/
config.yml
942 lines (910 loc) · 31.5 KB
/
config.yml
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# reusable anchors
_machine_defaults: &machine_defaults
environment:
TZ: "/usr/share/zoneinfo/America/Los_Angeles"
SCRATCH: "/scratch"
machine:
image: default
docker_layer_caching: true
working_directory: /tmp/src/smriprep
resource_class: large
_python_defaults: &python_defaults
docker:
- image: cimg/python:3.12.2
auth:
username: $DOCKER_USER
password: $DOCKER_PAT
working_directory: /tmp/src/smriprep
_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/smriprep
docker tag localhost:5000/smriprep nipreps/smriprep:latest
docs_deploy: &docs
docker:
- image: node:8.10.0
auth:
username: $DOCKER_USER
password: $DOCKER_PAT
working_directory: /tmp/gh-pages
steps:
- run:
name: Check whether this is the original repo
command: |
if [[ "$CIRCLE_PROJECT_USERNAME" != "nipreps" ]]; then
echo "Not in nipreps/smriprep - skipping docs deploy."
circleci step halt
fi
- add_ssh_keys:
fingerprints:
- "80:ec:ae:e8:92:1f:88:83:2a:e0:ee:35:39:79:85:88"
- run:
name: Install gh-pages tool
command: |
npm install -g --silent gh-pages@2.0.1
- checkout
- run:
name: Set git settings
command: |
git config user.email "nipreps@gmail.com"
git config user.name "nipreps-bot"
- attach_workspace:
at: docs/_build
- run:
name: Disable jekyll builds
command: touch docs/_build/html/.nojekyll
- run:
name: Deploy docs to gh-pages branch
command: gh-pages --dotfiles --message "doc(update) [skip ci]" --dist docs/_build/html
version: 2.1
orbs:
docker: circleci/docker@2.2.0
codecov: codecov/codecov@3.2.4
aliases:
- &src "/tmp/src/smriprep"
jobs:
build:
<<: *machine_defaults
environment:
DOCKER_BUILDKIT: 1
steps:
- checkout:
path: *src
- restore_cache:
keys:
- build-v1-{{ .Branch }}-{{ .Revision }}
- build-v1--{{ .Revision }}
- build-v1-{{ .Branch }}-
- build-v1-master-
- build-v1-
paths:
- /tmp/docker
- /tmp/images
- docker/install-docker-credential-helper
- run: *docker_auth
- run: *setup_docker_registry
- run:
name: Create named builder
command: docker buildx create --use --name=builder --driver=docker-container
- run:
name: Build Docker image
no_output_timeout: 60m
command: |
pyenv local 3
pip install hatch
# Get version, update files.
THISVERSION=$( hatch version )
if [[ ${THISVERSION:0:1} == "0" ]] ; then
echo "WARNING: latest git tag could not be found"
echo "Please, make sure you fetch all tags from upstream with"
echo "the command ``git fetch --tags --verbose`` and push"
echo "them to your fork with ``git push origin --tags``"
fi
# Build docker image
docker buildx build --load --builder builder \
--cache-from localhost:5000/smriprep \
--cache-from nipreps/smriprep:latest \
-t nipreps/smriprep:latest \
--build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
--build-arg VCS_REF=`git rev-parse --short HEAD` \
--build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" .
- run:
command: docker images
- run:
