miniconda_conda_remote_setup.md

Remote set-up using miniconda and conda

1. Add miniconda to your system path and create the aeon python env from the env.yml file:

module load miniconda
conda env create -f env_config/env.yml

2. Optionally install development dependencies:

conda activate aeon
conda env update -f env_config/env_dev.yml

3. Using the virtual environment:
   • conda activate aeon: activates the virtual environment; any commands now run within this terminal will take place within the virtual environment.
   • conda deactivate aeon: deactivates the virtual environment.
4. (Optional) Add commands to the .profile file to add miniconda as an environment module and Bonsai and its dependencies to your system path on startup (this will be initialized each time you SSH into the HPC).
   • Copy the commands in the .profile_example file in this folder to your HPC home directory .profile file (you will have to create this file if it doesn't already exist).
5. For instructions on developing within the aeon environment, see developing_on_hpc.md