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config.yml
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config.yml
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version: 2.1
orbs:
docker: circleci/docker@1.6.0
jobs:
build:
environment:
TZ: "/usr/share/zoneinfo/America/Los_Angeles"
SCRATCH: "/scratch"
machine:
# https://discuss.circleci.com/t/linux-machine-executor-images-2021-april-q2-update/39928
# upgrade Docker version
image: ubuntu-2004:202104-01
working_directory: /tmp/src/fmriprep
steps:
- checkout
- run:
name: Check whether build should be skipped
command: |
if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
echo "Only docs build"
circleci step halt
fi
- restore_cache:
keys:
- build-v4-{{ .Branch }}-{{ epoch }}
- build-v4-{{ .Branch }}-
- build-v4-master-
- build-v4-
paths:
- /tmp/docker
- /tmp/images
- docker/install-docker-credential-helper
- run:
name: Docker authentication
command: |
if [[ -n $DOCKER_PAT ]]; then
echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
fi
- run:
name: Set up Docker registry
command: |
if [[ -f /tmp/images/registry.tar.gz ]]; then
echo "Loading saved registry image"
docker load < /tmp/images/registry.tar.gz
else
echo "Pulling registry image from DockerHub"
docker pull registry:2
mkdir -p /tmp/images
docker save registry:2 | gzip > /tmp/images/registry.tar.gz
fi
docker run -d -p 5000:5000 --restart=always --name=registry \
-v /tmp/docker:/var/lib/registry registry:2
- run:
name: Pull images
command: |
set +e
docker pull localhost:5000/ubuntu
success=$?
set -e
if [[ "$success" = "0" ]]; then
echo "Pulling from local registry"
docker tag localhost:5000/ubuntu ubuntu:xenial-20200706
docker pull localhost:5000/fmriprep
docker tag localhost:5000/fmriprep nipreps/fmriprep:latest
docker tag localhost:5000/fmriprep nipreps/fmriprep
else
echo "Pulling from Docker Hub"
docker pull ubuntu:xenial-20200706
docker tag ubuntu:xenial-20200706 localhost:5000/ubuntu
docker push localhost:5000/ubuntu
docker pull nipreps/fmriprep:latest
fi
- run:
name: Build Docker image
no_output_timeout: 60m
command: |
export PY3=$(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:-$THISVERSION}'/" wrapper/fmriprep_docker.py
sed -i -E "s/(var version = )'[A-Za-z0-9.-]+'/\1'${CIRCLE_TAG:-$THISVERSION}'/" docs/citing.rst
sed -i "s/title = {FMRIPrep}/title = {FMRIPrep ${CIRCLE_TAG:-$THISVERSION}}/" fmriprep/data/boilerplate.bib
# 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-v4-{{ .Branch }}-{{ epoch }}
paths:
- /tmp/docker
- /tmp/images
get_data:
machine:
image: ubuntu-2004:202104-01
working_directory: /home/circleci/data
steps:
- restore_cache:
keys:
- data-v9-{{ .Branch }}-{{ .Revision }}
- data-v9-{{ .Branch }}
- 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 }}-{{ epoch }}
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:
image: ubuntu-2004:202104-01
working_directory: /tmp/src/fmriprep
steps:
- checkout:
path: /home/circleci/src/fmriprep
- run:
name: Check whether build should be skipped
command: |
cd /home/circleci/src/fmriprep
if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
echo "Only docs build"
circleci step halt
fi
if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?tests\]' )" != "" ]]; then
echo "Skipping pytest job"
circleci step halt
fi
- attach_workspace:
at: /tmp
- restore_cache:
keys:
- build-v4-{{ .Branch }}-{{ epoch }}
- build-v4-{{ .Branch }}-
- build-v4-
paths:
- /tmp/docker
- /tmp/images
- restore_cache:
keys:
- data-v9-{{ .Branch }}-{{ .Revision }}
- docker/install-docker-credential-helper
- run:
name: Docker authentication
command: |
if [[ -n $DOCKER_PAT ]]; then
echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
fi
- run:
name: Set-up a 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
- run:
name: Pull images from local registry
command: |
docker pull localhost:5000/fmriprep
docker tag localhost:5000/fmriprep nipreps/fmriprep:latest
- 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 $PY3
echo -n "Python version: "
python --version
pip install --upgrade pip setuptools
pip install --upgrade wrapper/
which fmriprep-docker
fmriprep-docker -i nipreps/fmriprep:latest --help
fmriprep-docker -i nipreps/fmriprep:latest --version
- store_artifacts:
path: /tmp/data/reports
ds005:
machine:
image: ubuntu-2004:202104-01
working_directory: /tmp/ds005
environment:
- FS_LICENSE: /tmp/fslicense/license.txt
- DATASET: ds005
steps:
- checkout:
path: /home/circleci/src/fmriprep
- run:
name: Check whether build should be skipped
command: |
cd /home/circleci/src/fmriprep
if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
echo "Only docs build"
circleci step halt
fi
if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?ds005\]' )" != "" ]]; then
echo "Skipping ds000005 build"
circleci step halt
fi
if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[no[ _-]?fasttrack\]' )" != "" ]]; then
touch /tmp/.nofasttrack
echo "Anatomical fasttrack reusing sMRIPrep's derivatives will not be used."
