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environment.yml
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environment.yml
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name: batch-msc
channels:
- conda-forge
- oddt
- rdkit # also try conda-forge build
- bioconda # only needed for more recent openbabel build
- pytorch # prefered for pytorch
dependencies:
- python >= 3.6
- pip
- joblib
- cython # for gpytorch
- docopt
#### standard data manipulation
- numpy
- pandas
#### ml libraries
- scipy
- scikit-learn>=0.23.1
- scikit-garden # Mondrian Forests
- xgboost
- pytorch::pytorch>=1.0 # needed for gpytorch
- gpytorch # gaussian processes
#### biochemical toolkits
- openbabel
- oddt
- rdkit::rdkit # try both rdkit and conda-forge versions
#### for replicating figures
- matplotlib
- seaborn
#### for using this env as a kernel in jupyterlab
- jupyter
- jupyterlab
- nb_conda_kernels
# install via pip (conda has outdated versions)
- pip:
- forestci>=0.4.1 # confidence intervals for random forests