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Merge pull request #2409 from mgxd/enh/update-dockerfile
ENH: Bump Dockerfile
2 parents 7e17dea + 72e1a73 commit 237523c

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‎.circleci/config.yml‎

Lines changed: 28 additions & 51 deletions
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,9 @@ jobs:
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TZ: "/usr/share/zoneinfo/America/Los_Angeles"
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SCRATCH: "/scratch"
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machine:
9-
image: ubuntu-1604:202007-01
9+
# https://discuss.circleci.com/t/linux-machine-executor-images-2021-april-q2-update/39928
10+
# upgrade Docker version
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image: ubuntu-2004:202104-01
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working_directory: /tmp/src/fmriprep
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steps:
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- checkout
@@ -118,15 +120,14 @@ jobs:
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get_data:
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machine:
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# Ubuntu 14.04 with Docker 17.10.0-ce
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image: ubuntu-1604:202007-01
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image: ubuntu-2004:202104-01
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working_directory: /home/circleci/data
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steps:
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- restore_cache:
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keys:
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- data-v8-{{ .Branch }}-{{ .Revision }}
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- data-v8-{{ .Branch }}
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- data-v8-
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- data-v9-{{ .Branch }}-{{ .Revision }}
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- data-v9-{{ .Branch }}
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- data-v9-
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- run:
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name: Get test data from ds000005
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command: |
@@ -203,7 +204,7 @@ jobs:
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echo "sMRIPrep derivatives of ds000210 were cached"
204205
fi
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- save_cache:
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key: data-v8-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
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key: data-v9-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
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paths:
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- /tmp/data
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- /tmp/ds005/freesurfer
@@ -235,7 +236,7 @@ jobs:
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test_pytest:
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machine:
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image: ubuntu-1604:202007-01
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image: ubuntu-2004:202104-01
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working_directory: /tmp/src/fmriprep
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steps:
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- checkout:
@@ -265,7 +266,7 @@ jobs:
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- /tmp/images
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- restore_cache:
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keys:
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- data-v8-{{ .Revision }}
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- data-v9-{{ .Branch }}-{{ .Revision }}
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- run:
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name: Docker authentication
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command: |
@@ -329,7 +330,7 @@ jobs:
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ds005:
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machine:
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image: ubuntu-1604:202007-01
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image: ubuntu-2004:202104-01
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working_directory: /tmp/ds005
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environment:
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- FS_LICENSE: /tmp/fslicense/license.txt
