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config.yml
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config.yml
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# reusable anchors
_machine_defaults: &machine_defaults
environment:
TZ: "/usr/share/zoneinfo/America/Los_Angeles"
SCRATCH: "/scratch"
machine:
image: ubuntu-2004:current
docker_layer_caching: true
working_directory: /tmp/src/fmriprep
resource_class: large
_python_defaults: &python_defaults
docker:
- image: circleci/python:3.9.6
working_directory: /tmp/src/fmriprep
_docker_auth: &docker_auth
name: Docker authentication
command: |
if [[ -n $DOCKER_PAT ]]; then
echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
fi
_setup_docker_registry: &setup_docker_registry
name: Set up Docker registry
command: |
if [[ -f /tmp/images/registry.tar.gz ]]; then
echo "Loading saved registry image"
docker load < /tmp/images/registry.tar.gz
else
echo "Pulling registry image from DockerHub"
docker pull registry:2
fi
docker run -d -p 5000:5000 --restart=always --name=registry \
-v /tmp/docker:/var/lib/registry registry:2
_pull_from_registry: &pull_from_registry
name: Pull and tag image from local registry
command: |
docker pull localhost:5000/fmriprep
docker tag localhost:5000/fmriprep nipreps/fmriprep:latest
_check_skip_job: &check_skip_job
name: Check commit message and determine if job should be skipped
command: |
set +e
cd /tmp/src/fmriprep
COMMIT_MSG="$(git show -s --format=%s)"
DOCBUILD="$(echo ${COMMIT_MSG} | grep -i -E '^docs?(\(\w+\))?:')"
SKIP_PYTEST="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?tests\]')"
SKIP_DS005="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?ds005\]' )"
SKIP_DS054="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?ds054\]' )"
SKIP_DS210="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?ds210\]' )"
NO_FASTTRACK="$(echo ${COMMIT_MSG} | grep -i -E '\[no[ _-]?fasttrack\]' )"
# no skipping if tagged build
if [[ -n "$NO_FASTTRACK" ]]; then
touch /tmp/.nofasttrack
echo "Anatomical fasttrack reusing sMRIPrep's derivatives will not be used."
elif [[ -n "$CIRCLETAG" ]]; then
exit 0
elif [[ -n "$DOCSBUILD" ]]; then # always try to skip docs builds
echo "Only docs build"
circleci step halt
elif [ -n "$CHECK_PYTEST" -a -n "$SKIP_PYTEST" ]; then
echo "Skipping pytest"
circleci step halt
elif [ -n "$CHECK_DS005" -a -n "$SKIP_DS005" ]; then
echo "Skipping DS005"
circleci step halt
elif [ -n "$CHECK_DS054" -a -n "$SKIP_DS054" ]; then
echo "Skipping DS054"
circleci step halt
elif [ -n "$CHECK_DS210" -a -n "$SKIP_DS210" ]; then
echo "Skipping DS210"
circleci step halt
fi
echo "No skip"
_setup_fmriprep_docker: &setup_fmriprep_docker
name: Install fMRIPrep's docker wrapper
command: |
export PY3=$(pyenv versions | grep '3\.' |
sed -e 's/.* 3\./3./' -e 's/ .*//')
pyenv local $PY3
mkdir -p /tmp/${DATASET}/derivatives
pip install --upgrade pip setuptools
pip install --upgrade /tmp/src/fmriprep/wrapper/
version: 2.1
aliases:
- &src "/tmp/src/fmriprep"
orbs:
docker: circleci/docker@2.1.4
jobs:
build:
<<: *machine_defaults
steps:
- checkout:
path: *src
- run: *check_skip_job
- restore_cache:
keys:
- build-v5-{{ .Branch }}-{{ .Revision }}
- build-v5--{{ .Revision }}
- build-v5-{{ .Branch }}-
- build-v5-master-
- build-v5-
paths:
- /tmp/docker
- /tmp/images
- docker/install-docker-credential-helper
- run: *docker_auth
- run: *setup_docker_registry
- run:
name: Save docker registry
command: |
if [[ ! -f /tmp/images/registry.tar.gz ]]; then
mkdir -p /tmp/images
docker save registry:2 | gzip > /tmp/images/registry.tar.gz
fi
- run:
name: Pull Ubuntu/focal image
command: |
set +e
docker pull localhost:5000/ubuntu
success=$?
