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Merge pull request #203 from QIICR/standalone-packaging-rebased
Standalone packaging
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| build/ | ||
| docker/dcmqi/dcmqi-linux/ | ||
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| *.[ao] | ||
| *~ | ||
| *.swp | ||
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| Original file line number | Diff line number | Diff line change |
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| machine: | ||
| # XXX: btrfs circleCI fix, see: https://github.com/docker/docker/issues/9939 and https://github.com/Sabayon/docker-stage3-base-amd64/commit/8c1bf737113a278dd2f | ||
| pre: | ||
| - sudo curl -L -o /usr/bin/docker 'https://s3-external-1.amazonaws.com/circle-downloads/docker-1.9.0-circleci' | ||
| - sudo chmod 0755 /usr/bin/docker | ||
| services: | ||
| - docker | ||
| python: | ||
| version: 2.7.11 | ||
| dependencies: | ||
| cache_directories: | ||
| - "~/dcmqi-build/zlib" | ||
| - "~/dcmqi-build/zlib-build" | ||
| - "~/dcmqi-build/ITK" | ||
| - "~/dcmqi-build/ITK-build" | ||
| - "~/dcmqi-build/DCMTK" | ||
| - "~/dcmqi-build/DCMTK-build" | ||
| - "~/dcmqi-build/SlicerExecutionModel" | ||
| - "~/dcmqi-build/SlicerExecutionModel-build" | ||
| - dicom3tools_1.00.snapshot.20160721064406 | ||
| pre: | ||
| # Install tools required to run DCMQI "doc" tests | ||
| - npm install jsonlint -g | ||
| - npm install ajv-cli -g | ||
| # Install xutils-dev package providing "imake" | ||
| - sudo apt-get update | ||
| - sudo apt-get install xutils-dev | ||
| # If needed, download and build dicom3tools | ||
| - | | ||
| dicom3tools_version=dicom3tools_1.00.snapshot.20160721064406 | ||
| if [[ ! -e $dicom3tools_version ]]; then | ||
| wget --no-check-certificate http://slicer.kitware.com/midas3/download/item/270310/dicom3tools_1.00.snapshot.20160721064406.tar.bz2 -O dicom3tools.tar.bz2 \ | ||
| && tar xjf dicom3tools.tar.bz2 \ | ||
| && (cd $dicom3tools_version/ \ | ||
| && ./Configure \ | ||
| && imake -I./config -DUseQIICRID \ | ||
| && make -j$(grep -c processor /proc/cpuinfo) World > /dev/null 2>&1) | ||
| else | ||
| echo "Reusing " | ||
| fi | ||
| cd $dicom3tools_version && sudo make install | ||
| # Install Ninja | ||
| - wget --no-check-certificate https://github.com/ninja-build/ninja/releases/download/v1.7.2/ninja-linux.zip | ||
| - unzip ninja-linux.zip && sudo cp ninja /usr/local/bin/ && sudo chmod 755 /usr/local/bin/ninja | ||
| # Use scikit-ci-addons to streamline installation of CMake | ||
| - pip install scikit-ci-addons==0.11.0 | ||
| - ci_addons circle/install_cmake 3.6.2 | ||
| - "~/dcmqi/build" | ||
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| post: | ||
| - mkdir -p ~/dcmqi-build && cd ~/dcmqi-build && cmake -G Ninja ../dcmqi && ninja | ||
| - cd docker && make dcmqi | ||
| # Install package required by convert.py | ||
| - pip install lxml==3.6.4 | ||
| - | | ||
| cd ~/dcmqi-build/dcmqi-build && \ | ||
| ctest -j4 -D ExperimentalTest -VV --no-compress-output && \ | ||
| python ../../dcmqi/util/junit/convert.py \ | ||
| ~/dcmqi-build/dcmqi-build/ \ | ||
| ../../dcmqi/util/junit/conv.xsl > ~/dcmqi-build/BaseTest.xml | ||
| cd docker && make dcmqi.test && \ | ||
| python ../util/junit/convert.py \ | ||
| ../build/dcmqi-build/ \ | ||
| ../util/junit/conv.xsl > ../build/BaseTest.xml | ||
| test: | ||
