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Merge pull request #1324 from poldracklab/sync/master_multiecho
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MAINT: Merge master into multiecho
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@effigies
effigies authored Oct 26, 2018
2 parents 66afc57 + c542dbf commit 02d1112
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Showing 35 changed files with 867 additions and 373 deletions.
144 changes: 102 additions & 42 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -165,8 +165,8 @@ jobs:
steps:
- restore_cache:
keys:
- regression-v0-{{ epoch }}
- regression-v0-
- regression-v2-{{ epoch }}
- regression-v2-
- run:
name: Get truncated BOLD series
command: |
Expand All @@ -193,7 +193,7 @@ jobs:
paths:
- data
- save_cache:
key: regression-v0-{{ epoch }}
key: regression-v2-{{ epoch }}
paths:
- /tmp/data

Expand Down Expand Up @@ -227,10 +227,6 @@ jobs:
fi
- attach_workspace:
at: /tmp
- restore_cache:
keys:
- regression-v0-{{ epoch }}
- regression-v0-
- run:
name: Check PyPi preconditions
command: |
Expand All @@ -252,13 +248,21 @@ jobs:
name: Run fMRIPrep tests
no_output_timeout: 2h
command: |
mkdir /tmp/data/reports && \
docker run -ti --rm=false \
-v /tmp/data:/tmp/data \
-e FMRIPREP_REGRESSION_SOURCE=/tmp/data/fmriprep_bold_truncated \
-e FMRIPREP_REGRESSION_TARGETS=/tmp/data/fmriprep_bold_mask \
-e FMRIPREP_REGRESSION_REPORTS=/tmp/data/reports \
--entrypoint="py.test" poldracklab/fmriprep:latest \
/root/src/fmriprep/ \
--doctest-modules --ignore=/root/src/fmriprep/docs --ignore=setup.py
-svx --doctest-modules --ignore=/root/src/fmriprep/docs --ignore=setup.py
- run:
name: Package new masks
no_output_timeout: 10m
working_directory: /tmp/data/reports
command: |
tar cfz fmriprep_bold_mask.tar.gz fmriprep_bold_mask/*/*.nii.gz
- run:
name: Test fmriprep-wrapper (Python 2)
command: |
Expand All @@ -284,7 +288,7 @@ jobs:
fmriprep-docker -i poldracklab/fmriprep:latest --help
fmriprep-docker -i poldracklab/fmriprep:latest --version
- store_artifacts:
path: /home/circleci/out/tests
path: /tmp/data/reports