set -e
if [[ "$success" = "0" ]]; then
echo "Pulling from local registry"
docker tag localhost:5000/ubuntu ubuntu:focal
else
echo "Pulling from Docker Hub"
docker pull ubuntu:focal
docker tag ubuntu:focal localhost:5000/ubuntu
docker push localhost:5000/ubuntu
fi
- run:
name: Pull fMRIPrep Docker image
command: |
set +e
docker pull localhost:5000/fmriprep
success=$?
set -e
if [[ "$success" = "0" ]]; then
echo "Pulled from local registry"
docker tag localhost:5000/fmriprep nipreps/fmriprep:latest
docker tag localhost:5000/fmriprep nipreps/fmriprep
else
echo "Pulling from Docker Hub"
docker pull nipreps/fmriprep:latest
fi
- run:
name: Build Docker image
no_output_timeout: 60m
command: |
export PY3=$(pyenv versions | grep '3\.' |
sed -e 's/.* 3\./3./' -e 's/ .*//')
pyenv local $PY3
# Get version, update files.
THISVERSION=$( python3 get_version.py )
if [[ ${THISVERSION:0:1} == "0" ]] ; then
echo "WARNING: latest git tag could not be found"
echo "Please, make sure you fetch all tags from upstream with"
echo "the command ``git fetch --tags --verbose`` and push"
echo "them to your fork with ``git push origin --tags``"
fi
sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'${CIRCLE_TAG:-$THISVERSION}'/" wrapper/fmriprep_docker.py
# Build docker image
e=1 && for i in {1..5}; do
docker build --rm \
--cache-from=nipreps/fmriprep \
-t nipreps/fmriprep:latest \
--build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
--build-arg VCS_REF=`git rev-parse --short HEAD` \
--build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" . \
&& e=0 && break || sleep 15
done && [ "$e" -eq "0" ]
- run:
name: Docker push to local registry
no_output_timeout: 40m
command: |
docker tag nipreps/fmriprep:latest localhost:5000/fmriprep
docker push localhost:5000/fmriprep
- run:
name: Docker registry garbage collection
command: |
docker exec -it registry /bin/registry garbage-collect --delete-untagged \
/etc/docker/registry/config.yml
- persist_to_workspace:
root: /tmp
paths:
- src/fmriprep
- save_cache:
key: build-v5-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
get_data:
<<: *machine_defaults
steps:
- restore_cache:
keys:
- data-v9-{{ .Branch }}-{{ .Revision }}
- data-v9--{{ .Revision }}
- data-v9-{{ .Branch }}-
- data-v9-master-
- data-v9-
- run:
name: Get test data from ds000005
command: |
mkdir -p /tmp/data
if [[ ! -d /tmp/data/ds005 ]]; then
wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
-O ds005_downsampled.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/57f32a429ad5a101f977eb75"
tar xvzf ds005_downsampled.tar.gz -C /tmp/data/
else
echo "Dataset ds000005 was cached"
fi
- run:
name: Get test data from ds000054
command: |
if [[ ! -d /tmp/data/ds054 ]]; then
wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
-O ds054_downsampled.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/57f32c22594d9001ef91bf9e"
tar xvzf ds054_downsampled.tar.gz -C /tmp/data/
else
echo "Dataset ds000054 was cached"
fi
- run:
name: Get test data from ds000210
command: |
if [[ ! -d /tmp/data/ds210 ]]; then
wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
-O ds210_downsampled.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5ae9e37b9a64d7000ce66c21"
tar xvzf ds210_downsampled.tar.gz -C /tmp/data/
else
echo "Dataset ds000210 was cached"
fi
- run:
name: Get FreeSurfer derivatives for ds000005
command: |
if [[ ! -d /tmp/ds005/freesurfer ]]; then
mkdir -p /tmp/ds005
wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
-O ds005_derivatives_freesurfer.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/58fe59eb594d900250960180"
