on KaTeX to render LaTeX maths.
• Upstream improvements to infrastructure files (e.g. theme, etc.).

Last release prior to transitioning to the new Carpentries Workbench
infrastructure.

What's Changed

• Ostanle2 edits - notebook 2 by @kaitj in #3
• Update organization and pull changes by @kaitj in #7
• Bump bleach from 3.1.0 to 3.1.4 by @dependabot in #9
• use remote themeUse remote theme by @fmichonneau in #13
• DOC: Add content to the lesson's overview page by @jhlegarreta in #15
• DOC: Fix spelling and capitalize acronyms in lesson 03 by @jhlegarreta in #16
• BUG: Rename eigenvalues and eigenvector images by @jhlegarreta in #17
• DOC: Add additional explanations to DTI scalar measures by @jhlegarreta in #18
• DOC: Fix typo in index.md by @jhlegarreta in #19
• BUG: Remove conflict-derived git traces in 03-DTI lesson by @jhlegarreta in #20
• DOC: Add instructor notes by @jhlegarreta in #22
• ENH: Add GitHub Actions CI builds for notebooks by @jhlegarreta in #23
• ENH: Add .idea folder to .gitignore by @jhlegarreta in #26
• ENH: Fix README GitHub Actions badge by @jhlegarreta in #32
• Bump notebook from 5.7.8 to 6.1.5 by @dependabot in #33
• update author and maintainer list by @kaitj in #25
• FIX: Trim Python package requirements by @josephmje in #35
• ENH: Add additional local reconstruction model lesson by @jhlegarreta in #27
• MAINT: Refactoring of notebook 2 & convert to carpentries format by @kaitj in #21
• DOC: Add reference for QSIPrep by @kaitj in #38
• ENH: Add osfclient to the requirements list by @jhlegarreta in #40
• FIX: Update .ipynb path and test on multiple Python versions by @josephmje in #39
• ENH: Make the FURY screenshots be displayed inline by @jhlegarreta in #42
• FIX: Update file paths for website build by @josephmje in #43
• STY: Rename files and folders to increase consistency with markdown files by @jhlegarreta in #45
• ENH: Add probabilistic tractography lesson by @jhlegarreta in #36
• ENH: Re-organize lessons by @jhlegarreta in #47
• DOC: Add lesson information to config file by @jhlegarreta in #49
• DOC: Add missing HTML code closing tag by @jhlegarreta in #53
• DOC: Add terms to glossary by @jhlegarreta in #54
• DOC: Improve lesson information in README by @jhlegarreta in #51
• BUG: Remove duplicate probabilistic tractography episode by @jhlegarreta in #52
• BUG: Remove the unnecessary code environment for the glossary terms by @jhlegarreta in #55
• DOC: Add setup instructions by @jhlegarreta in #50
• DOC: Remove redundant instructor notes title by @jhlegarreta in #58
• BUG: Fix setup instructions file syntax by @jhlegarreta in #57
• BUG: Fix links.md file comment tag syntax by @jhlegarreta in #56
• ENH: Remove unnecessary content from the CSD episode by @jhlegarreta in #60
• ENH: Refactor tractography episodes by @jhlegarreta in #59
• DOC: Improve syntax in prob tracking episode callout by @jhlegarreta in #62
• MAINT: Update dti episode image and dataset by @kaitj in #64
• MAINT: Update exercise solution by @kaitj in #65
• Manual episode order for Figures by @tobyhodges in #68
• STYLE: Use the episode order feature by @jhlegarreta in #67
• ENH: Add different orientations to CSD Episode by @kaitj in #69
• DOC: Add meaningful figure captions by @jhlegarreta in #72
• DOC: Fix typo in citation author name by @jhlegarreta in #70
• STY: Sync template and update Makefile/Gemfile by @josephmje in #73
• BUG: Mark output cell as Markdown in CSD episode by @jhlegarreta in #75
• DOC: Declare no reported problems in instructor notes by @jhlegarreta in #74
• STYLE: Prefer {{ relative_root_path }} to resolve figure paths by @jhlegarreta in #71
• ENH: Put the fury camera setup into a function by @jhlegarreta in #76
• DOC: Add discussion section about camera setup by @jhlegarreta in #77
• DOC: Improve the completeness of tractography method list by @jhlegarreta in #80
• DOC: Add further aspects of dMRI to discussion by @jhlegarreta in #79
• FIX: Update image display in DTI lesson by @josephmje in #84
• include base_path.html for relative_root_path by @tobyhodges in #86
• ENH: Add orientation concepts figure by @kaitj in #82
