MAINT: add docker image/circle build

.circleci/config.yml

@@ -0,0 +1,196 @@
+version: 2
+jobs:
+  build:
+    machine:
+      image: circleci/classic:201808-01
+    working_directory: /tmp/src/nitransforms
+    environment:
+      TZ: "/usr/share/zoneinfo/America/Los_Angeles"
+      SCRATCH: "/scratch"
+
+    steps:
+    - restore_cache:
+        keys:
+          - build-v1-{{ .Branch }}-{{ epoch }}
+          - build-v1-{{ .Branch }}-
+          - build-v1-master-
+          - build-v1-
+        paths:
+          - /tmp/docker
+    - run:
+        name: Set-up a Docker registry
+        command: |
+            docker run -d -p 5000:5000 --restart=always --name=registry \
+                -v /tmp/docker:/var/lib/registry registry:2
+    - run:
+        name: Pull existing 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-20200114
+                docker pull localhost:5000/nitransforms
+                docker tag localhost:5000/nitransforms nitransforms:latest
+            else
+                echo "Pulling from Docker Hub"
+                docker pull ubuntu:xenial-20200114
+                docker tag ubuntu:xenial-20200114 localhost:5000/ubuntu
+                docker push localhost:5000/ubuntu
+            fi
+    - checkout
+    - run:
+        name: Build Docker image & push to registry
+        no_output_timeout: 60m
+        command: |
+            e=1 && for i in {1..5}; do
+                docker build --rm --cache-from=nitransforms:latest \
+                -t nitransforms:latest \
+                --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
+                --build-arg VCS_REF=`git rev-parse --short HEAD` . \
+                && e=0 && break || sleep 15
+            done && [ "$e" -eq "0" ]
+            docker tag nitransforms:latest localhost:5000/nitransforms
+            docker push localhost:5000/nitransforms
+    - 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 }}-{{ epoch }}
+        paths:
+          - /tmp/docker
+    - 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
+
+  test_pytest:
+    machine:
+      image: circleci/classic:201808-01
+    environment:
+      FS_LICENSE: "/tmp/fslicense/license.txt"
+    working_directory: /tmp/tests
+    steps:
+      - attach_workspace:
+          at: /tmp
+      - checkout:
+          path: /tmp/src/nitransforms
+      - run:
+          name: Get codecov
+          command: python -m pip install codecov
+      - restore_cache:
+          keys:
+            - build-v1-{{ .Branch }}-{{ epoch }}
+            - build-v1-{{ .Branch }}-
+            - build-v1-master-
+            - build-v1-
+      - run:
+          name: Set-up a Docker registry & pull
+          command: |
+            docker run -d -p 5000:5000 --restart=always --name=registry \
+                -v /tmp/docker:/var/lib/registry registry:2
+            docker pull localhost:5000/nitransforms
+            docker tag localhost:5000/nitransforms nitransforms:latest
+      - run:
+          name: Run unit tests
+          no_output_timeout: 2h
+          command: |
+            mkdir -p $PWD/artifacts $PWD/summaries
+            sudo setfacl -d -m group:ubuntu:rwx $PWD
+            sudo setfacl -m group:ubuntu:rwx $PWD
+            docker run -u $( id -u ) -it --rm=false -w /src/nitransforms \
+              -e COVERAGE_FILE=/tmp/summaries/.pytest.coverage \
+              -v /tmp/fslicense/license.txt:/opt/freesurfer/license.txt:ro \
+              -v ${PWD}:/tmp nitransforms:latest \
+              pytest --junit-xml=/tmp/summaries/pytest.xml \
+                     --cov nitransforms --cov-report xml:/tmp/summaries/unittests.xml \
+                     nitransforms/
+      - run:
+          name: Submit unit test coverage
+          command: |
+            cd /tmp/src/nitransforms
+            python -m codecov --file /tmp/tests/summaries/unittests.xml \
+                --flags unittests -e CIRCLE_JOB