tar xvzf ds005_derivatives_freesurfer.tar.gz -C /tmp/ds005
else
echo "FreeSurfer derivatives of ds000005 were cached"
fi
- run:
name: Get sMRIPrep derivatives for ds000005
command: |
if [[ ! -d /tmp/ds005/smriprep-0.6 ]]; then
mkdir -p /tmp/ds005
wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
-O ds005_sub-01_smriprep.zip "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5e860c528140b402134249d1"
unzip -d /tmp/ds005 ds005_sub-01_smriprep.zip
else
echo "sMRIPrep derivatives of ds000005 were cached"
fi
- run:
name: Get sMRIPrep derivatives for ds000054
command: |
if [[ ! -d /tmp/ds054/smriprep-0.6 ]]; then
mkdir -p /tmp/ds054
wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
-O ds054_sub-100185_smriprep.zip "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5e86be591ab243025be0c6f1"
unzip -d /tmp/ds054 ds054_sub-100185_smriprep.zip
else
echo "sMRIPrep derivatives of ds000054 were cached"
fi
- run:
name: Get sMRIPrep derivatives for ds000210
command: |
if [[ ! -d /tmp/ds210/smriprep-0.6 ]]; then
mkdir -p /tmp/ds210
wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
-O ds210_sub-02_smriprep.zip "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5e86e9bb1ab2430268e03873"
unzip -d /tmp/ds210 ds210_sub-02_smriprep.zip
else
echo "sMRIPrep derivatives of ds000210 were cached"
fi
- save_cache:
key: data-v9-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/data
- /tmp/ds005/freesurfer
- /tmp/ds005/smriprep-0.6
- /tmp/ds054/smriprep-0.6
- /tmp/ds210/smriprep-0.6
- run:
name: Store FreeSurfer license file
command: |
mkdir -p /tmp/fslicense
cd /tmp/fslicense
echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IGxpY2Vuc2UudHh0Cg==" | base64 -d | sh
- run:
name: Create Nipype config files
command: |
mkdir -p /tmp/ds005 /tmp/ds054 /tmp/ds210
printf "[execution]\nstop_on_first_crash = true\n" > /tmp/ds005/nipype.cfg
echo "poll_sleep_duration = 0.01" >> /tmp/ds005/nipype.cfg
echo "hash_method = content" >> /tmp/ds005/nipype.cfg
cp /tmp/ds005/nipype.cfg /tmp/ds054/nipype.cfg
cp /tmp/ds005/nipype.cfg /tmp/ds210/nipype.cfg
- persist_to_workspace:
root: /tmp
paths:
- fslicense
- ds005/nipype.cfg
- ds054/nipype.cfg
- ds210/nipype.cfg
test_pytest:
<<: *machine_defaults
environment:
CHECK_PYTEST: true
steps:
- checkout:
path: *src
- run: *check_skip_job
- attach_workspace:
at: /tmp
- restore_cache:
keys:
- build-v5-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
- restore_cache:
keys:
- data-v9-{{ .Branch }}-{{ .Revision }}
- docker/install-docker-credential-helper
- run: *docker_auth
- run: *setup_docker_registry
- run: *pull_from_registry
- run:
name: Run fMRIPrep tests
no_output_timeout: 2h
command: |
docker run -ti --rm=false \
-e TEST_READONLY_FILESYSTEM=1 -v $HOME:/home/readonly:ro \
--entrypoint="pytest" nipreps/fmriprep:latest \
/src/fmriprep/fmriprep -svx --doctest-modules
- run:
name: Test fmriprep-wrapper (Python 2)
command: |
export PY2=$(pyenv versions | grep '2\.' |
sed -e 's/.* 2\./2./' -e 's/ .*//')
pyenv local $PY2
echo -n "Python version: "
python --version
pip install --upgrade "pip<21" "setuptools<45"
pip install --upgrade wrapper/
which fmriprep-docker
fmriprep-docker -i nipreps/fmriprep:latest --help
fmriprep-docker -i nipreps/fmriprep:latest --version
- run:
name: Test fmriprep-wrapper (Python 3)
command: |
export PY3=$(pyenv versions | grep '3\.' |
sed -e 's/.* 3\./3./' -e 's/ .*//')
pyenv local $PY3
echo -n "Python version: "
python --version
pip install --upgrade pip setuptools
pip install --upgrade wrapper/
which fmriprep-docker
fmriprep-docker -i nipreps/fmriprep:latest --help
fmriprep-docker -i nipreps/fmriprep:latest --version