@@ -366,7 +367,7 @@ jobs:
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- /tmp/images
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- restore_cache:
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keys:
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- data-v8-{{ .Branch }}-{{ .Revision }}
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- data-v9-{{ .Branch }}-{{ .Revision }}
370371
- restore_cache:
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keys:
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- ds005-anat-v18-{{ .Branch }}-{{ .Revision }}
@@ -403,22 +404,16 @@ jobs:
403404
sed -e 's/.* 3\./3./' -e 's/ .*//')
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pyenv local $PY3
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mkdir -p /tmp/${DATASET}/derivatives
406-
sudo setfacl -d -m group:$(id -gn):rwx /tmp/${DATASET}/derivatives
407-
sudo setfacl -m group:$(id -gn):rwx /tmp/${DATASET}/derivatives
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pip install --upgrade pip setuptools
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pip install --upgrade /tmp/src/fmriprep/wrapper/
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- run:
411410
name: Run anatomical workflow on ds005
412411
no_output_timeout: 2h
413412
command: |
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mkdir -p /tmp/${DATASET}/work /tmp/${DATASET}/derivatives
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sudo setfacl -d -m group:$(id -gn):rwx /tmp/${DATASET}/derivatives && \
416-
sudo setfacl -m group:$(id -gn):rwx /tmp/${DATASET}/derivatives
417-
sudo setfacl -d -m group:$(id -gn):rwx /tmp/${DATASET}/work && \
418-
sudo setfacl -m group:$(id -gn):rwx /tmp/${DATASET}/work
419414
if [ -f /tmp/.nofasttrack ]; then
420415
fmriprep-docker -i nipreps/fmriprep:latest \
421-
-e FMRIPREP_DEV 1 -u $(id -u) \
416+
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
422417
--network none \
423418
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
424419
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
@@ -443,16 +438,12 @@ jobs:
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name: Run full fMRIPrep on ds005 (LegacyMultiProc plugin)
444439
no_output_timeout: 2h
445440
command: |
446-
sudo setfacl -d -m group:$(id -gn):rwx /tmp/${DATASET}/derivatives && \
447-
sudo setfacl -m group:$(id -gn):rwx /tmp/${DATASET}/derivatives
448-
sudo setfacl -d -m group:$(id -gn):rwx /tmp/${DATASET}/work && \
449-
sudo setfacl -m group:$(id -gn):rwx /tmp/${DATASET}/work
450441
FASTRACK_ARG="--anat-derivatives /tmp/${DATASET}/smriprep-0.6"
451442
if [ -f /tmp/.nofasttrack ]; then
452443
FASTRACK_ARG=""
453444
fi
454445
fmriprep-docker -i nipreps/fmriprep:latest \
455-
-e FMRIPREP_DEV 1 -u $(id -u) \
446+
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
456447
--network none \
457448
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
458449
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
@@ -498,7 +489,7 @@ jobs:
498489
FASTRACK_ARG=""
499490
fi
500491
fmriprep-docker -i nipreps/fmriprep:latest \
501-
-e FMRIPREP_DEV 1 -u $(id -u) \
492+
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
502493
--network none \
503494
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work_bids \
504495
/tmp/data/${DATASET}/ /tmp/${DATASET}/bids participant \
@@ -528,7 +519,7 @@ jobs:
528519
FASTRACK_ARG=""
529520
fi
530521
fmriprep-docker -i nipreps/fmriprep:latest \
531-
-e FMRIPREP_DEV 1 -u $(id -u) \
522+
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
532523
--network none \
533524
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work_partial \
534525
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives_partial participant \
@@ -572,7 +563,7 @@ jobs:
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573564
ds054:
574565
machine:
575-
image: ubuntu-1604:202007-01
566+
image: ubuntu-2004:202104-01
576567
working_directory: /tmp/ds054
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environment:
578569
- FS_LICENSE: /tmp/fslicense/license.txt
@@ -605,7 +596,7 @@ jobs:
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- /tmp/images
606597
- restore_cache:
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keys:
608-
- data-v8-{{ .Branch }}-{{ .Revision }}
599+
- data-v9-{{ .Branch }}-{{ .Revision }}
609600
- restore_cache:
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keys:
611602
- ds054-anat-v14-{{ .Branch }}-{{ .Revision }}
@@ -619,8 +610,6 @@ jobs:
619610
sed -e 's/.* 3\./3./' -e 's/ .*//')
620611
pyenv local $PY3
621612
mkdir -p /tmp/${DATASET}/derivatives
622-
sudo setfacl -d -m group:$(id -gn):rwx /tmp/${DATASET}/derivatives
623-
sudo setfacl -m group:$(id -gn):rwx /tmp/${DATASET}/derivatives
624613