fi
- attach_workspace:
at: /tmp
- restore_cache:
keys:
- build-v4-{{ .Branch }}-{{ epoch }}
- build-v4-{{ .Branch }}-
- build-v4-
paths:
- /tmp/docker
- /tmp/images
- restore_cache:
keys:
- data-v9-{{ .Branch }}-{{ .Revision }}
- restore_cache:
keys:
- ds005-anat-v18-{{ .Branch }}-{{ .Revision }}
- ds005-anat-v18-{{ .Branch }}
- ds005-anat-v18-master
- ds005-anat-v18-
- docker/install-docker-credential-helper
- run:
name: Docker authentication
command: |
if [[ -n $DOCKER_PAT ]]; then
echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
fi
- run:
name: Set-up a Docker registry
command: |
if [[ -f /tmp/images/registry.tar.gz ]]; then
echo "Loading saved registry image"
docker load < /tmp/images/registry.tar.gz
else
echo "Pulling registry image from DockerHub"
docker pull registry:2
fi
docker run -d -p 5000:5000 --restart=always --name=registry \
-v /tmp/docker:/var/lib/registry registry:2
- run:
name: Pull images from local registry
command: |
docker pull localhost:5000/fmriprep
docker tag localhost:5000/fmriprep nipreps/fmriprep:latest
- run:
name: Setting up test
command: |
export PY3=$(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/
- 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 \
--fs-subjects-dir /tmp/${DATASET}/freesurfer \
--skull-strip-template OASIS30ANTs:res-1 \
--output-spaces MNI152NLin2009cAsym MNI152NLin6Asym \
--sloppy --write-graph --mem_mb 4096 \
--nthreads 2 --anat-only -vv
fi
- run:
name: Clean-up after anatomical run
command: |
rm -rf /tmp/${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 }}-{{ epoch }}
paths:
- /tmp/ds005/work
- 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
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 \
${FASTRACK_ARG} \
--sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
--use-aroma \
--skull-strip-template OASIS30ANTs:res-1 \
--output-spaces MNI152NLin2009cAsym fsaverage5 fsnative MNI152NLin6Asym anat \
--use-plugin /home/circleci/src/fmriprep/.circleci/legacy.yml \
--nthreads 2 --cifti-output -vv
- store_artifacts:
path: /tmp/ds005/derivatives
- run:
name: Copy intermediate results for re-runs
command: |
mkdir -p /tmp/${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="${DATASET}_fasttrack_outputs.txt"
if [ -f /tmp/.nofasttrack ]; then
CHECK_OUTPUTS_FILE="${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 $?