name: Check Docker image
command: |
pyenv local 3
# Get version, update files.
THISVERSION=$( hatch version )
BUILT_VERSION=$( docker run --rm nipreps/smriprep:latest --version )
BUILT_VERSION=${BUILT_VERSION%$'\r'}
BUILT_VERSION=${BUILT_VERSION#*"smriprep v"}
echo "VERSION: \"$THISVERSION\""
echo "BUILT: \"$BUILT_VERSION\""
set -e
test "$BUILT_VERSION" = "$THISVERSION"
- run:
name: Docker push to local registry
no_output_timeout: 40m
command: |
docker tag nipreps/smriprep:latest localhost:5000/smriprep
docker push localhost:5000/smriprep
- 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/smriprep
- save_cache:
key: build-v1-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
- run:
name: Docker push to local registry
no_output_timeout: 40m
command: |
docker tag nipreps/smriprep:latest localhost:5000/smriprep
docker push localhost:5000/smriprep
- run:
name: Docker registry garbage collection
command: |
docker exec -it registry /bin/registry garbage-collect --delete-untagged \
/etc/docker/registry/config.yml
- save_cache:
key: build-v1-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
- persist_to_workspace:
root: /tmp
paths:
- src/smriprep
- .force
get_data:
<<: *python_defaults
working_directory: /home/circleci/data
steps:
- restore_cache:
keys:
- testdata-v2-{{ .Branch }}-{{ epoch }}
- testdata-v2-{{ .Branch }}
- testdata-v2-
- 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 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: Store FreeSurfer license file
command: |
mkdir -p /tmp/fslicense
cd /tmp/fslicense
echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IGxpY2Vuc2UudHh0Cg==" | base64 -d | sh
- persist_to_workspace:
root: /tmp
paths:
- fslicense
- save_cache:
key: testdata-v2-{{ .Branch }}-{{ epoch }}
paths:
- /tmp/data
- /tmp/ds005/freesurfer
- checkout:
path: /tmp/src/smriprep
- restore_cache:
keys:
- templateflow-v1-{{ .Branch }}-{{ epoch }}
- templateflow-v1-{{ .Branch }}
- templateflow-v1-
- restore_cache:
keys:
- env-v1-{{ .Branch }}-{{ epoch }}
- env-v1-{{ .Branch }}
- env-v1-
- run:
name: Pull TemplateFlow down, pre-cache some templates
command: |
export TEMPLATEFLOW_HOME=/tmp/templateflow
pip install -U --user --no-cache-dir templateflow
python -c "from templateflow import api as tfapi; \
tfapi.get(['MNI152Lin', 'MNI152NLin2009cAsym', 'OASIS30ANTs'], suffix='T1w'); \
tfapi.get(['MNI152Lin', 'MNI152NLin2009cAsym', 'OASIS30ANTs'], desc='brain', suffix='mask'); \
tfapi.get('OASIS30ANTs', resolution=1, desc='4', suffix='dseg'); \
tfapi.get(['OASIS30ANTs', 'NKI'], resolution=1, label='brain', suffix='probseg'); \
tfapi.get(['MNI152NLin2009cAsym', 'OASIS30ANTs', 'NKI'], resolution=1, \
desc='BrainCerebellumExtraction', suffix='mask'); \
tfapi.get(['MNI152NLin2009cAsym', 'OASIS30ANTs', 'NKI'], resolution=1, \
desc='BrainCerebellumRegistration', suffix='mask'); \
tfapi.get('OASIS30ANTs', resolution=1, label=['WM', 'BS'], suffix='probseg'); \
tfapi.get('MNI152NLin2009cAsym', resolution=2, label='WM', suffix='probseg');"
- save_cache:
key: templateflow-v1-{{ .Branch }}-{{ epoch }}
paths:
- /tmp/templateflow
- save_cache:
key: env-v1-{{ .Branch }}-{{ epoch }}
paths:
- /home/circleci/.local
test:
<<: *machine_defaults
environment:
- FS_LICENSE: /tmp/fslicense/license.txt
steps:
- attach_workspace:
at: /tmp
- restore_cache:
keys:
- build-v1-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
- docker/install-docker-credential-helper
- run: *docker_auth
- run: *setup_docker_registry
- run: *pull_from_registry
- checkout
- run:
name: Test smriprep-wrapper (Python 2)
command: |
pyenv local 2.7
