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First install mamba and conda-lock into your base environment
conda activate base conda install mamba conda-lock
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Then create a lock file for your platform and use it to make a new environment
conda-lock -f environment.yml -p osx-64 (or linux-64 or win-64) mamba create --name test --file conda*lock* conda activate test
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Finally, install the command line utilities using an editable install:
pip install -e .
cd notebooks
filter_notebook two_layers.md new_layers.md