- run:
name: Prepare BIDS Derivatives dataset
command: |
mkdir -p /tmp/${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 \
${FASTRACK_ARG} \
--output-layout bids \
--sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
--output-spaces MNI152NLin2009cAsym \
--nthreads 2 -vv
- run:
name: Checking outputs of partial fMRIPrep run
command: |
mkdir -p /tmp/${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 \
${FASTRACK_ARG} \
--sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
--output-spaces MNI152NLin2009cAsym fsaverage5 fsnative MNI152NLin6Asym anat \
--aroma-melodic-dimensionality 2 --use-aroma \
--nthreads 2 --cifti-output -vv
- run:
name: Checking outputs of partial fMRIPrep run
command: |
mkdir -p /tmp/${DATASET}/test
CHECK_OUTPUTS_FILE="${DATASET}_partial_fasttrack_outputs.txt"
if [ -f /tmp/.nofasttrack ]; then
CHECK_OUTPUTS_FILE="${DATASET}_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:
image: ubuntu-2004:202104-01
working_directory: /tmp/ds054
environment:
- FS_LICENSE: /tmp/fslicense/license.txt
- DATASET: ds054
steps:
- checkout:
path: /home/circleci/src/fmriprep
- run:
name: Check whether build should be skipped
command: |
cd /home/circleci/src/fmriprep
if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
echo "Only docs build"
circleci step halt
fi
if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?ds054\]' )" != "" ]]; then
echo "Skipping ds000054 build"
circleci step halt
fi
- attach_workspace:
at: /tmp
- restore_cache:
keys:
- build-v4-{{ .Branch }}-{{ epoch }}
- build-v4-{{ .Branch }}-
- build-v4-
paths:
- /tmp/docker
- /tmp/images
- restore_cache:
keys:
- data-v9-{{ .Branch }}-{{ .Revision }}
- restore_cache:
keys:
- ds054-anat-v14-{{ .Branch }}-{{ .Revision }}
- ds054-anat-v14-{{ .Branch }}
- ds054-anat-v14-master
- ds054-anat-v14-
- run:
name: Setting up test
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/
- docker/install-docker-credential-helper
- run:
name: Docker authentication
command: |
if [[ -n $DOCKER_PAT ]]; then
echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
fi
- run:
name: Set-up a Docker registry
command: |
if [[ -f /tmp/images/registry.tar.gz ]]; then
echo "Loading saved registry image"
docker load < /tmp/images/registry.tar.gz
else
echo "Pulling registry image from DockerHub"
docker pull registry:2
fi
docker run -d -p 5000:5000 --restart=always --name=registry \
-v /tmp/docker:/var/lib/registry registry:2
- run:
name: Pull images from local registry
command: |
docker pull localhost:5000/fmriprep
docker tag localhost:5000/fmriprep nipreps/fmriprep:latest
- run:
name: Run anatomical workflow on ds054
no_output_timeout: 2h
command: |
mkdir -p /tmp/${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 \
--fs-no-reconall --sloppy --write-graph \
--output-spaces MNI152NLin2009cAsym \
--mem_mb 4096 --nthreads 2 --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/${DATASET}/derivatives/fmriprep
- save_cache:
key: ds054-anat-v14-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
paths:
- /tmp/ds054/work
- run:
name: Run full fMRIPrep on ds054
no_output_timeout: 2h
command: |
FASTRACK_ARG="--anat-derivatives /tmp/${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 \
${FASTRACK_ARG} \
--fs-no-reconall --sloppy \
--output-spaces MNI152NLin2009cAsym:res-2 anat func \
--mem_mb 4096 --nthreads 2 -vv --debug compcor
- run:
name: Checking outputs of fMRIPrep
command: |
mkdir -p /tmp/${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/${DATASET}/work/*/config.toml | cut -d\" -f 2)
cp /tmp/src/fmriprep/fmriprep/data/tests/crash_files/*.txt \
/tmp/${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 \
--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:
image: ubuntu-2004:202104-01
working_directory: /tmp/ds210
environment:
- FS_LICENSE: /tmp/fslicense/license.txt
- DATASET: ds210
steps:
- checkout:
path: /home/circleci/src/fmriprep
- run:
name: Check whether build should be skipped
command: |
cd /home/circleci/src/fmriprep
if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
echo "Only docs build"
circleci step halt
fi
if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?ds210\]' )" != "" ]]; then
echo "Skipping ds000210 build"
circleci step halt
fi
- attach_workspace:
at: /tmp
- restore_cache:
keys:
- build-v4-{{ .Branch }}-{{ epoch }}
- build-v4-{{ .Branch }}-
- build-v4-
paths:
- /tmp/docker
- /tmp/images
- restore_cache:
keys:
- data-v9-{{ .Branch }}-{{ .Revision }}
- restore_cache:
keys:
- ds210-anat-v12-{{ .Branch }}-{{ .Revision }}