- store_artifacts:
path: /tmp/data/reports
ds005:
<<: *machine_defaults
working_directory: /tmp/ds005
environment:
- FS_LICENSE: /tmp/fslicense/license.txt
- DATASET: ds005
- CHECK_DS005: true
steps:
- checkout:
path: *src
- run: *check_skip_job
- attach_workspace:
at: /tmp
- restore_cache:
keys:
- build-v5-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
- restore_cache:
keys:
- data-v9-{{ .Branch }}-{{ .Revision }}
- restore_cache:
keys:
- ds005-anat-v18-{{ .Branch }}-{{ .Revision }}
- ds005-anat-v18--{{ .Revision }}
- ds005-anat-v18-{{ .Branch }}-
- ds005-anat-v18-master-
- ds005-anat-v18-
- docker/install-docker-credential-helper
- run: *docker_auth
- run: *setup_docker_registry
- run: *pull_from_registry
- run: *setup_fmriprep_docker
- run:
name: Run anatomical workflow on ds005
no_output_timeout: 2h
command: |
mkdir -p /tmp/${DATASET}/work /tmp/${DATASET}/derivatives
if [ -f /tmp/.nofasttrack ]; then
fmriprep-docker -i nipreps/fmriprep:latest \
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
--network none \
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
--output-layout legacy \
--fs-subjects-dir /tmp/${DATASET}/freesurfer \
--skull-strip-template OASIS30ANTs:res-1 \
--output-spaces MNI152NLin2009cAsym MNI152NLin6Asym \
--sloppy --write-graph --mem-mb 14336 \
--nthreads 4 --anat-only -vv
fi
- run:
name: Clean-up after anatomical run
command: |
rm -rf /tmp/${DATASET}/work/fmriprep_wf/fsdir*
rm -rf /tmp/${DATASET}/work/reportlets
rm -rf /tmp/${DATASET}/derivatives/fmriprep
- save_cache:
key: ds005-anat-v18-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/ds005/work
- run:
name: Attempt run without PE metadata (should fail)
no_output_timeout: 2h
command: |
echo "TODO"
- run:
name: Run full fMRIPrep on ds005 (LegacyMultiProc plugin)
no_output_timeout: 2h
command: |
FASTRACK_ARG="--anat-derivatives /tmp/${DATASET}/smriprep-0.6"
if [ -f /tmp/.nofasttrack ]; then
FASTRACK_ARG=""
fi
# Inject pretend metadata
json_sidecar=/tmp/data/${DATASET}/task-mixedgamblestask_bold.json
awk 'NR==1{print; print " \"TotalReadoutTime\": 0.05,"} NR!=1' ${json_sidecar} > tmp && mv tmp ${json_sidecar}
awk 'NR==1{print; print " \"PhaseEncodingDirection\": \"j\","} NR!=1' ${json_sidecar} > tmp && mv tmp ${json_sidecar}
fmriprep-docker -i nipreps/fmriprep:latest \
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
--network none \
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
--fs-subjects-dir /tmp/${DATASET}/freesurfer \
${FASTRACK_ARG} \
--output-layout legacy \
--sloppy --write-graph --mem-mb 14336 \
--skull-strip-template OASIS30ANTs:res-1 \
--output-spaces fsaverage5 fsnative \
--use-plugin /tmp/src/fmriprep/.circleci/legacy.yml \
--nthreads 4 -vv
- store_artifacts:
path: /tmp/ds005/derivatives
destination: full-run
- run:
name: Copy intermediate results for re-runs
command: |
mkdir -p /tmp/${DATASET}/derivatives_partial
sudo cp -a /tmp/${DATASET}/work /tmp/${DATASET}/work_partial
sudo cp -a /tmp/${DATASET}/work /tmp/${DATASET}/work_bids
sudo rm -rf /tmp/${DATASET}/work_partial/fmriprep_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf
- run:
name: Checking outputs of full fMRIPrep run
command: |
mkdir -p /tmp/${DATASET}/test
CHECK_OUTPUTS_FILE="${DATASET}_legacy_fasttrack_outputs.txt"
if [ -f /tmp/.nofasttrack ]; then
CHECK_OUTPUTS_FILE="${DATASET}_legacy_outputs.txt"
fi
find /tmp/${DATASET}/derivatives \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/${DATASET}/derivatives/++ | sort > /tmp/${DATASET}/test/outputs.out
diff /tmp/src/fmriprep/.circleci/${CHECK_OUTPUTS_FILE} /tmp/${DATASET}/test/outputs.out
exit $?