• BUG: Add missing base path include by @jhlegarreta in #87
• STYLE: Change tabs to whitespaces by @jhlegarreta in #89
• BUG: Use the right bvec file in prob tractography episode by @jhlegarreta in #91
• BUG: Fix probabilistic tractography notebook by @jhlegarreta in #90
• BUG: Fix deterministic tractography notebook by @jhlegarreta in #94
• STYLE: Comply with PEP 8 by @jhlegarreta in #95
• ENH: Add coronal and sagittal views to GFA plot by @jhlegarreta in #97
• ENH: Fix GitHub actions notebook test workflow by @jhlegarreta in #96
• FIX: Fix broken paths in intro notebook by @josephmje in #99
• BUG: Update probabilistic tractography episode by @kaitj in #103
• ENH: Update deterministic tractography episode by @kaitj in #104
• ENH: Constrain the slices to be shown to three dimensions by @jhlegarreta in #98
• ENH: Add SH order theory by @kaitj in #106
• FIX: Clear deterministic tractography jupyter outputs by @kaitj in #109
• ENH: Define the SH order at a single location by @jhlegarreta in #107
• FIX: Update Binder link by @josephmje in #108
• ENH: Change SH order in probabilistic tractography notebook by @jhlegarreta in #113
• ENH: Save and show the probabilistic tracking episode peaks by @jhlegarreta in #114
• ENH: Remove Travis CI config file by @jhlegarreta in #111
• ENH: Reuse the anatomical orientation views generating method by @jhlegarreta in #92
• ENH: Bring 404 page from lesson example by @jhlegarreta in #112
• STYLE: Remove excessive whitespace around RGB FA map plot by @jhlegarreta in #119
• BUG: Fix the anatomical slice figure sorting by @jhlegarreta in #122
• ENH: Remove empty cell from CSD notebook by @jhlegarreta in #124
• STYLE: Mark numeric cell as Markdown in CSD episode by @jhlegarreta in #123
• ENH: Call NiBabel get_fdata() instead of get_data() by @jhlegarreta in #125
• DOC: Add info about downloading single subject from OSF by @kaitj in #126
• BUG: Fix call to visualization helper and skip fury visualizations in tests by @jhlegarreta in #128
• FIX: Fix slice orientations by @kaitj in #121
• BUG: Call to visualization module by @kaitj in #130
• FIX: Update and sync DTI episode by @kaitj in #116
• FIX: Update pythonpath by @kaitj in #133
• STY: Update DTI notebook by @kaitj in #132
• ENH: Update probabilistic tractography notebook by @kaitj in #134
• FIX: Actions workflow - rm zip by @kaitj in #135
• ENH: Update deterministic tractography by @kaitj in #120
• ENH: Increase the test workflow scheduled frequency by @jhlegarreta in #136
• FIX: Reset notebook kernel by @kaitj in #137
• ENH: Add csd exercise by @kaitj in #117
• FIX: add skip tag for utils by @kaitj in #139
• Update styles 2021-04-20 by @zkamvar in #140
• ENH: Split apart visualization cell in CSD exercise by @jhlegarreta in #142
• STYLE: Fix unknown code block warning by @jhlegarreta in #146
• STYLE: Use a separate, lesson-specific links file by @jhlegarreta in #145
• ENH: Add website build workflow status badge to README by @jhlegarreta in #144
• ENH: Fix cell test skip command by @jhlegarreta in #148
• MAINT: Migrate master branch to main by @josephmje in #149
• STYLE: Prefer using {{ relative_root_path }} to resolve episode links by @jhlegarreta in #151
• STYLE: Limit line length in Markdown files by @jhlegarreta in #150
• STYLE: Remove unnecessary whitespaces by @jhlegarreta in #152
• FIX: Update Github Actions caching by @josephmje in #153
• STYLE: Bump style changes by @jhlegarreta in #154
• FIX: Update to pip install cache by @josephmje in #155
• STYLE: Use inline image class by @jhlegarreta in #157
• STYLE: Remove the unnecessary img-responsive class for images by @jhlegarreta in #158
• STYLE: Bump style changes by @jhlegarreta in #156
• STYLE: Allow rendering LaTeX math syntax by @jhlegarreta in #161
• DOC: Fix figure generation method docstring by @jhlegarreta in #163
• ENH: Test non-solution notebooks by @jhlegarreta in #162
• BUG: Fix introduction episode non-solution notebook by @jhlegarreta in #166
• STYLE: Improve style by @jhlegarreta in #165
• BUG: Fix data location in non solution introduction notebook by @jhlegarreta in #167
