Merge pull request #379 from nipreps/ci/fix-smoke

CI: Fix smoke tests

Author: mgxd

.circleci/bcp_anat_outputs.txt

@@ -10,39 +10,34 @@ logs/CITATION.tex
 sub-01
 sub-01/ses-1mo
 sub-01/ses-1mo/anat
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-aparcaseg_dseg.nii.gz
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+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-preproc_T2w.json
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 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-brain_mask.json
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-brain_mask.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T1w.json
@@ -51,6 +46,12 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_dseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-CSF_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-GM_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-preproc_T2w.json
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-preproc_T2w.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-aparcaseg_dseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-aseg_dseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-ribbon_mask.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_desc-ribbon_mask.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_dseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_label-CSF_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_label-GM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T1w_label-WM_probseg.nii.gz
 sub-01_ses-1mo.html

.circleci/bcp_anat_t2only_outputs.txt

@@ -10,39 +10,32 @@ logs/CITATION.tex
 sub-01
 sub-01/ses-1mo
 sub-01/ses-1mo/anat
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 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T2w.json
@@ -51,4 +44,12 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_dseg.nii.gz
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 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz
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+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T2w_label-WM_probseg.nii.gz
 sub-01_ses-1mo.html

.circleci/bcp_full_outputs.txt

@@ -10,39 +10,34 @@ logs/CITATION.tex
 sub-01
 sub-01/ses-1mo
 sub-01/ses-1mo/anat
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@@ -51,27 +46,38 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_dseg.nii.gz
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-sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_from-scanner_to-boldref_mode-image_xfm.txt
-sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_from-T1w_to-scanner_mode-image_xfm.txt
+sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
+sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
+sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_from-boldref_to-auto00000_mode-image_xfm.json
+sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_from-boldref_to-auto00000_mode-image_xfm.txt
+sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
+sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
+sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_boldref.json
 sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_boldref.nii.gz
-sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_desc-aparcaseg_dseg.nii.gz
-sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_desc-aseg_dseg.nii.gz
 sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_desc-brain_mask.json
 sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_desc-brain_mask.nii.gz
 sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_cohort-1_desc-preproc_bold.json

.circleci/config.yml

@@ -10,7 +10,7 @@ _machine_defaults: &machine_defaults
 
 _python_defaults: &python_defaults
   docker:
-    - image: cimg/python:3.12.1
+    - image: cimg/python:3.12.5
       auth:
         username: $DOCKER_USER
         password: $DOCKER_PAT
@@ -160,17 +160,16 @@ jobs:
 
 
   get_data:
-    docker:
-      - image: cimg/python:3.12.1
+    <<: *python_defaults
     working_directory: /home/circleci/data
     steps:
       - restore_cache:
           keys:
-            - data-v0-{{ .Branch }}-{{ .Revision }}
-            - data-v0--{{ .Revision }}
-            - data-v0-{{ .Branch }}-
-            - data-v0-master-
-            - data-v0-
+            - data-v1-{{ .Branch }}-{{ .Revision }}
+            - data-v1--{{ .Revision }}
+            - data-v1-{{ .Branch }}-
+            - data-v1-master-
+            - data-v1-
       - run:
           name: Install datalad + git-annex
           command: |
@@ -180,7 +179,7 @@ jobs:
               git config --global filter.annex.process "git-annex filter-process"
               git config --global user.name "Nipreps CI"
               git config --global user.email "[email protected]"
-              pip install "datalad<0.18"
+              pip install datalad
             fi
       - run:
           name: Get bcp test data
@@ -334,7 +333,8 @@ jobs:
                 --output-spaces MNIInfant:cohort-1 func \
                 --sloppy --write-graph --mem-mb 14000 \
                 --nthreads 4 -vv --age-months 2 --sloppy \
-                --derivatives /tmp/data/${DATASET}/derivatives/precomputed \
+                --surface-recon-method infantfs \
+                --derivatives precomputed=/tmp/data/${DATASET}/derivatives/bibsnet \
                 --output-layout bids --anat-only
       - run:
           name: Checking outputs of anatomical nibabies run
@@ -362,7 +362,8 @@ jobs:
                 --output-spaces MNIInfant:cohort-1 func \
                 --sloppy --write-graph --mem-mb 14000 \
                 --nthreads 4 -vv --age-months 2 --sloppy \
-                --derivatives /tmp/data/${DATASET}/derivatives/precomputed \
+                --surface-recon-method infantfs \
+                --derivatives precomputed=/tmp/data/${DATASET}/derivatives/bibsnet \
                 --output-layout bids
       - run:
           name: Checking outputs of full nibabies run
@@ -390,12 +391,7 @@ jobs:
             rm -f /tmp/data/${DATASET}-t2only/sub-01/ses-1mo/anat/*_T1w.*
             tree /tmp/data/${DATASET}-t2only
             mkdir -p /tmp/data/${DATASET}-t2only/derivatives
-            cp -r /tmp/data/${DATASET}/derivatives/precomputed /tmp/data/${DATASET}-t2only/derivatives
-            # rename the derivatives for now - this is only possible since they share the same space
-            sudo apt install rename
-            rename 's/space-T1w/space-T2w/' /tmp/data/${DATASET}-t2only/derivatives/precomputed/sub-01/ses-1mo/anat/*
-            sed -i 's/_T1w./_T2w./g' /tmp/data/${DATASET}-t2only/derivatives/precomputed/sub-01/ses-1mo/anat/*json
-            tree /tmp/data/${DATASET}-t2only/derivatives/precomputed
+            cp -r /tmp/data/${DATASET}/derivatives/bibsnet /tmp/data/${DATASET}-t2only/derivatives
 
       - run:
           name: Run nibabies single anatomical workflow
@@ -412,7 +408,8 @@ jobs:
                 --output-spaces MNIInfant:cohort-1 func \
                 --sloppy --write-graph --mem-mb 14000 \
                 --nthreads 4 -vv --age-months 2 --sloppy \
-                --derivatives /tmp/data/${DATASET}-t2only/derivatives/precomputed \
+                --surface-recon-method infantfs \
+                --derivatives precomputed=/tmp/data/${DATASET}-t2only/derivatives/bibsnet \
                 --output-layout bids --anat-only
       - run:
           name: Checking outputs of T2-only nibabies anat