<commit_before>dependencies:
  cache_directories:
    - "~/examples/data"
    - "~/examples/fsdata"
    - "~/examples/feeds"
    - "~/mcr"
    - "~/spm12"
    - "~/examples/fsl_course_data"
  override:
    - pip install --upgrade pip
    - pip install -e .
    - pip install matplotlib sphinx ipython
    - if [[ ! -d ~/examples/data ]]; then wget "http://tcpdiag.dl.sourceforge.net/project/nipy/nipype/nipype-0.2/nipype-tutorial.tar.bz2"; tar jxvf nipype-tutorial.tar.bz2; mkdir ~/examples; mv nipype-tutorial/* ~/examples/; fi
    # we download this manually because CircleCI does not cache apt
    - if [[ ! -d ~/examples/feeds ]]; then wget "http://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.8-feeds.tar.gz"; tar zxvf fsl-5.0.8-feeds.tar.gz; mv feeds ~/examples/; fi
    - if [[ ! -d ~/examples/fsl_course_data ]]; then wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt1.tar.gz" ; wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt2.tar.gz"; wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/tbss.tar.gz"; mkdir ~/examples/fsl_course_data; tar zxvf fdt1.tar.gz -C ~/examples/fsl_course_data; tar zxvf fdt2.tar.gz -C ~/examples/fsl_course_data; tar zxvf tbss.tar.gz -C ~/examples/fsl_course_data; fi
    - wget -O- http://neuro.debian.net/lists/trusty.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
    - sudo apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 0xA5D32F012649A5A9
    - sudo apt-get update -y; sudo apt-get install -y fsl-core fsl-atlases
    - bash ~/nipype/tools/install_spm_mcr.sh
    - mkdir ~/.nipype && echo "[logging]" > ~/.nipype/nipype.cfg && echo "workflow_level = DEBUG" >> ~/.nipype/nipype.cfg && echo "interface_level = DEBUG" >> ~/.nipype/nipype.cfg && echo "filemanip_level = DEBUG" >> ~/.nipype/nipype.cfg
test:
  override:
    - . /usr/share/fsl/5.0/etc/fslconf/fsl.sh && nosetests --processes=1 --process-restartworker --process-timeout=2600 --with-doctest nipype --logging-level=DEBUG --verbosity=3:
        pwd: ../examples
        environment:
          SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
          FORCE_SPMMCR: 1
          FSL_COURSE_DATA: "$HOME/examples/fsl_course_data"
        timeout: 2600
    - set -o pipefail && cd doc && make html 2>&1 | tee ~/log.txt
    - cat ~/log.txt && if grep -q "ERROR" ~/log.txt; then false; else true; fi
    - . /usr/share/fsl/5.0/etc/fslconf/fsl.sh && python ~/nipype/tools/run_examples.py fmri_fsl_feeds Linear l1pipeline:
        pwd: ../examples
    - . /usr/share/fsl/5.0/etc/fslconf/fsl.sh && python ~/nipype/tools/run_examples.py fmri_spm_dartel Linear level1 l2pipeline:
        pwd: ../examples
        environment:
          SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
          FORCE_SPMMCR: 1
        timeout: 1600
    - . /usr/share/fsl/5.0/etc/fslconf/fsl.sh && python ~/nipype/tools/run_examples.py fmri_fsl_reuse Linear level1_workflow:<commit_msg>run tests in source folder, remove test isolation<commit_after>dependencies:
  cache_directories:
    - "~/examples/data"
    - "~/examples/fsdata"
    - "~/examples/feeds"
    - "~/mcr"
    - "~/spm12"
    - "~/examples/fsl_course_data"
  override:
    - pip install --upgrade pip
    - pip install -e .
    - pip install matplotlib sphinx ipython
    - if [[ ! -d ~/examples/data ]]; then wget "http://tcpdiag.dl.sourceforge.net/project/nipy/nipype/nipype-0.2/nipype-tutorial.tar.bz2"; tar jxvf nipype-tutorial.tar.bz2; mkdir ~/examples; mv nipype-tutorial/* ~/examples/; fi
    # we download this manually because CircleCI does not cache apt
    - if [[ ! -d ~/examples/feeds ]]; then wget "http://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.8-feeds.tar.gz"; tar zxvf fsl-5.0.8-feeds.tar.gz; mv feeds ~/examples/; fi
    - if [[ ! -d ~/examples/fsl_course_data ]]; then wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt1.tar.gz" ; wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt2.tar.gz"; wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/tbss.tar.gz"; mkdir ~/examples/fsl_course_data; tar zxvf fdt1.tar.gz -C ~/examples/fsl_course_data; tar zxvf fdt2.tar.gz -C ~/examples/fsl_course_data; tar zxvf tbss.tar.gz -C ~/examples/fsl_course_data; fi
    - wget -O- http://neuro.debian.net/lists/trusty.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
    - sudo apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 0xA5D32F012649A5A9
    - sudo apt-get update -y; sudo apt-get install -y fsl-core fsl-atlases
    - bash ~/nipype/tools/install_spm_mcr.sh
    - mkdir ~/.nipype && echo "[logging]" > ~/.nipype/nipype.cfg && echo "workflow_level = DEBUG" >> ~/.nipype/nipype.cfg && echo "interface_level = DEBUG" >> ~/.nipype/nipype.cfg && echo "filemanip_level = DEBUG" >> ~/.nipype/nipype.cfg
test:
  override:
    - . /usr/share/fsl/5.0/etc/fslconf/fsl.sh && nosetests --with-doctest --logging-level=DEBUG --verbosity=3:
        environment:
          SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
          FORCE_SPMMCR: 1
          FSL_COURSE_DATA: "$HOME/examples/fsl_course_data"
        timeout: 2600
    - set -o pipefail && cd doc && make html 2>&1 | tee ~/log.txt
    - cat ~/log.txt && if grep -q "ERROR" ~/log.txt; then false; else true; fi
    - . /usr/share/fsl/5.0/etc/fslconf/fsl.sh && python ~/nipype/tools/run_examples.py fmri_fsl_feeds Linear l1pipeline:
        pwd: ../examples
    - . /usr/share/fsl/5.0/etc/fslconf/fsl.sh && python ~/nipype/tools/run_examples.py fmri_spm_dartel Linear level1 l2pipeline:
        pwd: ../examples
        environment:
          SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
          FORCE_SPMMCR: 1
        timeout: 1600
    - . /usr/share/fsl/5.0/etc/fslconf/fsl.sh && python ~/nipype/tools/run_examples.py fmri_fsl_reuse Linear level1_workflow:
{'fraction_non_alphanumeric': 0.16478162519575432, 'fraction_numerical': 0.02418653210370628, 'mean_word_length': 2.7593198168737736, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 19, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2161245', 'n_tokens_mistral': 2501, 'n_tokens_neox': 2304, 'n_words': 420}