build_docs:
Expand Down Expand Up @@ -350,10 +354,10 @@ jobs:
at: /tmp
- restore_cache:
keys:
- ds005-anat-v7-{{ .Branch }}-{{ epoch }}
- ds005-anat-v7-{{ .Branch }}
- ds005-anat-v7-master
- ds005-anat-v7-
- ds005-anat-v9-{{ .Branch }}-{{ epoch }}
- ds005-anat-v9-{{ .Branch }}
- ds005-anat-v9-master
- ds005-anat-v9-
- run:
name: Setting up test
command: |
Expand Down Expand Up @@ -384,10 +388,10 @@ jobs:
-e FMRIPREP_DEV 1 -u $(id -u) \
--config $PWD/nipype.cfg -w /tmp/ds005/work \
/tmp/data/ds005 /tmp/ds005/derivatives participant \
--debug --write-graph --mem_mb 4096 \
--sloppy --write-graph --mem_mb 4096 \
--nthreads 2 --anat-only -vv
- save_cache:
key: ds005-anat-v7-{{ .Branch }}-{{ epoch }}
key: ds005-anat-v9-{{ .Branch }}-{{ epoch }}
paths:
- /tmp/ds005/work
- /tmp/ds005/derivatives/fmriprep
Expand All @@ -404,7 +408,7 @@ jobs:
-e FMRIPREP_DEV 1 -u $(id -u) \
--config $PWD/nipype.cfg -w /tmp/ds005/work \
/tmp/data/ds005 /tmp/ds005/derivatives participant \
--debug --write-graph --use-syn-sdc --mem_mb 4096 \
--sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
--ignore-aroma-denoising-errors --use-aroma \
--output-space T1w template fsaverage5 \
--template-resampling-grid native \
Expand All @@ -431,7 +435,7 @@ jobs:
-e FMRIPREP_DEV 1 -u $(id -u) \
--config $PWD/nipype.cfg -w /tmp/ds005/work \
/tmp/data/ds005 /tmp/ds005/derivatives_partial participant \
--debug --write-graph --use-syn-sdc --mem_mb 4096 \
--sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
--output-space T1w template fsaverage5 \
--ignore-aroma-denoising-errors --use-aroma \
--template-resampling-grid native \
Expand Down Expand Up @@ -479,10 +483,10 @@ jobs:
at: /tmp
- restore_cache:
keys:
- ds054-anat-v5-{{ .Branch }}-{{ epoch }}
- ds054-anat-v5-{{ .Branch }}
- ds054-anat-v5-master
- ds054-anat-v5-
- ds054-anat-v7-{{ .Branch }}-{{ epoch }}
- ds054-anat-v7-{{ .Branch }}
- ds054-anat-v7-master
- ds054-anat-v7-
- run:
name: Setting up test
command: |
Expand Down Expand Up @@ -513,10 +517,10 @@ jobs:
-e FMRIPREP_DEV 1 \
--config $PWD/nipype.cfg -w /tmp/ds054/work \
/tmp/data/ds054 /tmp/ds054/derivatives participant \
--fs-no-reconall --debug --write-graph \
--fs-no-reconall --sloppy --write-graph \
--mem_mb 4096 --nthreads 2 --anat-only -vv
- save_cache:
key: ds054-anat-v5-{{ .Branch }}-{{ epoch }}
key: ds054-anat-v7-{{ .Branch }}-{{ epoch }}
paths:
- /tmp/ds054/work
- /tmp/ds054/derivatives
Expand All @@ -533,7 +537,7 @@ jobs:
-e FMRIPREP_DEV 1 \
--config $PWD/nipype.cfg -w /tmp/ds054/work \
/tmp/data/ds054 /tmp/ds054/derivatives participant \
--fs-no-reconall --debug \
--fs-no-reconall --sloppy \
--output-space T1w template \
--template-resampling-grid 2mm \
--mem_mb 4096 --nthreads 2 -vv
Expand All @@ -558,7 +562,7 @@ jobs:
-e FMRIPREP_DEV 1 \
--config $PWD/nipype.cfg -w /tmp/ds054/work \
/tmp/data/ds054 /tmp/ds054/derivatives participant \
--fs-no-reconall --debug --write-graph \
--fs-no-reconall --sloppy --write-graph \
--output-space T1w template \
--template-resampling-grid 2mm \
--reports-only --run-uuid $UUID
Expand Down Expand Up @@ -597,8 +601,8 @@ jobs:
at: /tmp
- restore_cache:
keys:
- ds210-anat-v2-{{ epoch }}
- ds210-anat-v2-
- ds210-anat-v4-{{ epoch }}
- ds210-anat-v4-
- run:
name: Setting up test
command: |
Expand Down Expand Up @@ -629,10 +633,10 @@ jobs:
-e FMRIPREP_DEV 1 \
--config $PWD/nipype.cfg -w /tmp/ds210/work \
/tmp/data/ds210 /tmp/ds210/derivatives participant \
--fs-no-reconall --debug --write-graph \
--fs-no-reconall --sloppy --write-graph \
--mem_mb 4096 --nthreads 2 --anat-only -vv
- save_cache:
key: ds210-anat-v2-{{ epoch }}
key: ds210-anat-v4-{{ epoch }}
paths:
- /tmp/ds210/work
- /tmp/ds210/derivatives
Expand All @@ -647,7 +651,7 @@ jobs:
/tmp/data/ds210 /tmp/ds210/derivatives participant \
--fs-no-reconall --t2s-coreg --use-syn-sdc \
--template-resampling-grid native \
--debug --write-graph --mem_mb 4096 --nthreads 2 -vv
--sloppy --write-graph --mem_mb 4096 --nthreads 2 -vv
- run:
name: Checking outputs of fMRIPrep
command: |
Expand All @@ -666,7 +670,7 @@ jobs:
- store_artifacts:
path: /tmp/ds210