• ENH: Skip visualization cells in non-solution CSD notebook by @jhlegarreta in #168
• ENH: Update DIPY fiber response function method call by @jhlegarreta in #170
• ENH: Allow initial dot for BIDS extension entity by @jhlegarreta in #169
• BUG: Fix DIPY fiber response function method call parameter by @jhlegarreta in #174
• ENH: Run GitHub actions build test workflow on PRs by @jhlegarreta in #172
• BUG: Fix data paths in preprocessing episode solutions notebook by @jhlegarreta in #176
• BUG: Fix data paths in preprocessing episode solutions notebook p2 by @josephmje in #177
• BUG: Fix data paths in preprocessing episode solutions notebook by @jhlegarreta in #180
• ENH: Install FSL and ANTs within GitHub Actions by @josephmje in #175
• ENH: Update Binder environment by @josephmje in #178
• ENH: Use Exercise2 extension to synchronize solution and non-solution notebooks by @josephmje in #182
• DOC: Fix typo in Build, test workflow step name by @jhlegarreta in #183
• STYLE: Remove unused imports by @jhlegarreta in #186
• ENH: Allow initial dot for BIDS extension entity by @jhlegarreta in #187
• STYLE: Remove trailing whitespaces by @jhlegarreta in #189
• ENH: Add AD and RD map figures to DTI episode by @jhlegarreta in #191
• STYLE: Move imports closer to used location in prob tractogr episode by @jhlegarreta in #188
• fix formatting of block quote code by @zkamvar in #192
• DOC: Remove orphan character in Python code snippet by @jhlegarreta in #194
• ENH: Increase text style consistency by @jhlegarreta in #198
• ENH: Switch to JupyterLab by @jhlegarreta in #200
• DOC: Add memory limitation notes by @jhlegarreta in #201
• turn katex on by @fmichonneau in #202
• STYLE: Prefer f-strings over %-formatting for string substitution by @jhlegarreta in #203
• ENH: Allow running visualization cells in CI workflow by @jhlegarreta in #204
• ENH: Remove Python package cache restore in GHA workflow by @jhlegarreta in #206
• ENH: Add PyBIDS leading dot warning by @jhlegarreta in #211
• urgent: fix workflows by @zkamvar in #213
• ENH: Pin matplotlib package version by @jhlegarreta in #214
• ENH: Update actions versions to use Node.js 16 by @jhlegarreta in #215
• ENH: Update DIPY and FURY by @jhlegarreta in #218
• MAINT: Clarification and spelling updates by @kaitj in #212
• STYLE: Increase style consistency across episodes by @jhlegarreta in #219
• ENH: Drop Python 3.7 and add 3.10 to testing matrix by @jhlegarreta in #217
• STYLE: Fix DTI episode radial diffusivity inline picture markup by @jhlegarreta in #223
• Update setup-python version by @georgebisbas in #224
• ENH: Synchronize Binder environment package versions with requirements by @jhlegarreta in #227
• BUG: Fix package dependency spec in Binder when using pip by @jhlegarreta in #229
• ENH: Conform to current FSL installation instructions by @jhlegarreta in #231
• ENH: Bump DIPY to version 1.7.0 by @jhlegarreta in #232
• ENH: Clean up FSL installer download step by @jhlegarreta in #233
• BUG: Fix FSL eddy command by @jhlegarreta in #234
• ENH: Miscellaneous improvements to build, test GHA workflow by @jhlegarreta in #235
• BUG: Fix Ubuntu dependencies caching exception paths by @jhlegarreta in #236
• DOC: Fix preprocessing episode b0 brainmask image syntax by @jhlegarreta in #237
• STYLE: Allow rendering LaTeX math syntax: intro and preproc episodes by @jhlegarreta in #238
• DOC: Update introduction and preprocessing lessons by @Bradley-Karat in #222
• STYLE: Improve style across miscellaneous episode files by @jhlegarreta in #244
• ENH: Add Python 3.11 to the CI build matrix by @jhlegarreta in #243
• ENH: Set up correctly branches filter in build, test GHA workflow file by @jhlegarreta in #242

New Contributors

• @dependabot made their first contribution in #9
• @fmichonneau made their first contribution in #13
• @jhlegarreta made their first contribution in #15
• @josephmje made their first contribution in #35
• @tobyhodges made their first contribution in #68
• @zkamvar made their first contribution in #140
• @georgebisbas made their first contribution in #224
• @Bradley-Karat made their first contribution in #222

Full Changelog: v9.5.3...v10.0.0