pip install --upgrade pip setuptools
625614
pip install --upgrade /tmp/src/fmriprep/wrapper/
626615
- run:
@@ -651,13 +640,9 @@ jobs:
651640
no_output_timeout: 2h
652641
command: |
653642
mkdir -p /tmp/${DATASET}/work /tmp/${DATASET}/derivatives
654-
sudo setfacl -d -m group:$(id -gn):rwx /tmp/${DATASET}/derivatives && \
655-
sudo setfacl -m group:$(id -gn):rwx /tmp/${DATASET}/derivatives
656-
sudo setfacl -d -m group:$(id -gn):rwx /tmp/${DATASET}/work && \
657-
sudo setfacl -m group:$(id -gn):rwx /tmp/${DATASET}/work
658643
if [ -f /tmp/.nofasttrack ]; then
659644
fmriprep-docker -i nipreps/fmriprep:latest \
660-
-e FMRIPREP_DEV 1 \
645+
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
661646
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
662647
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
663648
--fs-no-reconall --sloppy --write-graph \
@@ -679,16 +664,12 @@ jobs:
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name: Run full fMRIPrep on ds054
680665
no_output_timeout: 2h
681666
command: |
682-
sudo setfacl -d -m group:$(id -gn):rwx /tmp/${DATASET}/derivatives && \
683-
sudo setfacl -m group:$(id -gn):rwx /tmp/${DATASET}/derivatives
684-
sudo setfacl -d -m group:$(id -gn):rwx /tmp/${DATASET}/work && \
685-
sudo setfacl -m group:$(id -gn):rwx /tmp/${DATASET}/work
686667
FASTRACK_ARG="--anat-derivatives /tmp/${DATASET}/smriprep-0.6"
687668
if [ -f /tmp/.nofasttrack ]; then
688669
FASTRACK_ARG=""
689670
fi
690671
fmriprep-docker -i nipreps/fmriprep:latest \
691-
-e FMRIPREP_DEV 1 \
672+
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
692673
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
693674
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
694675
${FASTRACK_ARG} \
@@ -717,7 +698,7 @@ jobs:
717698
/tmp/${DATASET}/derivatives/fmriprep/sub-100185/log/$UUID/
718699
set +e
719700
fmriprep-docker -i nipreps/fmriprep:latest \
720-
-e FMRIPREP_DEV 1 \
701+
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
721702
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
722703
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
723704
--fs-no-reconall --sloppy --write-graph \
@@ -744,7 +725,7 @@ jobs:
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745726
ds210:
746727
machine:
747-
image: ubuntu-1604:202007-01
728+
image: ubuntu-2004:202104-01
748729
working_directory: /tmp/ds210
749730
environment:
750731
- FS_LICENSE: /tmp/fslicense/license.txt
@@ -777,7 +758,7 @@ jobs:
777758
- /tmp/images
778759
- restore_cache:
779760
keys:
780-
- data-v8-{{ .Branch }}-{{ .Revision }}
761+
- data-v9-{{ .Branch }}-{{ .Revision }}
781762
- restore_cache:
782763
keys:
783764
- ds210-anat-v12-{{ .Branch }}-{{ .Revision }}
@@ -790,7 +771,7 @@ jobs:
790771
export PY3=$(pyenv versions | grep '3\.' |
791772
sed -e 's/.* 3\./3./' -e 's/ .*//')
792773
pyenv local $PY3
793-
mkdir -p /tmp/${DATASET}/derivatives && sudo setfacl -d -m group:$(id -gn):rwx /tmp/${DATASET}/derivatives && sudo setfacl -m group:$(id -gn):rwx /tmp/${DATASET}/derivatives
774+
mkdir -p /tmp/${DATASET}/derivatives
794775
pip install --upgrade pip setuptools
795776
pip install --upgrade /tmp/src/fmriprep/wrapper/
796777
- run:
@@ -821,13 +802,9 @@ jobs:
821802
no_output_timeout: 2h
822803
command: |
823804
mkdir -p /tmp/${DATASET}/work /tmp/${DATASET}/derivatives
824-
sudo setfacl -d -m group:$(id -gn):rwx /tmp/${DATASET}/derivatives && \
825-
sudo setfacl -m group:$(id -gn):rwx /tmp/${DATASET}/derivatives
826-
sudo setfacl -d -m group:$(id -gn):rwx /tmp/${DATASET}/work && \
827-
sudo setfacl -m group:$(id -gn):rwx /tmp/${DATASET}/work
828805
if [ -f /tmp/.nofasttrack ]; then
829806
fmriprep-docker -i nipreps/fmriprep:latest \
830-
-e FMRIPREP_DEV 1 \
807+
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
831808
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
832809
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
833810
--fs-no-reconall --sloppy --write-graph \
@@ -854,7 +831,7 @@ jobs:
854831
FASTRACK_ARG=""
855832
fi
856833
fmriprep-docker -i nipreps/fmriprep:latest \
857-
-e FMRIPREP_DEV 1 \
834+
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
858835
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
859836
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
860837
${FASTRACK_ARG} \
@@ -891,7 +868,7 @@ jobs:
891868

892869
deploy_docker_patches:
893870
machine:
894-
image: ubuntu-1604:202007-01
871+
image: ubuntu-2004:202104-01
895872
working_directory: /tmp/src/fmriprep
896873
steps:
897874

@@ -952,7 +929,7 @@ jobs:
952929
953930
deploy_docker:
954931
machine:
955-
image: ubuntu-1604:202007-01
932+
image: ubuntu-2004:202104-01
956933
working_directory: /tmp/src/fmriprep
957934
steps:
958935
- checkout:

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