echo -n "Python version: "
python --version
pip install --upgrade "pip<21"
pip install --upgrade setuptools
pip install --upgrade wrapper/
which smriprep-docker
smriprep-docker -i nipreps/smriprep:latest --help
smriprep-docker -i nipreps/smriprep:latest --version
- run:
name: Test smriprep-wrapper (Python 3)
command: |
pyenv local 3
echo -n "Python version: "
python --version
pip install --upgrade pip setuptools
pip install --upgrade wrapper/
which smriprep-docker
smriprep-docker -i nipreps/smriprep:latest --help
smriprep-docker -i nipreps/smriprep:latest --version
- restore_cache:
keys:
- testdata-v2-{{ .Branch }}-{{ epoch }}
- testdata-v2-{{ .Branch }}
- testdata-v2-
- restore_cache:
keys:
- templateflow-v1-{{ .Branch }}-{{ epoch }}
- templateflow-v1-{{ .Branch }}
- templateflow-v1-
- run:
name: Run Pytest
no_output_timeout: 2h
command: |
bash /tmp/src/smriprep/.circleci/pytest.sh
- codecov/upload:
file: /tmp/data/pytest_cov.xml
flags: pytest
test_deploy_pypi:
<<: *python_defaults
steps:
- checkout
- run:
name: Update build tools
command: pip install --upgrade build twine hatch
- run:
name: Build sMRIPrep
command: python -m build
- run:
name: Twine check smriprep
command: twine check dist/*
- run:
name: Pre-run hatch version
command: hatch version
- store_artifacts:
path: /tmp/src/smriprep/dist
- run:
name: Check sdist distribution
command: |
THISVERSION=$( hatch version )
THISVERSION=${CIRCLE_TAG:-$THISVERSION}
virtualenv --python=python sdist
source sdist/bin/activate
python -m pip install --upgrade pip
python -m pip install dist/smriprep*.tar.gz
which smriprep | grep sdist\\/bin
INSTALLED_VERSION=$(smriprep --version)
INSTALLED_VERSION=${INSTALLED_VERSION%$'\r'}
INSTALLED_VERSION=${INSTALLED_VERSION#*"smriprep v"}
echo "VERSION: \"$THISVERSION\""
echo "INSTALLED: \"$INSTALLED_VERSION\""
test "$INSTALLED_VERSION" = "$THISVERSION"
- run:
name: Check wheel distribution
command: |
THISVERSION=$( hatch version )
THISVERSION=${CIRCLE_TAG:-$THISVERSION}
virtualenv --python=python wheel
source wheel/bin/activate
python -m pip install dist/smriprep*.whl
which smriprep | grep wheel\\/bin
INSTALLED_VERSION=$(smriprep --version)
INSTALLED_VERSION=${INSTALLED_VERSION%$'\r'}
INSTALLED_VERSION=${INSTALLED_VERSION#*"smriprep v"}
echo "VERSION: \"$THISVERSION\""
echo "INSTALLED: \"$INSTALLED_VERSION\""
test "$INSTALLED_VERSION" = "$THISVERSION"
- run:
name: Build smriprep-docker
command: python -m build wrapper
- run:
name: Twine check wrapper
command: twine check wrapper/dist/*
- store_artifacts:
path: /tmp/src/smriprep/wrapper/dist
ds005:
<<: *machine_defaults
working_directory: /tmp/ds005
environment:
- FS_LICENSE: /tmp/fslicense/license.txt
steps:
- attach_workspace:
at: /tmp
- run:
name: Check whether build should be skipped
command: |
cd /tmp/src/smriprep
if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?ds005\]' )" != "" ]]; then
echo "Skipping ds000005 build"
circleci step halt
fi
- restore_cache:
keys:
- build-v1-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
- run:
name: Setting up test
command: |
mkdir -p /tmp/ds005/derivatives /tmp/ds005/work
- docker/install-docker-credential-helper
- run: *docker_auth
- run: *setup_docker_registry
- run: *pull_from_registry
- restore_cache:
keys:
- ds005-anat-v1-{{ .Branch }}-{{ epoch }}
- ds005-anat-v1-{{ .Branch }}
- ds005-anat-v1-master
- ds005-anat-v1-next
- restore_cache:
keys:
- testdata-v2-{{ .Branch }}-{{ epoch }}
- testdata-v2-{{ .Branch }}
- testdata-v2-
- restore_cache:
keys:
- templateflow-v1-{{ .Branch }}-{{ epoch }}
- templateflow-v1-{{ .Branch }}
- templateflow-v1-
