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Merge pull request #184 from connectomicslab/release/v3.0.4
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REL: v3.0.4
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@sebastientourbier
sebastientourbier authored Jun 15, 2022
2 parents d0dc006 + 330a7a4 commit 2ce5619
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10 changes: 8 additions & 2 deletions .circleci/config.yml
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Expand Up @@ -401,6 +401,7 @@ jobs:
- run:
name: Enable "--squash" feature of docker build
command: |
# Enable the --squash feature
sudo touch /etc/docker/daemon.json
echo "{\"experimental\": true}" | sudo tee -a /etc/docker/daemon.json
sudo service docker restart
Expand Down Expand Up @@ -442,8 +443,13 @@ jobs:
fi
# Build CMP BIDS App docker image
cd /home/circleci/src/connectomemapper3
ls -la .
DOCKER_BUILDKIT=1 docker build --progress=plain --squash --rm=true --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` --build-arg VCS_REF=`git rev-parse --short HEAD` --build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" -t sebastientourbier/connectomemapper3 /home/circleci/src/connectomemapper3 \
export DOCKER_BUILDKIT=1
docker build --progress=plain \
--squash --rm=true \
--build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
--build-arg VCS_REF=`git rev-parse --short HEAD` \
--build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" \
-t sebastientourbier/connectomemapper3 /home/circleci/src/connectomemapper3
#- run:
# name: Prune Docker cache (temporary)
# command: docker system prune -f
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232 changes: 116 additions & 116 deletions .circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt
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120 changes: 60 additions & 60 deletions .circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt
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@@ -1,22 +1,22 @@
cmp-v3.0.3/dataset_description.json
cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.graphml
cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.nii.gz
cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.tsv
cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_FreeSurferColorLUT.txt
cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_stats.tsv
cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz
cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz
cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
cmp-v3.0.3/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
cmp-v3.0.3/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
cmp-v3.0.4/dataset_description.json
cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.graphml
cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.nii.gz
cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.tsv
cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_FreeSurferColorLUT.txt
cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_stats.tsv
cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz
cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz
cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz
cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json
cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz
cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz
cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz
cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz
cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz
cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz
cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz
cmp-v3.0.4/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz
cmp-v3.0.4/sub-01/ses-01/sub-01_ses-01_anatomical_config.json
freesurfer-7.1.1/dataset_description.json
freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab
freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab
Expand Down Expand Up @@ -361,44 +361,44 @@ freesurfer-7.1.1/sub-01_ses-01/touch/talairach.touch
freesurfer-7.1.1/sub-01_ses-01/touch/wmaparc.stats.touch
freesurfer-7.1.1/sub-01_ses-01/touch/wmaparc.touch
freesurfer-7.1.1/sub-01_ses-01/touch/wmsegment.touch
nipype-1.7.0/dataset_description.json
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/anat_datasinker/_inputs.pklz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/anat_datasinker/_node.pklz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/anat_datasinker/_report/report.rst
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/anat_datasinker/result_anat_datasinker.pklz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/anat_datasource/_inputs.pklz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/anat_datasource/_node.pklz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/anat_datasource/_report/report.rst
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/anat_datasource/result_anat_datasource.pklz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/d3.js
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/graph1.json
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/graph.dot
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/graph.json
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/graph.svg
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/index.html
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/compute_roi_volumetry/freesurferaparc_roi_stats.tsv
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/compute_roi_volumetry/_inputs.pklz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/compute_roi_volumetry/_node.pklz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/compute_roi_volumetry/_report/report.rst
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/compute_roi_volumetry/result_compute_roi_volumetry.pklz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/_inputs.pklz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/_node.pklz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/_report/report.rst
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/result_createBIDSLabelIndexMappingFile.pklz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/aparc+aseg.native.nii.gz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/brain_eroded.nii.gz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/brain_mask.nii.gz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/brain.nii.gz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/csf_eroded.nii.gz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/csf_mask.nii.gz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/fsmask_1mm.nii.gz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/gmmask.nii.gz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_inputs.pklz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_node.pklz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_report/report.rst
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/result_NativeFreesurfer_parcellation.pklz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/ribbon.nii.gz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/ROIv_HR_th_freesurferaparc.nii.gz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/T1.nii.gz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/wm_eroded.nii.gz
nipype-1.7.0/sub-01/ses-01/anatomical_pipeline/pypeline.log
nipype-1.8.0/dataset_description.json
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/anat_datasinker/_inputs.pklz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/anat_datasinker/_node.pklz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/anat_datasinker/_report/report.rst
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/anat_datasinker/result_anat_datasinker.pklz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/anat_datasource/_inputs.pklz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/anat_datasource/_node.pklz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/anat_datasource/_report/report.rst
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/anat_datasource/result_anat_datasource.pklz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/d3.js
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/graph1.json
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/graph.dot
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/graph.json
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/graph.svg
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/index.html
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/compute_roi_volumetry/freesurferaparc_roi_stats.tsv
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/compute_roi_volumetry/_inputs.pklz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/compute_roi_volumetry/_node.pklz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/compute_roi_volumetry/_report/report.rst
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/compute_roi_volumetry/result_compute_roi_volumetry.pklz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/_inputs.pklz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/_node.pklz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/_report/report.rst
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/result_createBIDSLabelIndexMappingFile.pklz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/aparc+aseg.native.nii.gz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/brain_eroded.nii.gz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/brain_mask.nii.gz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/brain.nii.gz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/csf_eroded.nii.gz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/csf_mask.nii.gz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/fsmask_1mm.nii.gz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/gmmask.nii.gz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_inputs.pklz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_node.pklz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_report/report.rst
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/result_NativeFreesurfer_parcellation.pklz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/ribbon.nii.gz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/ROIv_HR_th_freesurferaparc.nii.gz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/T1.nii.gz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/wm_eroded.nii.gz
nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/pypeline.log
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