- run:
name: Prepare BIDS Derivatives dataset
command: |
mkdir -p /tmp/${DATASET}/bids/sourcedata
cp -r /tmp/${DATASET}/freesurfer /tmp/${DATASET}/bids/sourcedata/freesurfer
- run:
name: Re-run with BIDS layout
no_output_timeout: 2h
command: |
FASTRACK_ARG="--anat-derivatives /tmp/${DATASET}/smriprep-0.6"
if [ -f /tmp/.nofasttrack ]; then
FASTRACK_ARG=""
fi
fmriprep-docker -i nipreps/fmriprep:latest \
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
--network none \
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work_bids \
/tmp/data/${DATASET}/ /tmp/${DATASET}/bids participant \
${FASTRACK_ARG} \
--sloppy --write-graph --mem-mb 14336 \
--output-spaces fsaverage5 \
--nthreads 4 -vv
- store_artifacts:
path: /tmp/ds005/bids
destination: bids-run
- run:
name: Checking outputs of partial fMRIPrep run
command: |
mkdir -p /tmp/${DATASET}/test
CHECK_OUTPUTS_FILE="${DATASET}_bids_fasttrack_outputs.txt"
if [ -f /tmp/.nofasttrack ]; then
CHECK_OUTPUTS_FILE="${DATASET}_bids_outputs.txt"
fi
find /tmp/${DATASET}/bids \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/${DATASET}/++ | grep -v sourcedata | sort > /tmp/${DATASET}/test/outputs.out
diff /tmp/src/fmriprep/.circleci/${CHECK_OUTPUTS_FILE} /tmp/${DATASET}/test/outputs.out
exit $?
- run:
name: Re-run fMRIPrep on single run of task data
no_output_timeout: 2h
command: |
rm /tmp/data/${DATASET}/sub-01/func/*_run-01_*
FASTRACK_ARG="--anat-derivatives /tmp/${DATASET}/smriprep-0.6"
if [ -f /tmp/.nofasttrack ]; then
FASTRACK_ARG=""
fi
fmriprep-docker -i nipreps/fmriprep:latest \
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
--network none \
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work_partial \
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives_partial participant \
--fs-subjects-dir /tmp/${DATASET}/freesurfer \
${FASTRACK_ARG} \
--output-layout legacy \
--sloppy --write-graph --use-syn-sdc --mem-mb 14336 \
--output-spaces MNI152NLin2009cAsym fsaverage5 fsnative MNI152NLin6Asym anat \
--aroma-melodic-dimensionality 2 --use-aroma \
--nthreads 4 --cifti-output -vv
- store_artifacts:
path: /tmp/ds005/derivatives_partial
destination: partial-run
- run:
name: Checking outputs of partial fMRIPrep run
command: |
mkdir -p /tmp/${DATASET}/test
CHECK_OUTPUTS_FILE="${DATASET}_legacy_partial_fasttrack_outputs.txt"
if [ -f /tmp/.nofasttrack ]; then
CHECK_OUTPUTS_FILE="${DATASET}_legacy_partial_outputs.txt"
fi
sudo rm -rf /tmp/${DATASET}/derivatives_partial/freesurfer
find /tmp/${DATASET}/derivatives_partial \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/${DATASET}/derivatives_partial/++ | sort > /tmp/${DATASET}/test/outputs.out
diff /tmp/src/fmriprep/.circleci/${CHECK_OUTPUTS_FILE} /tmp/${DATASET}/test/outputs.out
exit $?
- run:
name: Clean working directory
when: on_success
command: |
sudo chown $(id -un):$(id -gn) -R /tmp/${DATASET}
sudo rm -rf /tmp/${DATASET}/work
sudo rm -rf /tmp/${DATASET}/work_partial
- run:
name: Clean working directory
when: on_fail
command: |
sudo chown $(id -un):$(id -gn) -R /tmp/${DATASET}
find /tmp/${DATASET}/work \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
-exec sh -c 'rm -f {}; touch {}' \;
find /tmp/${DATASET}/work_partial \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