- run:
name: Run anatomical workflow on ds005
no_output_timeout: 2h
command: |
# Remove part of FreeSurfer output to ensure that at least
# some of recon-all is attempted
rm /tmp/ds005/freesurfer/sub-01/mri/ribbon.mgz
bash /tmp/src/smriprep/.circleci/ds005_run.sh --write-graph
- run:
name: Combine coverage
no_output_timeout: 2h
command: |
# Combine coverage and convert to XML inside container because
# the file format is sensitive to changes in environment
docker run -it -e FMRIPREP_DEV=1 -u $(id -u):$(id -g) \
-v /tmp/ds005:/tmp/ds005 \
-v /tmp/src/smriprep:/src/smriprep \
-v /tmp/templateflow:/home/smriprep/.cache/templateflow \
-w /src/smriprep \
-e COVERAGE_FILE=/tmp/ds005/work/.coverage \
-e COVERAGE_RCFILE=/src/smriprep/docker/multiproc.coveragerc \
--entrypoint=coverage \
nipreps/smriprep:latest \
combine /tmp/ds005/work/.coverage.*
# Convert to XML to freeze
docker run -it -e FMRIPREP_DEV=1 -u $(id -u) \
-v /tmp/ds005:/tmp/ds005 \
-v /tmp/src/smriprep:/src/smriprep \
-v /tmp/templateflow:/home/smriprep/.cache/templateflow \
-w /src/smriprep \
-e COVERAGE_FILE=/tmp/ds005/work/.coverage \
-e COVERAGE_RCFILE=/src/smriprep/docker/multiproc.coveragerc \
--entrypoint=coverage \
nipreps/smriprep:latest \
xml
- codecov/upload:
file: /tmp/src/smriprep/coverage.xml
flags: ds005
- run:
name: Clean-up temporary directory of reportlets and fsdir_run_XXX nodes
when: always
command: |
sudo chown $(id -un):$(id -gn) -R /tmp/ds005
rm -rf /tmp/ds005/work/reportlets
rm -rf /tmp/ds005/work/smriprep_wf/fsdir_run_*/
- save_cache:
key: ds005-anat-v1-{{ .Branch }}-{{ epoch }}
paths:
- /tmp/ds005/work
- run:
name: Checking outputs of sMRIPrep
command: |
mkdir -p /tmp/ds005/test
find /tmp/ds005/derivatives -name "*" ! -path "*/figures*" -print | sed s+/tmp/ds005/derivatives/++ | sort > /tmp/ds005/test/outputs.out
sort /tmp/src/smriprep/.circleci/ds005_outputs.txt > /tmp/ds005/test/expected.out
diff /tmp/ds005/test/{expected,outputs}.out
exit $?
- store_artifacts:
path: /tmp/ds005/derivatives
- run:
name: Clean working directory
when: on_success
command: |
rm -rf /tmp/ds005/work
- run:
name: Clean working directory
when: on_fail
command: |
find /tmp/ds005/work \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
-exec sh -c 'rm -f {}; touch {}' \;
- store_artifacts:
path: /tmp/ds005/work
- run:
name: Check fast track using existing derivatives
no_output_timeout: 5m
command: |
bash /tmp/src/smriprep/.circleci/ds005_run.sh --fast-track
- run:
name: Clean working directory
when: on_fail
command: |
rm -rf /tmp/ds005/work/smriprep_wf/fsdir_run_*/
find /tmp/ds005/work \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
-exec sh -c 'rm -f {}; touch {}' \;
- store_artifacts:
path: /tmp/ds005/work
destination: fasttrack
- store_artifacts:
path: /tmp/ds005/derivatives
destination: fasttrack
- run:
name: Check fs-no-resume using existing freesufer output
no_output_timeout: 5m
command: |
bash /tmp/src/smriprep/.circleci/ds005_run.sh --fs-no-resume
- run:
name: Clean working directory
when: on_fail
command: |
rm -rf /tmp/ds005/work/smriprep_wf/fsdir_run_*/
find /tmp/ds005/work \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
-exec sh -c 'rm -f {}; touch {}' \;
- store_artifacts:
path: /tmp/ds005/work
destination: fs_no_resume
- store_artifacts:
path: /tmp/ds005/derivatives
destination: fs_no_resume
ds054:
<<: *machine_defaults
environment:
- FS_LICENSE: /tmp/fslicense/license.txt
steps:
- attach_workspace:
at: /tmp
- run:
name: Check whether build should be skipped
command: |
cd /tmp/src/smriprep
