1.0.0rc1

[tsalo]

This is a prerelease for the version that will be used by the HBCD project for their first data release.

We plan to not introduce any backwards-incompatible changes for a while.

What's Changed

🛠 Breaking Changes

• Rename QSIPrep to QSIRecon by @tsalo in Rename QSIPrep to QSIRecon #1
• Start removing QSIPrep-specific code and documentation by @tsalo in Start removing QSIPrep-specific code and documentation #4
• Remove QSIPrep-specific parameters and Config elements by @tsalo in Remove QSIPrep-specific parameters and Config elements #6
• Drop Docker wrapper by @tsalo in Drop Docker wrapper #52
• Restructure outputs into BIDS datasets by @tsalo in Restructure outputs into BIDS datasets #66
• Combine mfp and mdp entities into single param entity by @tsalo in Combine mfp and mdp entities into single param entity #72
• Replace --recon-input-pipeline with --input-type by @tsalo in Replace --recon-input-pipeline with --input-type #68
• Remove unused --longitudinal argument by @tsalo in Remove unused --longitudinal argument #88
• Make all params and models lower-case by @tsalo in Make all params and models lower-case #90
• Reorganize atlas management based on XCP-D and BIDS-Atlas by @tsalo in Reorganize atlas management based on XCP-D and BIDS-Atlas #123
• Rename --freesurfer-input to --fs-subjects-dir by @tsalo in Rename --freesurfer-input to --fs-subjects-dir #152
• [ENH] Read session-specific anat data by @mattcieslak in [ENH] Read session-specific anat data #151
• Remove underscore versions of all parameters by @tsalo in Remove underscore versions of all parameters #159
• Make connectivity field names compatible with MATLAB by @tsalo in Make connectivity field names compatible with MATLAB #166

🎉 Exciting New Features

• Add ng, perng, parng, and mapcoeffs to Dipy MAPMRI outputs by @tsalo in Add ng, perng, parng, and mapcoeffs to Dipy MAPMRI outputs #55
• Add DatasetLinks to dataset_description.json by @tsalo in Add DatasetLinks to dataset_description.json #77
• Pass DWI file metadata to reconstruction workflows by @tsalo in Pass DWI file metadata to reconstruction workflows #154
• Add HBCD Release1 recon workflow by @mattcieslak in Add HBCD Release1 recon workflow #169

🐛 Bug Fixes

• Write out QSIRecon pipeline-wise reports by @tsalo in Write out QSIRecon pipeline-wise reports #7
• Write out reports to individual reconstruction derivative folders by @tsalo in Write out reports to individual reconstruction derivative folders #53
• Add summary reportlets to HTML report by @tsalo in Add summary reportlets to HTML report #61
• Fix QSIRecon Entrypoint by @smeisler in Fix QSIRecon Entrypoint #76
• Use file lock to avoid concurrent edits to dataset_description.json by @cookpa in Use file lock to avoid concurrent edits to dataset_description.json #91
• Compress the tck files by @tsalo in Compress the tck files #93
• Add missing filename patterns by @tsalo in Add missing filename patterns #131
• Fix infant anatomical ingression by @tsalo in Fix infant anatomical ingression #126
• Fix extension in ds_fs_5tt_hsvs by @tsalo in Fix extension in ds_fs_5tt_hsvs #165
• Fix extension in ds_qsiprep_5tt_hsvs by @tsalo in Fix extension in ds_qsiprep_5tt_hsvs #172
• Fix space in ds_qsiprep_5tt_hsvs by @tsalo in Fix space in ds_qsiprep_5tt_hsvs #175
• Make PlotPeaks robust enough that we don't need --writable-tempfs in singularity/apptainer by @mattcieslak in Make PlotPeaks robust enough that we don't need --writable-tempfs in singularity/apptainer #174