-exec sh -c 'rm -f {}; touch {}' \;
- store_artifacts:
path: /tmp/ds005/work
ds054:
<<: *machine_defaults
working_directory: /tmp/ds054
environment:
- FS_LICENSE: /tmp/fslicense/license.txt
- DATASET: ds054
- CHECK_DS054: true
steps:
- checkout:
path: *src
- run: *check_skip_job
- attach_workspace:
at: /tmp
- restore_cache:
keys:
- build-v5-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
- restore_cache:
keys:
- data-v9-{{ .Branch }}-{{ .Revision }}
- restore_cache:
keys:
- ds054-anat-v14-{{ .Branch }}-{{ .Revision }}
- ds054-anat-v14--{{ .Revision }}
- ds054-anat-v14-{{ .Branch }}-
- ds054-anat-v14-master-
- ds054-anat-v14-
- docker/install-docker-credential-helper
- run: *docker_auth
- run: *setup_docker_registry
- run: *pull_from_registry
- run: *setup_fmriprep_docker
- run:
name: Run anatomical workflow on ds054
no_output_timeout: 2h
command: |
mkdir -p /tmp/${DATASET}/work /tmp/${DATASET}/derivatives
if [ -f /tmp/.nofasttrack ]; then
fmriprep-docker -i nipreps/fmriprep:latest \
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
--output-layout legacy \
--fs-no-reconall --sloppy --write-graph \
--output-spaces MNI152NLin2009cAsym \
--mem-mb 14336 --nthreads 4 --anat-only -vv
fi
- run:
name: Clean-up after anatomical run
command: |
rm -rf /tmp/${DATASET}/work/fmriprep_wf/fsdir*
rm -rf /tmp/${DATASET}/work/reportlets
rm -rf /tmp/${DATASET}/derivatives/fmriprep
- save_cache:
key: ds054-anat-v14-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/ds054/work
- run:
name: Run full fMRIPrep on ds054
no_output_timeout: 2h
command: |
FASTRACK_ARG="--anat-derivatives /tmp/${DATASET}/smriprep-0.6"
if [ -f /tmp/.nofasttrack ]; then
FASTRACK_ARG=""
fi
fmriprep-docker -i nipreps/fmriprep:latest \
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
${FASTRACK_ARG} \
--output-layout legacy \
--fs-no-reconall --sloppy \
--output-spaces MNI152NLin2009cAsym:res-2 anat func \
--mem-mb 14336 --nthreads 4 -vv --debug compcor
- run:
name: Checking outputs of fMRIPrep
command: |
mkdir -p /tmp/${DATASET}/test
CHECK_OUTPUTS_FILE="${DATASET}_fasttrack_outputs.txt"
if [ -f /tmp/.nofasttrack ]; then
CHECK_OUTPUTS_FILE="${DATASET}_outputs.txt"
fi
find /tmp/${DATASET}/derivatives \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/${DATASET}/derivatives/++ | sort > /tmp/${DATASET}/test/outputs.out
diff /tmp/src/fmriprep/.circleci/${CHECK_OUTPUTS_FILE} /tmp/${DATASET}/test/outputs.out
exit $?
- run:
name: Generate report with one artificial error
command: |
set -x
sudo mv /tmp/${DATASET}/derivatives/fmriprep/sub-100185.html \
/tmp/${DATASET}/derivatives/fmriprep/sub-100185_noerror.html
UUID=$(grep uuid /tmp/${DATASET}/work/*/config.toml | cut -d\" -f 2 | tail -n 1)
mkdir -p /tmp/${DATASET}/derivatives/fmriprep/sub-100185/log/$UUID/
cp /tmp/src/fmriprep/fmriprep/data/tests/crash_files/*.txt \
/tmp/${DATASET}/derivatives/fmriprep/sub-100185/log/$UUID/
set +e
fmriprep-docker -i nipreps/fmriprep:latest \
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
--output-layout legacy \
--fs-no-reconall --sloppy --write-graph \
--output-spaces MNI152NLin2009cAsym:res-2 anat func \
--reports-only --config-file /tmp/${DATASET}/work/${UUID}/config.toml -vv
RET=$?