if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?ds054\]' )" != "" ]]; then
echo "Skipping ds000054 build"
circleci step halt
fi
- restore_cache:
keys:
- build-v1-{{ .Branch }}-{{ .Revision }}
paths:
- /tmp/docker
- /tmp/images
- run:
name: Setting up test
command: |
mkdir -p /tmp/ds054/derivatives /tmp/ds054/work
- docker/install-docker-credential-helper
- run: *docker_auth
- run: *setup_docker_registry
- run: *pull_from_registry
- restore_cache:
keys:
- ds054-anat-v9-{{ .Branch }}-{{ epoch }}
- ds054-anat-v9-{{ .Branch }}
- ds054-anat-v9-master
- restore_cache:
keys:
- testdata-v2-{{ .Branch }}-{{ epoch }}
- testdata-v2-{{ .Branch }}
- testdata-v2-
- restore_cache:
keys:
- templateflow-v1-{{ .Branch }}-{{ epoch }}
- templateflow-v1-{{ .Branch }}
- templateflow-v1-
- run:
name: Run sMRIPrep on ds054 (with --fs-no-reconall)
no_output_timeout: 2h
command: |
bash /tmp/src/smriprep/.circleci/ds054_run.sh --write-graph
- run:
name: Combine coverage
no_output_timeout: 2h
command: |
# Combine coverage and convert to XML inside container because
# the file format is sensitive to changes in environment
docker run --rm=false -it \
-v /tmp/ds054:/tmp/ds054 \
-v /tmp/src/smriprep:/src/smriprep \
-v /tmp/templateflow:/home/smriprep/.cache/templateflow \
-w /src/smriprep \
-e FMRIPREP_DEV=1 -u $(id -u):$(id -g) \
-e COVERAGE_FILE=/tmp/ds054/work/.coverage \
-e COVERAGE_RCFILE=/src/smriprep/docker/multiproc.coveragerc \
--entrypoint=coverage \
nipreps/smriprep:latest \
combine /tmp/ds054/work/.coverage.*
# Convert to XML to freeze
docker run --rm=false -it \
-v /tmp/ds054:/tmp/ds054 \
-v /tmp/src/smriprep:/src/smriprep \
-v /tmp/templateflow:/home/smriprep/.cache/templateflow \
-w /src/smriprep \
-e FMRIPREP_DEV=1 -u $(id -u):$(id -g) \
-e COVERAGE_FILE=/tmp/ds054/work/.coverage \
-e COVERAGE_RCFILE=/src/smriprep/docker/multiproc.coveragerc \
--entrypoint=coverage \
nipreps/smriprep:latest \
xml
- codecov/upload:
file: /tmp/src/smriprep/coverage.xml
flags: ds054
- run:
name: Clean-up temporary directory of reportlets
when: always
command: |
sudo chown $(id -un):$(id -gn) -R /tmp/ds054
rm -rf /tmp/ds054/work/reportlets
- save_cache:
key: ds054-anat-v7-{{ .Branch }}-{{ epoch }}
paths:
- /tmp/ds054/work
- run:
name: Checking outputs of sMRIPrep
command: |
mkdir -p /tmp/ds054/test
find /tmp/ds054/derivatives -path */figures -prune -o -name "*" -print | sed s+/tmp/ds054/derivatives/++ | sort > /tmp/ds054/test/outputs.out
sort /tmp/src/smriprep/.circleci/ds054_outputs.txt > /tmp/ds054/test/expected.out
diff /tmp/ds054/test/{expected,outputs}.out
exit $?
- run:
name: Clean working directory
when: on_success
command: |
sudo rm -rf /tmp/ds054/work
- run:
name: Clean working directory
when: on_fail
command: |
find /tmp/ds054/work \( -name "*.nii.gz" -or -name "*.nii" -or -name "*.gii" -or -name "*.h5" \) \
-exec sh -c 'rm -f {}; touch {}' \;
- store_artifacts:
path: /tmp/ds054
- run:
name: Check fast track using existing derivatives (with --fs-no-reconall)
no_output_timeout: 5m
command: |
bash /tmp/src/smriprep/.circleci/ds054_run.sh --fast-track
- store_artifacts:
path: /tmp/ds054/work
destination: fasttrack-work
- store_artifacts:
path: /tmp/ds054/derivatives
destination: fasttrack-derivatives
build_docs:
<<: *python_defaults
working_directory: /tmp/gh-pages
environment:
- FSLOUTPUTTYPE: NIFTI
- SUBJECTS_DIR: /tmp/subjects
steps:
- checkout
- run:
name: Install Graphviz
command: sudo apt update && sudo apt -y install graphviz
- run:
name: Update pip
command: pip install --upgrade pip
- run:
name: Install deps and package
command: pip install -r docs/requirements.txt .