- ds210-anat-v12-{{ .Branch }}-
- ds210-anat-v12-master
- ds210-anat-v12-
- run:
name: Setting up test
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/
- docker/install-docker-credential-helper
- run:
name: Docker authentication
command: |
if [[ -n $DOCKER_PAT ]]; then
echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
fi
- run:
name: Set-up a Docker registry
command: |
if [[ -f /tmp/images/registry.tar.gz ]]; then
echo "Loading saved registry image"
docker load < /tmp/images/registry.tar.gz
else
echo "Pulling registry image from DockerHub"
docker pull registry:2
fi
docker run -d -p 5000:5000 --restart=always --name=registry \
-v /tmp/docker:/var/lib/registry registry:2
- run:
name: Pull images from local registry
command: |
docker pull localhost:5000/fmriprep
docker tag localhost:5000/fmriprep nipreps/fmriprep:latest
- run:
name: Run anatomical workflow on ds000210
no_output_timeout: 2h
command: |
mkdir -p /tmp/${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 \
--fs-no-reconall --sloppy --write-graph \
--output-spaces MNI152NLin2009cAsym \
--mem_mb 4096 --nthreads 2 --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/${DATASET}/derivatives/fmriprep
- save_cache:
key: ds210-anat-v12-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
paths:
- /tmp/ds210/work
- run:
name: Run full fMRIPrep on ds000210
no_output_timeout: 2h
command: |
FASTRACK_ARG="--anat-derivatives /tmp/${DATASET}/smriprep-0.6"
if [ -f /tmp/.nofasttrack ]; then
FASTRACK_ARG=""
fi
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 \
${FASTRACK_ARG} \
--fs-no-reconall --use-syn-sdc \
--dummy-scans 1 --sloppy --write-graph \
--output-spaces MNI152NLin2009cAsym \
--mem_mb 4096 --nthreads 2 -vv
- run:
name: Checking outputs of fMRIPrep
command: |
mkdir -p /tmp/${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:
image: ubuntu-2004:202104-01
working_directory: /tmp/src/fmriprep
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
- checkout:
path: /home/circleci/src/fmriprep
- run:
name: Check whether build should be skipped
command: |
cd /home/circleci/src/fmriprep
if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
echo "Only docs build"
circleci step halt
fi
- restore_cache:
keys:
- build-v4-{{ .Branch }}-{{ epoch }}
- build-v4-{{ .Branch }}-
- build-v4-
paths:
- /tmp/docker
- /tmp/images
- docker/install-docker-credential-helper
- run:
name: Docker authentication
command: |
if [[ -n $DOCKER_PAT ]]; then
echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
fi
- run:
name: Setup a Docker registry
command: |
if [[ -f /tmp/images/registry.tar.gz ]]; then
echo "Loading saved registry image"
docker load < /tmp/images/registry.tar.gz
else
echo "Pulling registry image from DockerHub"
docker pull registry:2
fi
docker run -d -p 5000:5000 --restart=always --name=registry \
-v /tmp/docker:/var/lib/registry registry:2
- run:
name: Pull images from local registry
command: |
docker pull localhost:5000/fmriprep
docker tag localhost:5000/fmriprep nipreps/fmriprep:latest
- run:
name: Deploy to Docker Hub
no_output_timeout: 40m
command: |
docker tag nipreps/fmriprep nipreps/fmriprep:${CIRCLE_BRANCH#docker/}
docker push nipreps/fmriprep:${CIRCLE_BRANCH#docker/}
deploy_docker:
machine:
image: ubuntu-2004:202104-01
working_directory: /tmp/src/fmriprep
steps:
- checkout:
path: /home/circleci/src/fmriprep
- run:
name: Check whether build should be skipped
command: |
cd /home/circleci/src/fmriprep
if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
echo "Only docs build"
circleci step halt
fi
- restore_cache:
keys:
- build-v4-{{ .Branch }}-{{ epoch }}
- build-v4-{{ .Branch }}-
- build-v4-
paths:
- /tmp/docker
- /tmp/images
- docker/install-docker-credential-helper
- run:
name: Docker authentication
command: |
if [[ -n $DOCKER_PAT ]]; then
echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
fi
- run:
name: Set-up a Docker registry
command: |
if [[ -f /tmp/images/registry.tar.gz ]]; then
echo "Loading saved registry image"
docker load < /tmp/images/registry.tar.gz
else
echo "Pulling registry image from DockerHub"
docker pull registry:2
fi
docker run -d -p 5000:5000 --restart=always --name=registry \
-v /tmp/docker:/var/lib/registry registry:2
- run:
name: Pull images from local registry
command: |
docker pull localhost:5000/fmriprep
docker tag localhost:5000/fmriprep nipreps/fmriprep:latest
- run:
name: Deploy to Docker Hub
no_output_timeout: 40m
command: |
if [[ -n "$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: