ShapeWorks/install_shapeworks.bat at master · ben2k/ShapeWorks · GitHub

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REM remove existing shapeworks env if any
set CONDAENV=shapeworks
IF NOT "%1"=="" SET CONDAENV=%1
echo "creating new conda environment for ShapeWorks called %CONDAENV%..."

REM remove any existing environment with this name
call conda env remove -n %CONDAENV%

REM update anaconda
call conda config --add channels anaconda
call conda config --add channels conda-forge

call conda create --yes --name %CONDAENV% python=3.7
call conda activate %CONDAENV%

REM install shapeworks deps
call conda install --yes colorama=0.4.3
call conda install --yes requests=2.22.0
call conda install --yes openblas=0.3.3
call conda install --yes numpy=1.17.4
call conda install --yes scikit-learn=0.22.1
call conda install --yes trimesh=3.9.35
call conda install --yes gtest=1.10.0 cmake-3.15.5
call conda install --yes notebook=6.1.5

REM reactivate shapeworks environment
call conda activate base
call conda activate %CONDAENV%

call conda install --yes pip=21.2.4

call pip install torch==1.7.1+cpu torchvision==0.8.2+cpu torchaudio===0.7.2 -f https://download.pytorch.org/whl/torch_stable.html
call pip install termcolor==1.1.0
call pip install matplotlib==3.1.2
call pip install hotelling==0.5.0
call pip install statsmodels==0.13.0
call pip install itk==5.2.1.post1
call pip install itk-elastix==0.13.0
call pip install SimpleITK==2.1.1
call pip install vtk==8.1.2
call pip install bokeh==2.2.0
call pip install shapely==1.8.0
call pip install seaborn==0.11.2
call pip install mdutils==1.3.0
call pip install mkdocs==1.1.2
call pip install python-markdown-math==0.8
call pip install fontawesome-markdown==0.2.6
call pip install pymdown-extensions==8.0.1
call pip install jinja2==3.0.3

REM install the local GirderConnector code as a package
call pip install Python/DatasetUtilsPackage
call pip install Python/DocumentationUtilsPackage
call pip install Python/DataAugmentationUtilsPackage
call pip install Python/DeepSSMUtilsPackage
call pip install Python/ShapeCohortGenPackage

REM install the shapeworks python module and conda [de]activate scripts
call .\Installation\install_python_module.bat
call .\Installation\conda_env_setup.bat

REM installs for jupyter notebooks
call pip install nbstripout==0.5.0
call pip install pyvista==0.30.1
call pip install ipyvtklink==0.2.1
call pip install ipyvtk_simple==0.1.4
call pip install ipywidgets==7.6.5
call pip install itkwidgets==0.32.1
call pip install mkdocs-jupyter==0.17.3

REM for spell check markdown cells in jupyter notebooks and table of content
call conda install --yes jupyter_contrib_nbextensions=0.5.1
call jupyter contrib nbextension install --user
call jupyter nbextension enable spellchecker/main
call jupyter nbextension enable toc2/main

md %USERPROFILE%\.shapeworks
python -c "import sys; print('\n'.join(sys.path))" > %USERPROFILE%\.shapeworks\python_path.txt
python -c "import sys; print(sys.prefix)" > %USERPROFILE%\.shapeworks\python_home.txt
echo %PATH% > %USERPROFILE%\.shapeworks\path.txt
call conda info