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Merge pull request #1730 from jdkent/code_server
[ENH] Set up code-server docker recipe for interactive development
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‎.circleci/config.yml

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@@ -67,6 +67,15 @@ jobs:
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--build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" . \
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&& e=0 && break || sleep 15
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done && [ "$e" -eq "0" ]
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# test if development image should be built
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if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[build[ _]?devel\]' )" != "" ]]; then
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echo "building development container"
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docker tag poldracklab/fmriprep poldracklab/fmriprep:unstable
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docker build \
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--rm=false \
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-t poldracklab/fmriprep_devel \
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-f Dockerfile_devel .
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fi
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- run:
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name: Smoke test Docker image
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command: |

‎.gitignore

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# pycharm project settings
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.idea
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# vscode project settings
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.vscode
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# Spyder project settings
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.spyderproject
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.spyproject

‎.vscode/launch.json

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{
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// Use IntelliSense to learn about possible attributes.
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// Hover to view descriptions of existing attributes.
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// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
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"version": "0.2.0",
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"configurations": [
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{
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"name": "ds005-anat",
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"type": "python",
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"request": "launch",
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"program": "/usr/local/miniconda/bin/fmriprep",
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"args": [
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"-w", "/tmp/ds005/work",
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"/tmp/data/ds005",
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"/tmp/ds005/derivatives",
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"participant",
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"--skull-strip-template", "OASIS30ANTs:res-1",
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"--output-spaces", "MNI152NLin2009cAsym", "MNI152NLin6Asym",
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"--sloppy", "--write-graph",
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"--anat-only", "-vv", "--notrack"
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],
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"console": "integratedTerminal",
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"justMyCode": false
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},
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{
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"name": "ds005-full",
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"type": "python",
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"request": "launch",
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"program": "/usr/local/miniconda/bin/fmriprep",
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"args": [
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"-w", "/tmp/ds005/work",
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"/tmp/data/ds005",
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"/tmp/ds005/derivatives",
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"participant",
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"--sloppy", "--write-graph",
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"--use-aroma",
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"--skull-strip-template", "OASIS30ANTs:res-1",
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"--output-space", "T1w", "template", "fsaverage5", "fsnative",
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"--template-resampling-grid", "native",
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"--use-plugin", "/src/fmriprep/.circleci/legacy.yml",
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"--cifti-output", "-vv", "--notrack"
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],
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"console": "integratedTerminal",
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"justMyCode": false
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},
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{
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"name": "ds054",
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"type": "python",
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"request": "launch",
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"program": "/usr/local/miniconda/bin/fmriprep",
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"args": [
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"-w", "/tmp/ds054/work",
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"/tmp/data/ds054",
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"/tmp/ds054/derivatives",
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"participant",
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"--fs-no-reconall", "--sloppy",
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"--output-spaces", "MNI152NLin2009cAsym:res-2", "anat", "func",
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"-vv",
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"--notrack"
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],
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"console": "integratedTerminal",
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"justMyCode": false
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},
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{
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"name": "ds210-anat",
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"type": "python",
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"request": "launch",
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"program": "/usr/local/miniconda/bin/fmriprep",
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"args": [
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"-w", "/tmp/ds210/work",
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"/tmp/data/ds210",
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"/tmp/ds210/derivatives",
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"participant",
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"--fs-no-reconall", "--sloppy", "--write-graph",
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"--anat-only", "-vv", "--notrack"
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],
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"console": "integratedTerminal",
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"justMyCode": false
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},
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{
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"name": "ds210-full",
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"type": "python",
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"request": "launch",
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"program": "/usr/local/miniconda/bin/fmriprep",
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"args": [
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"-w", "/tmp/ds210/work",
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"/tmp/data/ds210",
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"/tmp/ds210/derivatives",
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"participant",
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"--t2s-coreg", "--use-syn-sdc",
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"--template-resampling-grid", "native",
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"--dummy-scans", "1",
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"--fs-no-reconall", "--sloppy", "--write-graph",
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"--anat-only", "-vv", "--notrack"
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],
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"console": "integratedTerminal",
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"justMyCode": false
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}
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]
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}