- run:
name: Build only this commit
no_output_timeout: 30m
command: make -C docs NO_ET=1 SPHINXOPTS="-W" BUILDDIR="_build/no_version_html" html
- store_artifacts:
path: ./docs/_build/no_version_html/html
destination: noversion
- run:
name: Stop or generate versioned docs?
command: |
set +e
force_versioned="$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[docs?[ _]?versions?\]' )"
set -e
if [[ "x${CIRCLE_TAG}" = "x" && "${CIRCLE_BRANCH}" != "master" && "x${force_versioned}" = "x" ]]; then
echo "Not a tag or master branch - skipping versioned docs."
circleci step halt
fi
- run:
name: Clean-up unversioned docs
command: make -C docs clean
- restore_cache:
keys:
- docs-v2-{{ .Branch }}-{{ .Revision }}
- docs-v2-{{ .Branch }}-
- docs-v2-master
- docs-v2-
paths:
- ./docs/_build
- run:
name: Generate Versioned Docs
command: make -f ./docs/Makefile NO_ET=1 versioned CURBRANCH=${CIRCLE_TAG:-$CIRCLE_BRANCH}
- save_cache:
key: docs-v2-{{ .Branch }}-{{ .Revision }}
paths:
- ./docs/_build
- persist_to_workspace:
root: docs/_build
paths: html
- store_artifacts:
path: ./docs/_build/html
destination: versioned
deploy_pypi:
<<: *python_defaults
steps:
- checkout
- run:
name: Update build tools
command: pip install --upgrade build twine
- run:
name: Build sMRIPrep
command: python -m build
- run:
name: Build smriprep-docker
command: python -m build wrapper/
- run:
name: Upload packages to PyPI
command: python -m twine upload dist/smriprep* wrapper/dist/smriprep*
deploy_docker:
<<: *machine_defaults
working_directory: *src
steps:
- run:
name: Check whether image should be deployed to Docker Hub
command: |
if [[ "$CIRCLE_PROJECT_USERNAME" != "nipreps" ]]; then
echo "Nothing to deploy for $CIRCLE_PROJECT_USERNAME/$CIRCLE_PROJECT_REPONAME."
circleci step halt
fi
- restore_cache:
keys:
- build-v1-{{ .Branch }}-{{ epoch }}
- build-v1-{{ .Branch }}-
- build-v1-master-
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 "$DOCKER_PAT" ]]; then
docker tag nipreps/smriprep nipreps/smriprep:unstable
docker push nipreps/smriprep:unstable
if [[ -n "$CIRCLE_TAG" ]]; then
docker push nipreps/smriprep:latest
docker tag nipreps/smriprep nipreps/smriprep:$CIRCLE_TAG
docker push nipreps/smriprep:$CIRCLE_TAG
fi
fi
deploy_docs_tag:
<<: *docs
deploy_docs_master:
<<: *docs
workflows:
version: 2
build_test_deploy:
jobs:
- build:
context:
- nipreps-common
filters:
branches:
ignore:
- /docs?\/.*/
tags:
only: /.*/
- get_data:
filters:
branches:
ignore:
- /docs?\/.*/
- /tests?\/.*/
tags:
only: /.*/
- test_deploy_pypi:
context:
- nipreps-common
filters:
branches:
only:
- /rel\/.*/
- /maint\/.*/
tags:
only: /.*/
- test:
context:
- nipreps-common
requires:
- get_data
- build
filters:
branches:
ignore:
- /docs?\/.*/
- /ds005\/.*/
- /ds054\/.*/
tags:
only: /.*/
- build_docs:
filters:
branches:
ignore:
- /tests?\/.*/
- /ds005\/.*/
- /ds054\/.*/
tags:
only: /.*/
- ds005:
context:
- nipreps-common
requires:
- get_data
- build
filters:
branches:
ignore:
- /docs?\/.*/
- /tests?\/.*/
- /ds054\/.*/
tags:
only: /.*/
- ds054:
context:
- nipreps-common
requires:
- get_data
- build
filters:
branches:
ignore:
- /docs?\/.*/
- /tests?\/.*/
- /ds005\/.*/
tags:
only: /.*/
- deploy_docs_master:
requires:
- build_docs
- ds005
- ds054
- test
filters:
branches:
only: /master/
tags:
ignore: /.*/
- deploy_docs_tag:
requires:
- build_docs
- ds005
- ds054
- test_deploy_pypi
- test
filters:
branches:
ignore: /.*/
tags:
only: /.*/
- deploy_pypi:
context:
- nipreps-common
requires:
- deploy_docs_tag
filters:
branches:
ignore: /.*/
tags:
only: /.*/
- deploy_docker:
context:
- nipreps-common
requires:
- build
- ds005
- ds054
filters:
branches:
only: master
tags:
only: /.*/