Merge pull request #135 from khanlab/fix-ci

add requirements.txt from poetry export
khanlab · Dec 18, 2021 · 7af816c · 7af816c
2 parents 69a9088 + 34d485c
commit 7af816c
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diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml
@@ -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

diff --git a/requirements.txt b/requirements.txt
@@ -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"