set -e
[[ "$RET" -eq "1" ]]
- run:
name: Clean working directory
when: on_success
command: |
sudo chown $(id -un):$(id -gn) -R /tmp/${DATASET}
sudo rm -rf /tmp/${DATASET}/work
- run:
name: Clean working directory
when: on_fail
command: |
sudo chown $(id -un):$(id -gn) -R /tmp/${DATASET}
find /tmp/${DATASET}/work \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
-exec sh -c 'rm -f {}; touch {}' \;
- store_artifacts:
path: /tmp/ds054
ds210:
<<: *machine_defaults
working_directory: /tmp/ds210
environment:
- FS_LICENSE: /tmp/fslicense/license.txt
- DATASET: ds210
- CHECK_DS210: true
steps:
- checkout:
path: *src
- run: *check_skip_job
- attach_workspace:
at: /tmp
- restore_cache:
keys:
- build-v5-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
- restore_cache:
keys:
- data-v9-{{ .Branch }}-{{ .Revision }}
- restore_cache:
keys:
- ds210-anat-v12-{{ .Branch }}-{{ .Revision }}
- ds210-anat-v12--{{ .Revision }}
- ds210-anat-v12-{{ .Branch }}-
- ds210-anat-v12-master-
- ds210-anat-v12-
- docker/install-docker-credential-helper
- run: *docker_auth
- run: *setup_docker_registry
- run: *pull_from_registry
- run: *setup_fmriprep_docker
- run:
name: Run anatomical workflow on ds000210
no_output_timeout: 2h
command: |
mkdir -p /tmp/${DATASET}/work /tmp/${DATASET}/derivatives
if [ -f /tmp/.nofasttrack ]; then
fmriprep-docker -i nipreps/fmriprep:latest \
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
--output-layout legacy \
--fs-no-reconall --sloppy --write-graph \
--output-spaces MNI152NLin2009cAsym \
--mem-mb 14336 --nthreads 4 --anat-only -vv
fi
- run:
name: Clean-up after anatomical run
command: |
rm -rf /tmp/${DATASET}/work/fmriprep_wf/fsdir*
rm -rf /tmp/${DATASET}/work/reportlets
rm -rf /tmp/${DATASET}/derivatives/fmriprep
- save_cache:
key: ds210-anat-v12-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/ds210/work
- run:
name: Attempt run without PE metadata (should fail)
no_output_timeout: 2h
command: |
echo "TODO"
- run:
name: Run full fMRIPrep on ds000210
no_output_timeout: 2h
command: |
FASTRACK_ARG="--anat-derivatives /tmp/${DATASET}/smriprep-0.6"
if [ -f /tmp/.nofasttrack ]; then
FASTRACK_ARG=""
fi
# Inject pretend metadata for SDCFlows not to crash
# TODO / open question - do all echos need the metadata?
chmod +w /tmp/data/${DATASET}
echo '{"PhaseEncodingDirection": "j", "TotalReadoutTime": 0.058}' >> /tmp/data/${DATASET}/task-cuedSGT_bold.json
chmod -R -w /tmp/data/${DATASET}
fmriprep-docker -i nipreps/fmriprep:latest \
-e FMRIPREP_DEV 1 --user $(id -u):$(id -g) \
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work \
/tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
${FASTRACK_ARG} \
--output-layout legacy --me-output-echos \
--fs-no-reconall --use-syn-sdc --ignore slicetiming \
--dummy-scans 1 --sloppy --write-graph \
--output-spaces MNI152NLin2009cAsym \
--mem-mb 14336 --nthreads 4 -vv
- run:
name: Checking outputs of fMRIPrep
command: |
mkdir -p /tmp/${DATASET}/test
CHECK_OUTPUTS_FILE="${DATASET}_fasttrack_outputs.txt"
if [ -f /tmp/.nofasttrack ]; then
CHECK_OUTPUTS_FILE="${DATASET}_outputs.txt"
fi
find /tmp/${DATASET}/derivatives \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/${DATASET}/derivatives/++ | sort > /tmp/${DATASET}/test/outputs.out
diff /tmp/src/fmriprep/.circleci/${CHECK_OUTPUTS_FILE} /tmp/${DATASET}/test/outputs.out
exit $?
- run:
name: Clean working directory
when: on_success
command: |
sudo chown $(id -un):$(id -gn) -R /tmp/${DATASET}
sudo rm -rf /tmp/${DATASET}/work
- run:
name: Clean working directory
when: on_fail
command: |
sudo chown $(id -un):$(id -gn) -R /tmp/${DATASET}
find /tmp/${DATASET}/work \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
-exec sh -c 'rm -f {}; touch {}' \;
- store_artifacts:
path: /tmp/ds210
deploy_docker_patches:
<<: *machine_defaults
working_directory: *src
steps:
- run:
name: Check whether image should be deployed to Docker Hub
command: |
if [[ "$CIRCLE_PROJECT_USERNAME" != "nipreps" ]]; then
echo "Nothing to deploy for $CIRCLE_PROJECT_USERNAME/$CIRCLE_PROJECT_REPONAME."