‎.vscode/settings.json

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{
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"python.linting.flake8Enabled": true,
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"python.pythonPath": "/usr/local/miniconda/bin/python",
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"restructuredtext.confPath": "${workspaceFolder}/docs",
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"python.testing.pytestEnabled": true,
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"python.testing.unittestEnabled": false,
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"python.testing.nosetestsEnabled": false,
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"python.linting.enabled": true,
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"python.testing.pytestArgs": [],
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"python.linting.pylintEnabled": false
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}

‎Dockerfile_devel

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FROM poldracklab/fmriprep:unstable
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# net-tools needed for code-server
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# wget necessary for data downloads
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RUN apt-get update &&\
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apt-get install -y \
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net-tools \
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wget
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# necessary to find fmriprep in /src/fmriprep
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ENV PYTHONNOUSERSITE=0
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RUN cd /src/fmriprep &&\
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pip install --no-use-pep517 -e .[all] &&\
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cp -R /src/fmriprep/fmriprep.egg-info /src/
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# create freesurfer license
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RUN cd /tmp &&\
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echo 'cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IGxpY2Vuc2UudHh0Cg==' | base64 -d | sh
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ENV FS_LICENSE=/tmp/license.txt
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# set the fmriprep development variables
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ENV FMRIPREP_REGRESSION_SOURCE=/tmp/data/fmriprep_bold_truncated \
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FMRIPREP_REGRESSION_TARGETS=/tmp/data/fmriprep_bold_mask \
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FMRIPREP_REGRESSION_REPORTS=/tmp/data/reports \
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FMRIPREP_DEV=1
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# use flake8 as linter
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RUN conda install -y flake8
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RUN mkdir -p /tmp/data
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# Download ds005
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RUN wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
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-O ds005_downsampled.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/57f32a429ad5a101f977eb75" &&\
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tar xvzf ds005_downsampled.tar.gz -C /tmp/data/ &&\
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rm ds005_downsampled.tar.gz
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# Download ds210
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RUN wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
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-O ds210_downsampled.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5ae9e37b9a64d7000ce66c21" &&\
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tar xvzf ds210_downsampled.tar.gz -C /tmp/data &&\
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rm ds210_downsampled.tar.gz
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# Download ds054
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RUN wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
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-O ds054_downsampled.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/57f32c22594d9001ef91bf9e" &&\
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tar xvzf ds054_downsampled.tar.gz -C /tmp/data &&\
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rm ds054_downsampled.tar.gz
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# Download freesurfer results for ds005
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RUN mkdir -p /tmp/ds005/derivatives &&\
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wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
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-O ds005_derivatives_freesurfer.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/58fe59eb594d900250960180" &&\
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tar xvzf ds005_derivatives_freesurfer.tar.gz -C /tmp/ds005/derivatives &&\
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rm ds005_derivatives_freesurfer.tar.gz
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# Download truncated bold images
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RUN wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
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-O fmriprep_bold_truncated.tar.gz "https://osf.io/286yr/download" &&\
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tar xvzf fmriprep_bold_truncated.tar.gz -C /tmp/data &&\
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rm fmriprep_bold_truncated.tar.gz
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# Download precomputed masks
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RUN wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
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-O fmriprep_bold_mask.tar.gz "https://osf.io/s4f7b/download" &&\
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tar xvzf fmriprep_bold_mask.tar.gz -C /tmp/data &&\
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rm fmriprep_bold_mask.tar.gz
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# set up code-server (need net-tools for initialization)
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RUN curl -o /tmp/code-server.tar.gz -SL https://github.com/cdr/code-server/releases/download/2.preview.9-vsc1.37.0/code-server2.preview.9-vsc1.37.0-linux-x86_64.tar.gz
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RUN mkdir /src/codeserver &&\
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tar -xvf /tmp/code-server.tar.gz -C /src/codeserver --strip-components=1
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RUN /src/codeserver/code-server --install-extension eamodio.gitlens &&\
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/src/codeserver/code-server --install-extension ms-python.python
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ENTRYPOINT ["/src/codeserver/code-server", "/src/fmriprep"]
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# usage example (assuming in local fmriprep directory):
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#
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# docker run -it \
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# -p 127.0.0.1:8445:8080 \
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# -v ${PWD}:/src/fmriprep \
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# fmriprep_devel:latest
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#
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# then type 127.0.0.1:8445 in your browser address bar