| post: | ||
| - mkdir -p ${CIRCLE_TEST_REPORTS}/junit | ||
| - cp ~/dcmqi-build/BaseTest.xml ${CIRCLE_TEST_REPORTS}/junit | ||
| - cp ~/dcmqi/build/BaseTest.xml ${CIRCLE_TEST_REPORTS}/junit | ||
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| deployment: | ||
| release: # just a label | ||
| branch: master | ||
| commands: | ||
| - | | ||
| [ "$DOCKER_EMAIL" != "" ] \ | ||
| && docker login -e $DOCKER_EMAIL -u $DOCKER_USER -p $DOCKER_PASS \ | ||
| && docker push qiicr/dcmqi:`git describe --exact-match 2> /dev/null || echo "latest"` \ | ||
| || echo "skipping docker push" |
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| # | ||
| # Parameters | ||
| # | ||
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| # Name of the docker executable | ||
| DOCKER = docker | ||
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| # Docker organization to pull the images from | ||
| ORG = qiicr | ||
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| # Directories | ||
| ROOT_DIR = $(shell pwd)/.. | ||
| BUILD_DIR = build | ||
| DOCKER_DIR = $(ROOT_DIR)/docker | ||
| TMP = /tmp | ||
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| dicom3tools_version=dicom3tools_1.00.snapshot.20160721064406 | ||
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| # | ||
| # Targets | ||
| # | ||
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| image: dcmqi dcmqi.test | ||
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| # Pull dockcross image | ||
| prereq.pull_dockcross: | ||
| $(DOCKER) pull dockcross/manylinux-x64 | ||
| $(DOCKER) run --rm dockcross/manylinux-x64 > $(TMP)/dockcross | ||
| chmod u+x $(TMP)/dockcross | ||
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| # Download and build dicom3tools | ||
| prereq.build_dicom3tools: prereq.pull_dockcross | ||
| mkdir -p $(ROOT_DIR)/$(BUILD_DIR) | ||
| cd $(ROOT_DIR)/$(BUILD_DIR) \ | ||
| && [ ! -e $(dicom3tools_version) ] \ | ||
| && wget --no-check-certificate http://slicer.kitware.com/midas3/download/item/270310/dicom3tools_1.00.snapshot.20160721064406.tar.bz2 -O dicom3tools.tar.bz2 \ | ||
| && tar xjf dicom3tools.tar.bz2 \ | ||
| && cd $(dicom3tools_version)/ \ | ||
| && $(TMP)/dockcross ./Configure \ | ||
| && $(TMP)/dockcross imake -I./config -DUseQIICRID \ | ||
| && ( $(TMP)/dockcross make -j$(grep -c processor /proc/cpuinfo) World > /dev/null 2>&1 )\ | ||
| || echo "Reusing " | ||
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| # Download and install "ajv" and "jsonlint" tools | ||
| prereq.install_npm_packages: prereq.pull_dockcross | ||
| mkdir -p $(ROOT_DIR)/$(BUILD_DIR) | ||
| # If needed, download node | ||
| cd $(ROOT_DIR)/$(BUILD_DIR) && \ | ||
| [ ! -e node-v6.9.5-linux-x64 ] && \ | ||
| wget --no-check-certificate https://nodejs.org/dist/v6.9.5/node-v6.9.5-linux-x64.tar.xz && \ | ||
| tar xf node-v6.9.5-linux-x64.tar.xz || true | ||
| # Install tools required to run DCMQI "doc" tests | ||
| cd $(ROOT_DIR) && \ | ||
| $(TMP)/dockcross bash -c "export PATH=/work/build/node-v6.9.5-linux-x64/bin:$$PATH && npm install jsonlint -g && npm install ajv-cli -g" | ||
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| # Configure, build and package | ||
| dcmqi.generate_package: prereq.pull_dockcross | ||
| cd $(ROOT_DIR) && \ | ||
| $(TMP)/dockcross cmake -B$(BUILD_DIR) -H. -GNinja -DCMAKE_BUILD_TYPE:STRING=Release && \ | ||