Other Changes

• Remove internal version of LiterateWorkflow by @tsalo in Remove internal version of LiterateWorkflow #8
• Drop and modify infrastructure files by @tsalo in Drop and modify infrastructure files #40
• Remove QSIPrep-specific tests by @tsalo in Remove QSIPrep-specific tests #5
• Drop unused modules, classes, and functions by @tsalo in Drop unused modules, classes, and functions #11
• [CI] Speed up pyafq test by @mattcieslak in [CI] Speed up pyafq test #57
• [DOCS] Reorganize documentation by @mattcieslak in [DOCS] Reorganize documentation #56
• Collect templates from TemplateFlow instead of package data by @tsalo in Collect templates from TemplateFlow instead of package data #49
• Remove unused data files by @tsalo in Remove unused data files #63
• Replace hyperlinks with BibTeX references by @tsalo in Replace hyperlinks with BibTeX references #67
• [DOCS] Add scalar tables by @mattcieslak in [DOCS] Add scalar tables #80
• Move scalar file configs to YAMLs and use a recon scalar workflow by @tsalo in Move scalar file configs to YAMLs and use a recon scalar workflow #79
• [WIP] Make a system for keeping docs and file names in sync by @mattcieslak in [WIP] Make a system for keeping docs and file names in sync #86
• Convert pipeline configs from JSON to YAML by @tsalo in Convert pipeline configs from JSON to YAML #84
• [DOCS] clean up by @mattcieslak in [DOCS] clean up #101
• Draft pre-init ingression by @tsalo in Draft pre-init ingression #102
• [ENH] Update AMICO by @mattcieslak in [ENH] Update AMICO #115
• [FIX] mif2fib by @ameliecr in [FIX] mif2fib #116
• Fix how bundles to be tracked are selected for DSIstudio autotrack by @ameliecr in Fix how bundles to be tracked are selected for DSIstudio autotrack #121
• [FIX] workflow connection in dsi_studio_gqi by @mattcieslak in [FIX] workflow connection in dsi_studio_gqi #142
• [CI] add hsvs test by @mattcieslak in [CI] add hsvs test #136
• [FIX] dsi_studio_gqi workflow connect by @mattcieslak in [FIX] dsi_studio_gqi workflow connect #146
• [DOC] Minor addition for skipping connectivity matrices step by @chiuhoward in [DOC] Minor addition for skipping connectivity matrices step #150
• Add page documenting output structure by @tsalo in Add page documenting output structure #156
• Add information about QSIPrep/QSIRecon releases by @tsalo in Add information about QSIPrep/QSIRecon releases #158
• [CI] Add tests for reading pre-1.0 outputs from qsiprep by @mattcieslak in [CI] Add tests for reading pre-1.0 outputs from qsiprep #155
• [ENH] Support outputs from qsiprep 1.0.0rc0 by @mattcieslak in [ENH] Support outputs from qsiprep 1.0.0rc0 #160
• [FIX] get rid of logging error calc_connectivity failed to run in dsi_studio_gqi pipeline #145 by @mattcieslak in [FIX] get rid of logging error #145 #161
• Add UKB ingression by @smeisler in Add UKB ingression #147
• [FIX] set TMPDIR before running plot_peaks by @mattcieslak in [FIX] set TMPDIR before running plot_peaks #163
• [ENH] match to qsiprep nipype/nireports versions by @mattcieslak in [ENH] match to qsiprep nipype/nireports versions #167
• Add in Val's text for connectivity matrices by @mattcieslak in Add in Val's text for connectivity matrices #173
• Disable test_main in the CI integration tests by @mattcieslak in Disable test_main in the CI integration tests #177

New Contributors

• @tsalo made their first contribution in Rename QSIPrep to QSIRecon #1
• @mattcieslak made their first contribution in [CI] Speed up pyafq test #57
• @cookpa made their first contribution in Use file lock to avoid concurrent edits to dataset_description.json #91
• @dependabot made their first contribution in Update nireports requirement from ~=23.2.2 to ~=24.0.2 #100
• @ameliecr made their first contribution in [FIX] mif2fib #116
• @chiuhoward made their first contribution in [DOC] Minor addition for skipping connectivity matrices step #150

Full Changelog: https://github.com/PennLINC/qsirecon/commits/1.0.0rc1

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This discussion was created from the release 1.0.0rc1.