Merge branch 'maint/run-docker-as-user' into pin/niworkflows-0.8

Author: oesteban

.circleci/config.yml

@@ -389,7 +389,7 @@ jobs:
             sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds005/work && \
                 sudo setfacl -m group:$(id -gn):rwx /tmp/ds005/work
             fmriprep-docker -i poldracklab/fmriprep:latest \
-                -e FMRIPREP_DEV 1 \
+                -e FMRIPREP_DEV 1 -u $(id -u) \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work \
                 /tmp/data/ds005 /tmp/ds005/derivatives participant \
                 --sloppy --write-graph --mem_mb 4096 \
@@ -408,7 +408,7 @@ jobs:
             sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds005/work && \
                 sudo setfacl -m group:$(id -gn):rwx /tmp/ds005/work
             fmriprep-docker -i poldracklab/fmriprep:latest \
-                -e FMRIPREP_DEV 1 \
+                -e FMRIPREP_DEV 1 -u $(id -u) \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work \
                 /tmp/data/ds005 /tmp/ds005/derivatives participant \
                 --sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
@@ -437,7 +437,7 @@ jobs:
           command: |
             rm /tmp/data/ds005/sub-01/func/*_run-01_*
             fmriprep-docker -i poldracklab/fmriprep:latest \
-                -e FMRIPREP_DEV 1 \
+                -e FMRIPREP_DEV 1 -u $(id -u) \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work_partial \
                 /tmp/data/ds005 /tmp/ds005/derivatives_partial participant \
                 --sloppy --write-graph --use-syn-sdc --mem_mb 4096 \

CHANGES.rst

@@ -1,3 +1,9 @@
+1.3.0.post2 (February 14, 2019)
+===============================
+
+Hotfix release intended for Singularity users, amending the previous iteration
+that didn't fix the problem (#1510) @effigies.
+
 1.3.0.post1 (February 8, 2019)
 ==============================
 

Dockerfile

@@ -2,7 +2,7 @@
 FROM ubuntu:xenial-20161213
 
 # Pre-cache neurodebian key
-COPY docker/files/neurodebian.gpg /root/.neurodebian.gpg
+COPY docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg
 
 # Prepare environment
 RUN apt-get update && \
@@ -67,7 +67,7 @@ ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
 
 # Installing Neurodebian packages (FSL, AFNI, git)
 RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && \
-    apt-key add /root/.neurodebian.gpg && \
+    apt-key add /usr/local/etc/neurodebian.gpg && \
     (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true)
 
 RUN apt-get update && \
@@ -98,6 +98,11 @@ RUN mkdir -p $ANTSPATH && \
     | tar -xzC $ANTSPATH --strip-components 1
 ENV PATH=$ANTSPATH:$PATH
 
+# Create a shared $HOME directory
+RUN useradd -m -s /bin/bash -G users fmriprep
+WORKDIR /home/fmriprep
+ENV HOME="/home/fmriprep"
+
 # Installing SVGO
 RUN curl -sL https://deb.nodesource.com/setup_10.x | bash -
 RUN apt-get install -y nodejs
@@ -142,41 +147,30 @@ RUN conda install -y python=3.7.1 \
                      zlib; sync && \
     chmod -R a+rX /usr/local/miniconda; sync && \
     chmod +x /usr/local/miniconda/bin/*; sync && \
-    conda clean --all -y; sync && \
+    conda build purge-all; sync && \
     conda clean -tipsy && sync
 
-# Precaching fonts, set 'Agg' as default backend for matplotlib
-RUN python -c "from matplotlib import font_manager" && \
-    sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
-RUN pip install "datalad==0.10.0" && \
-    rm -rf ~/.cache/pip
-
 # Unless otherwise specified each process should only use one thread - nipype
 # will handle parallelization
 ENV MKL_NUM_THREADS=1 \
     OMP_NUM_THREADS=1
 
+# Precaching fonts, set 'Agg' as default backend for matplotlib
+RUN python -c "from matplotlib import font_manager" && \
+    sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
+
 # Precaching atlases
-RUN git config --global user.name "fMRIPrep User" && \
-    git config --global user.email "[email protected]"
-ENV TEMPLATEFLOW_HOME="/opt/templateflow"
-WORKDIR /opt
-RUN datalad install -r https://github.com/templateflow/templateflow.git
-RUN datalad get $TEMPLATEFLOW_HOME/tpl-MNI152NLin2009cAsym/* \
-                $TEMPLATEFLOW_HOME/tpl-MNI152Lin/* \
-                $TEMPLATEFLOW_HOME/tpl-OASIS30ANTs/* \
-                $TEMPLATEFLOW_HOME/tpl-NKI/*
-RUN git -C $TEMPLATEFLOW_HOME config annex.merge-annex-branches false && \
-    git -C $TEMPLATEFLOW_HOME/tpl-MNI152NLin2009cAsym config annex.merge-annex-branches false && \
-    git -C $TEMPLATEFLOW_HOME/tpl-MNI152Lin config annex.merge-annex-branches false && \
-    git -C $TEMPLATEFLOW_HOME/tpl-OASIS30ANTs config annex.merge-annex-branches false && \
-    git -C $TEMPLATEFLOW_HOME/tpl-NKI config annex.merge-annex-branches false
+RUN pip install --no-cache-dir "templateflow>=0.0.5.post1" && \
+    python -c "from templateflow import api as tfapi; \
+               tfapi.get('MNI152Lin'); \
+               tfapi.get('MNI152NLin2009cAsym'); \
+               tfapi.get('OASIS30ANTs'); \
+               tfapi.get('NKI');"
 
 # Installing dev requirements (packages that are not in pypi)
 WORKDIR /src/
 COPY requirements.txt requirements.txt
-RUN pip install -r requirements.txt && \
-    rm -rf ~/.cache/pip
+RUN pip install --no-cache-dir -r requirements.txt
 
 # Installing FMRIPREP
 COPY . /src/fmriprep
@@ -185,13 +179,15 @@ ARG VERSION
 RUN echo "${VERSION}" > /src/fmriprep/fmriprep/VERSION && \
     echo "include fmriprep/VERSION" >> /src/fmriprep/MANIFEST.in && \
     cd /src/fmriprep && \
-    pip install .[all] && \
-    rm -rf ~/.cache/pip
+    pip install --no-cache-dir .[all]
 
 RUN install -m 0755 \
     /src/fmriprep/scripts/generate_reference_mask.py \
     /usr/local/bin/generate_reference_mask
 
+RUN find $HOME -type d -exec chmod go=u {} + && \
+    find $HOME -type f -exec chmod go=u {} +
+
 ENV IS_DOCKER_8395080871=1
 
 RUN ldconfig

fmriprep/__about__.py

@@ -104,8 +104,8 @@
 
 
 LINKS_REQUIRES = [
-    'git+https://github.com/oesteban/smriprep@'
-    '1cfa100ab7fc92d07d988f0a99b720739d3812d3#smriprep-0.0.5',
+    'git+https://github.com/poldracklab/smriprep@'
+    '8d238200484ef4f4ea957a380758211612b8a265#smriprep-0.0.5',
 ]
 
 TESTS_REQUIRES = [

requirements.txt

@@ -1 +1 @@
-git+https://github.com/oesteban/smriprep@1cfa100ab7fc92d07d988f0a99b720739d3812d3#smriprep-0.0.5
+git+https://github.com/poldracklab/smriprep@8d238200484ef4f4ea957a380758211612b8a265#smriprep-0.0.5