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add requirements.txt from poetry export #135

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Dec 18, 2021
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2 changes: 1 addition & 1 deletion hippunfold/config/snakebids.yml
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
bids_dir: '../test_data/bids_singleT2w'
output_dir: 'test_output' #don't use '.'

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
snakemake_dir: '.' #do not modify this variable -- is used to refer to files needed by the workflow when running with CLI

#enable printing debug statements during parsing -- disable if generating dag visualization
debug: False
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103 changes: 103 additions & 0 deletions requirements.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,103 @@
appdirs==1.4.4
argparse==1.4.0
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"
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"
astropy==4.3.1; python_version >= "3.7"
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"
batchgenerators==0.21
bids-validator==1.8.9; python_version >= "3.7" and python_version < "3.11"
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"
certifi==2021.10.8; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0"
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"
charset-normalizer==2.0.9; python_full_version >= "3.6.0" and python_version >= "3"
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"
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"
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"
connection-pool==0.0.3; python_version >= "3.7" and python_version < "3.11"
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"
cycler==0.11.0; python_version >= "3.7"
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"
dicom2nifti==2.3.0
docopt==0.6.2; python_version >= "3.7" and python_version < "3.11"
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"
filelock==3.4.0; python_version >= "3.7" and python_version < "3.11"
fonttools==4.28.4; python_version >= "3.7"
formulaic==0.2.4; python_version >= "3.7" and python_version < "3.11"
future==0.18.2; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
gitdb==4.0.9; python_version >= "3.7"
gitpython==3.1.24; python_version >= "3.7" and python_version < "3.11"
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"
imageio==2.13.3; python_version >= "3.7"
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"
importlib-resources==5.4.0; python_version < "3.9" and python_version >= "3.7"
interface-meta==1.2.4; python_version >= "3.7" and python_version < "3.11"
ipython-genutils==0.2.0; python_version >= "3.5"
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"
jinja2==3.0.3; python_version >= "3.6"
joblib==1.1.0; python_version >= "3.7"
jsonschema==4.3.1; python_version >= "3.7" and python_version < "3.11"
jupyter-core==4.9.1; python_version >= "3.6"
kiwisolver==1.3.2; python_version >= "3.7"
linecache2==1.0.0
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"
matplotlib==3.5.1; python_version >= "3.7"
medpy==0.4.0
nbformat==5.1.3; python_version >= "3.7" and python_version < "3.11"
networkx==2.6.3; python_version >= "3.7"
nibabel==3.2.1; python_version >= "3.6"
nilearn==0.8.1; python_version >= "3.6"
nnunet-inference-on-cpu-and-gpu==1.6.6
num2words==0.5.10; python_version >= "3.7" and python_version < "3.11"
numpy==1.21.4; python_version >= "3.7" and python_version < "3.11"
packaging==21.3; python_version >= "3.7"
pandas==1.3.5; python_full_version >= "3.7.1"
pillow==8.4.0; python_version >= "3.7"
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"
progress==1.6; python_version >= "3.7" and python_version < "3.11"
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"
pulp==2.6.0; python_version >= "3.7" and python_version < "3.11"
pybids==0.14.0; python_version >= "3.7" and python_version < "3.11"
pydicom==2.2.2; python_full_version >= "3.6.1"
pyerfa==2.0.0.1; python_version >= "3.7"
pygments==2.10.0; python_version >= "3.5"
pygraphviz==1.7; python_version >= "3.7"
pyparsing==3.0.6; python_version >= "3.7"
pyrsistent==0.18.0; python_version >= "3.7"
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")
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"
pytz==2021.3; python_full_version >= "3.7.1"
pywavelets==1.2.0; python_version >= "3.7"
pywin32==302; sys_platform == "win32" and platform_python_implementation != "PyPy" and python_version >= "3.6"
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"
ratelimiter==1.2.0.post0; python_version >= "3.7" and python_version < "3.11"
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"
scikit-fmm==2021.10.29
scikit-image==0.19.1; python_version >= "3.7"
scikit-learn==1.0.1; python_version >= "3.7"
scipy==1.7.3; python_version >= "3.7" and python_version < "3.11"
seaborn==0.11.2; python_version >= "3.6"
setuptools-scm==6.3.2; python_version >= "3.7"
simpleitk==2.1.1
six==1.16.0; python_version >= "3.7" and python_version < "3.11" and python_full_version >= "3.7.1"
sklearn==0.0
smart-open==5.2.1; python_version >= "3.7" and python_version < "3.11"
smmap==5.0.0; python_version >= "3.7"
snakebids==0.4.1; python_version >= "3.7" and python_version < "3.11"
snakemake==6.12.3
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"
stopit==1.1.2; python_version >= "3.7" and python_version < "3.11"
tabulate==0.8.9; python_version >= "3.7" and python_version < "3.11"
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"
threadpoolctl==3.0.0; python_version >= "3.7"
tifffile==2021.11.2; python_version >= "3.7"
tomli==1.2.3; python_version >= "3.7"
toposort==1.7; python_version >= "3.7" and python_version < "3.11"
torch==1.10.1; python_full_version >= "3.6.2"
tqdm==4.62.3; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
traceback2==1.4.0
traitlets==5.1.1; python_version >= "3.7"
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")
unittest2==1.1.0
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"
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"
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"