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Merge pull request #135 from khanlab/fix-ci
add requirements.txt from poetry export
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‎hippunfold/config/snakebids.yml

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bids_dir: '../test_data/bids_singleT2w'
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output_dir: 'test_output' #don't use '.'
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snakemake_dir: '/localscratch/hippunfold_warps/hippunfold' #do not modify this variable -- is used to refer to files needed by the workflow when running with CLI
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snakemake_dir: '.' #do not modify this variable -- is used to refer to files needed by the workflow when running with CLI
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#enable printing debug statements during parsing -- disable if generating dag visualization
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debug: False

‎requirements.txt

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appdirs==1.4.4
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argparse==1.4.0
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arrow==1.2.1; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.5.0"
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astor==0.8.1; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.4.0"
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astropy==4.3.1; python_version >= "3.7"
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attrs==21.2.0; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.7"
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batchgenerators==0.21
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bids-validator==1.8.9; python_version >= "3.7" and python_version < "3.11"
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binaryornot==0.4.4; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.5.0"
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certifi==2021.10.8; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
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chardet==4.0.0; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.5.0"
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charset-normalizer==2.0.9; python_full_version >= "3.6.0" and python_version >= "3"
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click==7.1.2; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.5.0"
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colorama==0.4.4; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" and platform_system == "Windows" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.5.0" and platform_system == "Windows"
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configargparse==1.5.3; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.5.0"
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connection-pool==0.0.3; python_version >= "3.7" and python_version < "3.11"
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cookiecutter==1.7.3; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.5.0"
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cycler==0.11.0; python_version >= "3.7"
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datrie==0.8.2; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.4.0"
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dicom2nifti==2.3.0
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docopt==0.6.2; python_version >= "3.7" and python_version < "3.11"
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docutils==0.18.1; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.5.0"
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filelock==3.4.0; python_version >= "3.7" and python_version < "3.11"
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fonttools==4.28.4; python_version >= "3.7"
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formulaic==0.2.4; python_version >= "3.7" and python_version < "3.11"
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future==0.18.2; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
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gitdb==4.0.9; python_version >= "3.7"
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gitpython==3.1.24; python_version >= "3.7" and python_version < "3.11"
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idna==3.3; python_version >= "3.5" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.5"
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imageio==2.13.3; python_version >= "3.7"
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importlib-metadata==1.7.0; python_version == "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version == "3.7"
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importlib-resources==5.4.0; python_version < "3.9" and python_version >= "3.7"
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interface-meta==1.2.4; python_version >= "3.7" and python_version < "3.11"
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ipython-genutils==0.2.0; python_version >= "3.5"
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jinja2-time==0.2.0; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.5.0"
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jinja2==3.0.3; python_version >= "3.6"
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joblib==1.1.0; python_version >= "3.7"
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jsonschema==4.3.1; python_version >= "3.7" and python_version < "3.11"
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jupyter-core==4.9.1; python_version >= "3.6"
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kiwisolver==1.3.2; python_version >= "3.7"
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linecache2==1.0.0
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markupsafe==2.0.1; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.5.0"
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matplotlib==3.5.1; python_version >= "3.7"
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medpy==0.4.0
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nbformat==5.1.3; python_version >= "3.7" and python_version < "3.11"
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networkx==2.6.3; python_version >= "3.7"
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nibabel==3.2.1; python_version >= "3.6"
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nilearn==0.8.1; python_version >= "3.6"
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nnunet-inference-on-cpu-and-gpu==1.6.6
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num2words==0.5.10; python_version >= "3.7" and python_version < "3.11"
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numpy==1.21.4; python_version >= "3.7" and python_version < "3.11"
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packaging==21.3; python_version >= "3.7"
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pandas==1.3.5; python_full_version >= "3.7.1"
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pillow==8.4.0; python_version >= "3.7"
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poyo==0.5.0; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.5.0"
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progress==1.6; python_version >= "3.7" and python_version < "3.11"
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psutil==5.8.0; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.4.0"
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pulp==2.6.0; python_version >= "3.7" and python_version < "3.11"
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pybids==0.14.0; python_version >= "3.7" and python_version < "3.11"
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pydicom==2.2.2; python_full_version >= "3.6.1"
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pyerfa==2.0.0.1; python_version >= "3.7"
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pygments==2.10.0; python_version >= "3.5"
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pygraphviz==1.7; python_version >= "3.7"
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pyparsing==3.0.6; python_version >= "3.7"
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pyrsistent==0.18.0; python_version >= "3.7"
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python-dateutil==2.8.2; python_full_version >= "3.7.1" and python_version >= "3.7" and (python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.5.0")
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python-slugify==5.0.2; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.5.0"
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pytz==2021.3; python_full_version >= "3.7.1"
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pywavelets==1.2.0; python_version >= "3.7"
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pywin32==302; sys_platform == "win32" and platform_python_implementation != "PyPy" and python_version >= "3.6"
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pyyaml==5.4.1; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.6.0"
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ratelimiter==1.2.0.post0; python_version >= "3.7" and python_version < "3.11"
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requests==2.26.0; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_full_version >= "3.6.0" and python_version >= "3.7" and python_version < "3.11"
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scikit-fmm==2021.10.29
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scikit-image==0.19.1; python_version >= "3.7"
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scikit-learn==1.0.1; python_version >= "3.7"
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scipy==1.7.3; python_version >= "3.7" and python_version < "3.11"
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seaborn==0.11.2; python_version >= "3.6"
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setuptools-scm==6.3.2; python_version >= "3.7"
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simpleitk==2.1.1
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six==1.16.0; python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.7.1"
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sklearn==0.0
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smart-open==5.2.1; python_version >= "3.7" and python_version < "3.11"
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smmap==5.0.0; python_version >= "3.7"
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snakebids==0.4.1; python_version >= "3.7" and python_version < "3.11"
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snakemake==6.12.3
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sqlalchemy==1.3.24; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.4.0"
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stopit==1.1.2; python_version >= "3.7" and python_version < "3.11"
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tabulate==0.8.9; python_version >= "3.7" and python_version < "3.11"
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text-unidecode==1.3; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.5.0"
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threadpoolctl==3.0.0; python_version >= "3.7"
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tifffile==2021.11.2; python_version >= "3.7"
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tomli==1.2.3; python_version >= "3.7"
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toposort==1.7; python_version >= "3.7" and python_version < "3.11"
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torch==1.10.1; python_full_version >= "3.6.2"
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tqdm==4.62.3; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
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traceback2==1.4.0
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traitlets==5.1.1; python_version >= "3.7"
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typing-extensions==3.10.0.2; python_version >= "3.7" and python_version < "3.8" and python_full_version >= "3.6.2" and (python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.8" or python_version >= "3.7" and python_version < "3.8" and python_full_version >= "3.5.0")
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unittest2==1.1.0
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urllib3==1.26.7; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version < "4"
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wrapt==1.13.3; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.11" or python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.5.0"
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zipp==3.6.0; python_version == "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version == "3.7"

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