| $(TMP)/dockcross bash -c "export PATH=/work/build/node-v6.9.5-linux-x64/bin:/work/build/$(dicom3tools_version)/appsrc/dcfile:$$PATH && ninja -C$(BUILD_DIR) -v" && \ | ||
| $(TMP)/dockcross ninja -C$(BUILD_DIR)/dcmqi-build package | ||
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| # Build "dcmqi" docker image | ||
| dcmqi.docker_image: | ||
| tar -xzvf $(ROOT_DIR)/$(BUILD_DIR)/dcmqi-build/dcmqi-linux.tar.gz -C $(DOCKER_DIR)/dcmqi | ||
| cd $(DOCKER_DIR) && \ | ||
| docker build -t $(ORG)/dcmqi:`git describe --exact-match 2> /dev/null || echo "latest"` \ | ||
| --build-arg IMAGE=$(ORG)/dcmqi \ | ||
| --build-arg VCS_REF=`git describe --exact-match 2> /dev/null || git rev-parse --short HEAD` \ | ||
| --build-arg VCS_URL=`git config --get remote.origin.url` \ | ||
| --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \ | ||
| dcmqi | ||
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| dcmqi: prereq.build_dicom3tools prereq.install_npm_packages dcmqi.generate_package dcmqi.docker_image | ||
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| dcmqi.test: | ||
| cd $(ROOT_DIR) && \ | ||
| $(TMP)/dockcross bash -c "export PATH=/work/build/node-v6.9.5-linux-x64/bin:/work/build/$(dicom3tools_version)/appsrc/dcfile:/opt/python/cp27-cp27mu/bin/:$$PATH && cd /work/build/dcmqi-build && ctest -j4 -D ExperimentalTest -VV --no-compress-output" | ||
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| dcmqi.clean: | ||
| rm -rf $(ROOT_DIR)/$(BUILD_DIR) | ||
| rm -rf $(DOCKER_DIR)/dcmqi/dcmqi-linux | ||
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| .PHONY: image dcmqi dcmqi.% prereq.% |
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| FROM centos:5 | ||
| MAINTAINER http://github.com/QIICR | ||
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| COPY imagefiles/docker_entry.sh /dcmqi/ | ||
| COPY dcmqi-linux/bin/* /usr/bin/ | ||
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| WORKDIR /work | ||
| ENTRYPOINT ["/bin/bash","/dcmqi/docker_entry.sh"] | ||
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| # Build-time metadata as defined at http://label-schema.org | ||
| ARG BUILD_DATE | ||
| ARG IMAGE | ||
| ARG VCS_REF | ||
| ARG VCS_URL | ||
| LABEL org.label-schema.build-date=$BUILD_DATE \ | ||
| org.label-schema.name=$IMAGE \ | ||
| org.label-schema.vcs-ref=$VCS_REF \ | ||
| org.label-schema.vcs-url=$VCS_URL \ | ||
| org.label-schema.schema-version="1.0" |
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| Original file line number | Diff line number | Diff line change |
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| #!/bin/bash | ||
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| case "$1" in | ||
| itkimage2paramap|paramap2itkimage|itkimage2segimage|segimage2itkimage|tid1500reader|tid1500writer) | ||
| $1 "${@:2}" | ||
| ;; | ||
| *) | ||
| echo "ERROR: Unknown command" | ||
| echo "" | ||
| cat >&2 <<ENDHELP | ||
| Usage: docker run [-v <HOST_DIR>:<CONTAINER_DIR>] qiicr/dcmqi <command> [args] | ||
| Run the given dcmqi *command*. | ||
| Available commands are: | ||
| itkimage2paramap | ||
| paramap2itkimage | ||
| itkimage2segimage | ||
| segimage2itkimage | ||
| tid1500reader | ||
| tid1500writer | ||
| For *command* help use: docker run qiicr/dcmqi <command> --help | ||
| ENDHELP | ||
| exit 1 | ||
| ;; | ||
| esac | ||
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