Final revisions for next branch (#3134)

With the merge of this PR, we will merge `next` into `master` and begin
the process of releasing 23.2.0a1.

Starting by running without fasttrack to pin down expected results.

.circleci/config.yml

@@ -87,9 +87,30 @@ _setup_fmriprep_docker: &setup_fmriprep_docker
     pip install --upgrade /tmp/src/fmriprep/wrapper/
 
 _check_outputs: &check_outputs
-  name: Show outputs of fMRIPrep run
+  name: Check outputs of fMRIPrep run
   command: |
-    find /tmp/${DATASET}/${SUBDIR:-fmriprep} \( -path '*/figures' -o -path '*/log' -o -path '*/sourcedata' \) -prune -o -name "*" -print | cut -d/ -f 5- | sort
+    set +e -x
+    mkdir -p /tmp/${DATASET}/test
+    find /tmp/${DATASET}/${SUBDIR:-fmriprep} \
+      \( -path '*/figures' -o -path '*/log' -o -path '*/sourcedata' \) \
+      -prune -o -name "*" -print | cut -d/ -f 5- | sort > /tmp/${DATASET}/test/outputs.out
+
+    FASTTRACK_OUTPUTS="${DATASET}${VARIANT}_fasttrack_outputs.txt"
+    FULL_OUTPUTS="${DATASET}${VARIANT}_outputs.txt"
+    RET=1
+    if [ ! -f /tmp/.nofasttrack ]; then
+        echo "Checking fasttrack..."
+        sort /tmp/src/fmriprep/.circleci/${FASTTRACK_OUTPUTS} > /tmp/${DATASET}/test/fasttrack.out
+        diff /tmp/${DATASET}/test/{fasttrack,outputs}.out
+        RET=$?
+    fi
+    if [ $RET -ne 0 ]; then
+        echo "Checking full..."
+        sort /tmp/src/fmriprep/.circleci/${FULL_OUTPUTS} > /tmp/${DATASET}/test/full.out
+        diff /tmp/${DATASET}/test/{full,outputs}.out
+        RET=$?
+    fi
+    exit $RET
 
 version: 2.1
 aliases:

.circleci/ds005_fasttrack_outputs.txt

@@ -0,0 +1,70 @@
+
+.bidsignore
+dataset_description.json
+desc-aparcaseg_dseg.tsv
+desc-aseg_dseg.tsv
+logs
+logs/CITATION.bib
+logs/CITATION.html
+logs/CITATION.md
+logs/CITATION.tex
+sub-01
+sub-01/anat
+sub-01/anat/sub-01_desc-ribbon_mask.json
+sub-01/anat/sub-01_desc-ribbon_mask.nii.gz
+sub-01/anat/sub-01_hemi-L_desc-preproc_sphere.surf.gii
+sub-01/anat/sub-01_hemi-L_desc-preproc_white.surf.gii
+sub-01/anat/sub-01_hemi-L_desc-reg_sphere.surf.gii
+sub-01/anat/sub-01_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
+sub-01/anat/sub-01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
+sub-01/anat/sub-01_hemi-R_desc-preproc_sphere.surf.gii
+sub-01/anat/sub-01_hemi-R_desc-preproc_white.surf.gii
+sub-01/anat/sub-01_hemi-R_desc-reg_sphere.surf.gii
+sub-01/anat/sub-01_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
+sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
+sub-01/func
+sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.json
+sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.nii.gz
+sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
+sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
+sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.json
+sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.nii.gz
+sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-hmc_boldref.json
+sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-hmc_boldref.nii.gz
+sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.json
+sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.nii.gz
+sub-01/func/sub-01_task-mixedgamblestask_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
+sub-01/func/sub-01_task-mixedgamblestask_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
+sub-01/func/sub-01_task-mixedgamblestask_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
+sub-01/func/sub-01_task-mixedgamblestask_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
+sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.func.gii
+sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.json
+sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsnative_bold.func.gii
+sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsnative_bold.json
+sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.func.gii
+sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
+sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.func.gii
+sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
+sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
+sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.nii.gz
+sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.nii.gz
+sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.nii.gz
+sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
+sub-01/func/sub-01_task-mixedgamblestask_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
+sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii
+sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsnative_bold.func.gii
+sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsnative_bold.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsaverage5_bold.func.gii
+sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsaverage5_bold.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsnative_bold.func.gii
+sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsnative_bold.json
+sub-01.html