+      - run:
+          name: Clean up tests directory
+          when: on_success
+          command: |
+            rm -rf /tmp/tests/pytest-of-root
+      - store_artifacts:
+          path: /tmp/tests/artifacts
+
+      - store_test_results:
+          path: /tmp/tests/summaries/
+
+  test_packaging_and_deploy:
+    machine:
+      image: circleci/classic:201808-01
+    working_directory: /tmp/src/nitransforms
+    steps:
+      - checkout
+      - run: pyenv local 3.7.0
+      - run:
+          name: Install build depends
+          command: python3 -m pip install "setuptools>=30.4.0" "pip>=10.0.1" "twine<2.0" docutils
+      - run:
+          name: Build and check
+          command: |
+            python3 setup.py check -r -s
+            python3 setup.py sdist
+            python3 -m twine check dist/*
+      - run:
+          name: Validate version
+          command: |
+            THISVERSION=$( python3 get_version.py )
+            python3 -m pip install dist/*.tar.gz
+            mkdir empty
+            cd empty
+            INSTALLED=$( python3 -c 'import nitransforms; print(nitransforms.__version__)' )
+            test "${CIRCLE_TAG:-$THISVERSION}" == "$INSTALLED"
+      - run:
+          name: Upload to PyPi
+          command: |
+            python3 -m twine upload dist/*
+
+
+workflows:
+  version: 2
+  build_test_deploy:
+    jobs:
+      - build:
+          filters:
+            branches:
+              ignore:
+                - /docs?\/.*/
+            tags:
+              only: /.*/
+
+      - test_pytest:
+          requires:
+            - build
+          filters:
+            branches:
+              ignore:
+                - /docs?\/.*/
+                - /docker\/.*/
+            tags:
+              only: /.*/
+
+      - test_packaging_and_deploy:
+          requires:
+            - test_pytest
+          filters:
+            branches:
+              ignore: /.*/
+            tags:
+              only: /.*/

Dockerfile

@@ -0,0 +1,155 @@
+FROM ubuntu:xenial-20200114
+
+# Pre-cache neurodebian key
+COPY docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg
+
+# Prepare environment
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+                    curl \
+                    bzip2 \
+                    ca-certificates \
+                    xvfb \
+                    build-essential \
+                    autoconf \
+                    libtool \
+                    pkg-config \
+                    git && \
+    curl -sL https://deb.nodesource.com/setup_10.x | bash - && \
+    apt-get install -y --no-install-recommends \
+                    nodejs && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# Installing freesurfer
+RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz | tar zxv --no-same-owner -C /opt \
+    --exclude='freesurfer/diffusion' \
+    --exclude='freesurfer/docs' \
+    --exclude='freesurfer/fsfast' \
+    --exclude='freesurfer/lib/cuda' \
+    --exclude='freesurfer/lib/qt' \
+    --exclude='freesurfer/matlab' \
+    --exclude='freesurfer/mni/share/man' \
+    --exclude='freesurfer/subjects/fsaverage_sym' \
+    --exclude='freesurfer/subjects/fsaverage3' \
+    --exclude='freesurfer/subjects/fsaverage4' \
+    --exclude='freesurfer/subjects/cvs_avg35' \
+    --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
+    --exclude='freesurfer/subjects/bert' \
+    --exclude='freesurfer/subjects/lh.EC_average' \
+    --exclude='freesurfer/subjects/rh.EC_average' \
+    --exclude='freesurfer/subjects/sample-*.mgz' \
+    --exclude='freesurfer/subjects/V1_average' \
+    --exclude='freesurfer/trctrain'
+
+ENV FSL_DIR="/usr/share/fsl/5.0" \
+    OS="Linux" \
+    FS_OVERRIDE=0 \
+    FIX_VERTEX_AREA="" \
+    FSF_OUTPUT_FORMAT="nii.gz" \
+    FREESURFER_HOME="/opt/freesurfer"
+ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
