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Arno Klein
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Revert back from circleci v2 to v1 until figure out new format. Keep v2 attempt in DOTcircleci folder.
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‎.circleci/config.yml renamed to ‎DOTcircleci/config.yml

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MB: ${SITEPKGS}/mindboggle
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steps:
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- checkout
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#-----------------------------------------------------------------------
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# Dependencies
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#-----------------------------------------------------------------------
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- run:
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name: install requirements/dev.txt
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command: pip install -r requirements/dev.txt

‎.circleci/requirements/dev.txt renamed to ‎DOTcircleci/requirements/dev.txt

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‎circle.yml

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## Configuration file for circleci.com continuous integration (testing)
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##
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## All dependencies are accounted for in the environment.yml file.
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##
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## Authors:
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## - Arno Klein, 2016 ([email protected]) http://binarybottle.com
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##
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## Copyright 2016, Mindboggle team (mindboggle.info), Apache v2.0 License
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#-----------------------------------------------------------------------------
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# Customize the test machine:
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#-----------------------------------------------------------------------------
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machine:
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# Add some environment variables
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environment:
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HOME: /home/ubuntu
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CONDA_ROOT: ${HOME}/miniconda
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ENV_NAME: mindboggle-env
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ENV_PREFIX: ${CONDA_ROOT}/envs/${ENV_NAME}
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python: ${ENV_PREFIX}/bin/python
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vtk_cpp_tools: ${HOME}/mindboggle/vtk_cpp_tools/bin
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PATH: ${ENV_PREFIX}/bin:${CONDA_ROOT}/bin:${vtk_cpp_tools}:${PATH}
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SITEPKGS: ${ENV_PREFIX}/lib/python3.5/site-packages
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PYTHONPATH: ${SITEPKGS}/vtk:${PYTHONPATH}
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MB: ${SITEPKGS}/mindboggle
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#-----------------------------------------------------------------------------
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# Customize dependencies:
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#-----------------------------------------------------------------------------
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dependencies:
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#cache_directories:
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# - $CONDA_ROOT
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pre:
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- sudo apt-get update; sudo apt-get install libllvm-3.3
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override:
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#-------------------------------------------------------------------------
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# Download/install conda (if not already cached)
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#-------------------------------------------------------------------------
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- >
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if [[ ! -d $CONDA_ROOT ]]; then
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echo "Installing Miniconda3...";
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wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh &&
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bash Miniconda3-latest-Linux-x86_64.sh -b -p $CONDA_ROOT;
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else
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echo "Using cached Miniconda install";
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fi
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- conda config --set show_channel_urls yes --set always_yes yes
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- conda update conda conda-env
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#-------------------------------------------------------------------------
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# Create a Python environment (see environment.yml file):
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#-------------------------------------------------------------------------
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- conda env create
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- source activate mindboggle-env
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- conda info --envs
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#-------------------------------------------------------------------------
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# Install Mindboggle and its C++ code:
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#-------------------------------------------------------------------------
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- $python setup.py install
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- mkdir $vtk_cpp_tools && cd $vtk_cpp_tools && cmake ../ && make
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#-----------------------------------------------------------------------------
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# Customize test commands:
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#-----------------------------------------------------------------------------
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test:
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override:
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- $python -m "nose" --with-doctest ${MB}/thirdparty/
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- $python -m "nose" --with-doctest ${MB}/mio/
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- $python -m "nose" --with-doctest ${MB}/guts/
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- $python -m "nose" --with-doctest ${MB}/shapes/
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- $python -m "nose" --with-doctest ${MB}/features/
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#- $python -m "nose" --with-doctest --with-coverage ${MB}/evaluate/
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#- coveralls

‎environment.yml

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# Environment for installing Mindboggle
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#
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# This environment is configured for circleci.com continuous integration
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# (testing).
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#
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# Authors:
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# - Arno Klein, 2016-2017 ([email protected]) http://binarybottle.com
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#
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# Copyright 2016-2017, Mindboggle team (mindboggle.info), Apache v2.0 License
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#-----------------------------------------------------------------------------
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# mindboggle-env environment:
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#-----------------------------------------------------------------------------
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name: mindboggle-env
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#-----------------------------------------------------------------------------
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# anaconda cloud channel for installing VTK 7.0.0:
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#-----------------------------------------------------------------------------
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channels:
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- clinicalgraphics
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#-----------------------------------------------------------------------------
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# mindboggle dependencies:
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#-----------------------------------------------------------------------------
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dependencies:
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- python=3.5.1
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- vtk=7.0.0
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- matplotlib
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- numpy
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- scipy
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- pandas
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- cmake
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- pip
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- pip:
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- nibabel
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- nipype
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- prov
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- traits
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- xvfbwrapper
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- colormath
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- pydotplus
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- networkx
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- lxml
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- simplejson
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- future
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- nose
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#-------------------------------------------------------------------------
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# additional testing tools:
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#-------------------------------------------------------------------------
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- ipython
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- pytest
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- coverage
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