circleci step halt
fi
- restore_cache:
keys:
- build-v5-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
- docker/install-docker-credential-helper
- run: *docker_auth
- run: *setup_docker_registry
- run: *pull_from_registry
- run:
name: Deploy to Docker Hub
no_output_timeout: 40m
command: |
docker tag nipreps/fmriprep nipreps/fmriprep:${CIRCLE_BRANCH#docker/}
docker push nipreps/fmriprep:${CIRCLE_BRANCH#docker/}
deploy_docker:
<<: *machine_defaults
steps:
- checkout:
path: *src
- run: *check_skip_job
- restore_cache:
keys:
- build-v5-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
- docker/install-docker-credential-helper
- run: *docker_auth
- run: *setup_docker_registry
- run: *pull_from_registry
- run:
name: Deploy to Docker Hub
no_output_timeout: 40m
command: |
if [[ -n "$DOCKER_PAT" ]]; then
echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
docker tag nipreps/fmriprep nipreps/fmriprep:unstable
docker push nipreps/fmriprep:unstable
if [[ -n "$CIRCLE_TAG" ]]; then
docker push nipreps/fmriprep:latest
docker tag nipreps/fmriprep nipreps/fmriprep:$CIRCLE_TAG
docker push nipreps/fmriprep:$CIRCLE_TAG
fi
fi
test_deploy_pypi:
<<: *python_defaults
steps:
- checkout
- run:
name: Update build tools
command: python -m pip install --user pip build twine
- run:
name: Build fMRIPrep
command: python -m build
- store_artifacts:
path: /tmp/src/fmriprep/dist
- run:
name: Check sdist distribution
command: |
THISVERSION=$( python get_version.py )
THISVERSION=${THISVERSION%.dirty*}
THISVERSION=${CIRCLE_TAG:-$THISVERSION}
python -m twine check dist/fmriprep*.tar.gz
virtualenv --python=python sdist
source sdist/bin/activate
python -m pip install --upgrade "pip>=19.1" numpy
python -m pip install dist/fmriprep*.tar.gz
which fmriprep | grep sdist\\/bin
INSTALLED_VERSION=$(fmriprep --version)
INSTALLED_VERSION=${INSTALLED_VERSION%$'\r'}
INSTALLED_VERSION=${INSTALLED_VERSION#*"fMRIPrep v"}
echo "VERSION: \"$THISVERSION\""
echo "INSTALLED: \"$INSTALLED_VERSION\""
test "$INSTALLED_VERSION" = "$THISVERSION"
- run:
name: Check wheel distribution
command: |
THISVERSION=$( python get_version.py )
THISVERSION=${THISVERSION%.dirty*}
THISVERSION=${CIRCLE_TAG:-$THISVERSION}
python -m twine check dist/fmriprep*.whl
virtualenv --python=python wheel
source wheel/bin/activate
python -m pip install dist/fmriprep*.whl
which fmriprep | grep wheel\\/bin
INSTALLED_VERSION=$(fmriprep --version)
INSTALLED_VERSION=${INSTALLED_VERSION%$'\r'}
INSTALLED_VERSION=${INSTALLED_VERSION#*"fMRIPrep v"}
echo "VERSION: \"$THISVERSION\""
echo "INSTALLED: \"$INSTALLED_VERSION\""
test "$INSTALLED_VERSION" = "$THISVERSION"
- run:
name: Build fmriprep-docker
command: |
THISVERSION=$( python get_version.py )
THISVERSION=${THISVERSION%.dirty*}
sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'${CIRCLE_TAG:-$THISVERSION}'/" wrapper/fmriprep_docker.py
python -m build wrapper/
- store_artifacts:
path: /tmp/src/fmriprep/wrapper/dist
deploy_pypi:
<<: *python_defaults
steps:
- checkout
- run:
name: Update build tools
command: python -m pip install --user build twine
- run:
name: Build fMRIPrep
command: python -m build
- run:
name: Build fmriprep-docker
command: |
THISVERSION=$( python get_version.py )
THISVERSION=${THISVERSION%.dirty*}
sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'${CIRCLE_TAG:-$THISVERSION}'/" wrapper/fmriprep_docker.py
python -m build wrapper/
- run:
name: Upload packages to PyPI
command: |
python -m twine upload dist/fmriprep* wrapper/dist/fmriprep*
deployable:
docker:
- image: busybox:latest
steps:
- run: echo Deploying!
workflows:
version: 2
build_test_deploy:
jobs:
- build:
filters:
branches:
ignore:
- /docs?\/.*/
tags:
only: /.*/
- get_data:
filters:
branches:
ignore:
- /docs?\/.*/
- /tests?\/.*/
- /docker\/.*/
tags:
only: /.*/
- test_deploy_pypi:
filters:
branches:
only:
- /rel\/.*/