+    FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
+    MNI_DIR="$FREESURFER_HOME/mni" \
+    LOCAL_DIR="$FREESURFER_HOME/local" \
+    MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
+    MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
+    MNI_DATAPATH="$FREESURFER_HOME/mni/data"
+ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
+    MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
+    PATH="$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
+
+# Installing Neurodebian packages (FSL, AFNI, git)
+RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && \
+    apt-key add /usr/local/etc/neurodebian.gpg && \
+    (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true)
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+                    fsl-core=5.0.9-5~nd16.04+1 \
+                    fsl-mni152-templates=5.0.7-2 \
+                    afni=16.2.07~dfsg.1-5~nd16.04+1 \
+                    convert3d \
+                    connectome-workbench=1.3.2-2~nd16.04+1 \
+                    git-annex-standalone && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+ENV FSLDIR="/usr/share/fsl/5.0" \
+    FSLOUTPUTTYPE="NIFTI_GZ" \
+    FSLMULTIFILEQUIT="TRUE" \
+    POSSUMDIR="/usr/share/fsl/5.0" \
+    LD_LIBRARY_PATH="/usr/lib/fsl/5.0:$LD_LIBRARY_PATH" \
+    FSLTCLSH="/usr/bin/tclsh" \
+    FSLWISH="/usr/bin/wish" \
+    AFNI_MODELPATH="/usr/lib/afni/models" \
+    AFNI_IMSAVE_WARNINGS="NO" \
+    AFNI_TTATLAS_DATASET="/usr/share/afni/atlases" \
+    AFNI_PLUGINPATH="/usr/lib/afni/plugins"
+ENV PATH="/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH"
+
+# Installing ANTs 2.2.0 (NeuroDocker build)
+ENV ANTSPATH=/usr/lib/ants
+RUN mkdir -p $ANTSPATH && \
+    curl -sSL "https://dl.dropbox.com/s/2f4sui1z6lcgyek/ANTs-Linux-centos5_x86_64-v2.2.0-0740f91.tar.gz" \
+    | tar -xzC $ANTSPATH --strip-components 1
+ENV PATH=$ANTSPATH:$PATH
+
+# Installing and setting up miniconda
+RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh && \
+    bash Miniconda3-4.5.11-Linux-x86_64.sh -b -p /usr/local/miniconda && \
+    rm Miniconda3-4.5.11-Linux-x86_64.sh
+
+# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
+ENV PATH="/usr/local/miniconda/bin:$PATH" \
+    CPATH="/usr/local/miniconda/include/:$CPATH" \
+    LANG="C.UTF-8" \
+    LC_ALL="C.UTF-8" \
+    PYTHONNOUSERSITE=1
+
+# Installing precomputed python packages
+RUN conda install -y python=3.7.1 \
+                     pip=19.1 \
+                     mkl=2018.0.3 \
+                     mkl-service \
+                     numpy=1.15.4 \
+                     scipy=1.1.0 \
+                     libxml2=2.9.8 \
+                     libxslt=1.1.32 \
+                     zlib; sync && \
+    chmod -R a+rX /usr/local/miniconda; sync && \
+    chmod +x /usr/local/miniconda/bin/*; sync && \
+    conda build purge-all; sync && \
+    conda clean -tipsy && sync
+
+# Unless otherwise specified each process should only use one thread - nipype
+# will handle parallelization
+ENV MKL_NUM_THREADS=1 \
+    OMP_NUM_THREADS=1
+
+# Create a shared $HOME directory
+RUN useradd -m -s /bin/bash -G users neuro
+WORKDIR /home/neuro
+ENV HOME="/home/neuro"
+
+# Install package
+COPY . /src/nitransforms
+ARG VERSION
+# Force static versioning within container
+RUN echo "${VERSION}" > /src/nitransforms/nitransforms/VERSION && \
+    echo "include nitransforms/VERSION" >> /src/nitransforms/MANIFEST.in && \
+    pip install --no-cache-dir "/src/nitransforms[all]"
+
+RUN find $HOME -type d -exec chmod go=u {} + && \
+    find $HOME -type f -exec chmod go=u {} +
+
+
+RUN ldconfig
+WORKDIR /tmp/
+
+ARG BUILD_DATE
+ARG VCS_REF
+ARG VERSION
+LABEL org.label-schema.build-date=$BUILD_DATE \
+      org.label-schema.name="nitransforms" \
+      org.label-schema.vcs-url="https://github.com/poldracklab/nitransforms" \
+      org.label-schema.version=$VERSION \
+      org.label-schema.schema-version="1.0"