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| Original file line number | Diff line number | Diff line change |
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| name: Build using conda environment | ||
| on: [push, pull_request] | ||
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| jobs: | ||
| build-linux: | ||
| runs-on: ubuntu-latest | ||
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| steps: | ||
| - uses: actions/checkout@v2 | ||
| with: | ||
| submodules: 'recursive' | ||
| - uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| activate-environment: nighres | ||
| environment-file: conda-nighres.yml | ||
| python-version: 3.9 | ||
| auto-activate-base: false | ||
| - name: Run build process | ||
| shell: bash -l {0} | ||
| run: | | ||
| ./build.sh | ||
| - name: Run pip install | ||
| run: | | ||
| python3 -m pip install . |
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| __pycache__/ | ||
| *.pyc | ||
| *~ | ||
| *.zip | ||
| *.nt.bz2 | ||
| *.tar.gz | ||
| *.tgz | ||
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| env/ | ||
| build/ | ||
| cbstools-public/ | ||
| imcn-imaging/ | ||
| nighresjava/ | ||
| develop-eggs/ | ||
| dist/ | ||
| downloads/ | ||
| lib/ | ||
| lib64/ | ||
| parts/ | ||
| sdist/ | ||
| var/ | ||
| eggs/ | ||
| .eggs/ | ||
| nighres.egg-info/ | ||
| nighres.egg | ||
| .installed.cfg | ||
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| .so | ||
| .jar | ||
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| travis.log | ||
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| doc/_build | ||
| doc/auto_examples | ||
| doc/gen_modules | ||
| doc/modules/generated | ||
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| nighres_examples |
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| matrix: | ||
| include: | ||
| - dist: bionic | ||
| language: java | ||
| jdk: openjdk11 | ||
| before_install: | ||
| - export JCC_JDK=/usr/lib/jvm/java-11-openjdk-amd64 | ||
| - sudo ln -s /usr/lib/jvm/java-11-openjdk-amd64/lib/server/libjvm.so /usr/lib/libjvm.so | ||
| - sudo ln -s /usr/lib/jvm/java-11-openjdk-amd64/lib/libjava.so /usr/lib/libjava.so | ||
| - sudo apt-get update | ||
| - sudo apt-get install python3.6 | ||
| - sudo apt-get install python3-pip | ||
| - python3 -m pip install --upgrade --user setuptools | ||
| - python3 -m pip install --upgrade --user wheel | ||
| - python3 -m pip install --upgrade --user JCC | ||
| script: "travis/make_dist.sh" | ||
| # before_deploy: | ||
| # - python3 -m pip install --user twine | ||
| # - python3 -m pip install --user urllib3[secure] | ||
| # deploy: | ||
| # provider: pypi | ||
| # #server: https://test.pypi.org/legacy/ | ||
| # user: "nighres" | ||
| # # using plain text password for testpypi, when switching to real pypi use encrypted (below) | ||
| # password: | ||
| # secure: "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" | ||
| # skip_cleanup: true | ||
| # on: | ||
| # tags: true | ||
| # branch: master | ||
| # condition: $TRAVIS_PYTHON_VERSION = "2.7" once we run travis against | ||
| # multiple python versions, this ensures that the package will be deployed only once | ||
|
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| notifications: | ||
| email: false |
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| FROM ubuntu:16.04 | ||
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| RUN apt-get update && \ | ||
| apt-get -y install sudo && \ | ||
| sudo apt-get update -qq && \ | ||
| apt-get install -y python3 \ | ||
| python3-pip \ | ||
| python3-dev \ | ||
| build-essential \ | ||
| software-properties-common \ | ||
| openjdk-8-jdk \ | ||
| git \ | ||
| wget && \ | ||
| sudo add-apt-repository ppa:openjdk-r/ppa && \ | ||
| apt-get update -qq && \ | ||
| apt-get install -y openjdk-8-jdk | ||
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| RUN ln -svT "/usr/lib/jvm/java-8-openjdk-$(dpkg --print-architecture)" /docker-java-home | ||
| ENV JAVA_HOME=/docker-java-home \ | ||
| JCC_JDK=/docker-java-home | ||
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| RUN apt-get install libffi-dev && \ | ||
| python3 -m pip install --upgrade "pip < 21.0" \ | ||
| wheel \ | ||
| JCC \ | ||
| urllib3 && \ | ||
| python3 -m pip install jupyter \ | ||
| nilearn \ | ||
| sklearn \ | ||
| nose \ | ||
| matplotlib \ | ||
| scipy \ | ||
| psutil | ||
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| RUN useradd --no-user-group --create-home --shell /bin/bash neuro && \ | ||
| mkdir /home/neuro/nighres | ||
| COPY build.sh cbstools-lib-files.sh setup.py MANIFEST.in README.rst LICENSE imcntk-lib-files.sh /home/neuro/nighres/ | ||
| COPY nighres /home/neuro/nighres/nighres | ||
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| RUN cd /home/neuro/nighres && \ | ||
| ./build.sh && \ | ||
| cd /home/neuro/nighres && python3 -m pip install . && \ | ||
| mkdir /home/neuro/notebooks && \ | ||
| chown -R neuro /home/neuro | ||
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| COPY docker/jupyter_notebook_config.py /etc/jupyter/ | ||
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| EXPOSE 8888 | ||
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| ENV TINI_VERSION v0.6.0 | ||
| ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /usr/bin/tini | ||
| RUN chmod +x /usr/bin/tini | ||
| ENTRYPOINT ["/usr/bin/tini", "--"] | ||
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| EXPOSE 8888 | ||
| CMD ["jupyter", "notebook", "--port=8888", "--no-browser", "--ip=0.0.0.0"] | ||
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| USER neuro |
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