deploy:
deploy_docker:
machine:
image: circleci/classic:201711-01
working_directory: /tmp/src/fmriprep
Expand All @@ -690,10 +694,22 @@ jobs:
command: |
if [[ -n "$DOCKER_PASS" ]]; then
docker login -u $DOCKER_USER -p $DOCKER_PASS
docker push poldracklab/fmriprep:latest
docker tag poldracklab/fmriprep poldracklab/fmriprep:$CIRCLE_TAG
docker push poldracklab/fmriprep:$CIRCLE_TAG
docker tag poldracklab/fmriprep poldracklab/fmriprep:unstable
docker push poldracklab/fmriprep:unstable
if [[ -n "$CIRCLE_TAG" ]]; then
docker push poldracklab/fmriprep:latest
docker tag poldracklab/fmriprep poldracklab/fmriprep:$CIRCLE_TAG
docker push poldracklab/fmriprep:$CIRCLE_TAG
fi
fi
deploy_pypi:
machine:
image: circleci/classic:201711-01
working_directory: /tmp/src/fmriprep
steps:
- attach_workspace:
at: /tmp
- run:
name: Deploy to PyPi
command: |
Expand All @@ -717,19 +733,31 @@ workflows:
- get_data:
filters:
branches:
ignore: /docs?\/.*/
ignore:
- /docs?\/.*/
- /tests?\/.*/
tags:
only: /.*/

- get_regression_data:
filters:
branches:
ignore: /docs?\/.*/
ignore:
- /docs?\/.*/
- /ds005\/.*/
- /ds054\/.*/
- /ds210\/.*/

- build_docs:
requires:
- build
filters:
branches:
ignore:
- /tests?\/.*/
- /ds005\/.*/
- /ds054\/.*/
- /ds210\/.*/
tags:
only: /.*/

Expand All @@ -738,7 +766,9 @@ workflows:
- build
filters:
branches:
ignore: /docs?\/.*/
ignore:
- /docs?\/.*/
- /tests?\/.*/
tags:
only: /.*/

Expand All @@ -748,7 +778,11 @@ workflows:
- get_regression_data
filters:
branches:
ignore: /docs?\/.*/
ignore:
- /docs?\/.*/
- /ds005\/.*/
- /ds054\/.*/
- /ds210\/.*/
tags:
only: /.*/

Expand All @@ -758,7 +792,11 @@ workflows:
- build
filters:
branches:
ignore: /docs?\/.*/
ignore:
- /docs?\/.*/
- /tests?\/.*/
- /ds054\/.*/
- /ds210\/.*/
tags:
only: /.*/

Expand All @@ -768,7 +806,11 @@ workflows:
- build
filters:
branches:
ignore: /docs?\/.*/
ignore:
- /docs?\/.*/
- /tests?\/.*/
- /ds005\/.*/
- /ds210\/.*/
tags:
only: /.*/

Expand All @@ -779,11 +821,29 @@ workflows:
filters:
branches:
# only: /meepi.*/
ignore: /docs?\/.*/
ignore:
- /docs?\/.*/
- /tests?\/.*/
- /ds005\/.*/
- /ds054\/.*/
tags:
only: /.*/

- deploy_docker:
requires:
- build
- test_pytest
- build_docs
- ds005
- ds054
- ds210
filters:
branches:
only: master
tags:
only: /.*/

- deploy:
- deploy_pypi:
requires:
- build
- test_pytest
Expand Down
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