‎docs/contributors.rst

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Development in Docker is encouraged, for the sake of consistency and
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portability.
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By default, work should be built off of `poldracklab/fmriprep:latest
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<https://hub.docker.com/r/poldracklab/fmriprep/>`_ (see the
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By default, work should be built off of `poldracklab/fmriprep:unstable
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<https://hub.docker.com/r/poldracklab/fmriprep/>`_, which tracks the ``master`` branch,
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or ``poldracklab/fmriprep:latest``, which tracks the latest release version (see the
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installation_ guide for the basic procedure for running).
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It will be assumed the developer has a working repository in
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$ fmriprep-docker -i fmriprep --shell
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Code-Server Development Environment (Experimental)
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==================================================
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To get the best of working with containers and having an interactive
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development environment, we have an experimental setup with `code-server
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<https://github.com/cdr/code-server>`_.
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.. Note::
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We have `a video walking through the process
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<https://youtu.be/bkZ-NyUaTvg>`_ if you want a visual guide.
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1. Build the Docker image
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~~~~~~~~~~~~~~~~~~~~~~~~~
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We will use the ``Dockerfile_devel`` file to build
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our development docker image::
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$ cd $HOME/projects/fmriprep
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$ docker build -t fmriprep_devel -f Dockerfile_devel .
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2. Run the Docker image
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~~~~~~~~~~~~~~~~~~~~~~~
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We can start a docker container using the image we built (``fmriprep_devel``)::
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$ docker run -it -p 127.0.0.1:8445:8080 -v ${PWD}:/src/fmriprep fmriprep_devel:latest
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.. Note::
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If you are using windows shell, ${PWD} may not be defined, instead use the absolute
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path to your fmriprep directory.
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.. Note::
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If you are using Docker-Toolbox, you will need to change your virtualbox settings
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using `these steps as a guide
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<https://github.com/jdkent/tutDockerRstudio#additional-setup-for-docker-toolbox>`_.
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(For step ``6``, instead of ``Name = rstudio; Host Port = 8787; Guest Port = 8787``,
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have ``Name = code-server; Host Port = 8443; Guest Port = 8080``.)
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Then in the docker command above, change ``127.0.0.1:8445:8080``
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to ``192.168.99.100:8445:8080``.
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If the container started correctly, you should see the following on your console::
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INFO Server listening on http://localhost:8080
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INFO - No authentication
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INFO - Not serving HTTPS
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Now you can switch to your favorite browser and go to: ``127.0.0.1:8445``
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(or ``192.168.99.100:8445`` for Docker Toolbox).
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3. Copy fmriprep.egg-info into your fmriprep directory
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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``fmriprep.egg-info`` makes the fmriprep package exacutable inside the docker container.
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Open a terminal in vscode and type the following::
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$ cp -R /src/fmriprep.egg-info /src/fmriprep/
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Code-Server Development Environment Features
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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- The editor is `vscode <https://code.visualstudio.com/docs>`_
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- There are several preconfigured debugging tests under
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the debugging icon in the activity bar
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- see `vscode debugging python <https://code.visualstudio.com/docs/python/debugging>`_
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for details.
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- The ``gitlens`` and ``python`` extensions are preinstalled to improve
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the development experience in vscode.
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Adding new features to the citation boilerplate
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===============================================
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(transformation matrices, and six corresponding rotation and translation
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parameters) are estimated before any spatiotemporal filtering using
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`mcflirt` [FSL {fsl_ver}, @mcflirt].
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""".format(fsl_ver=fsl.Info().version() or '<ver>')
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""".format(fsl_ver=fsl.Info().version() or '<ver>')

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