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User Install (Deprecated)

Deprecated

This installation method is deprecated. We recommend following the main Installation guide instead, which provides a full developer setup with editable submodule installations.

Requirements

  1. conda (miniconda or miniforge)
  2. git (install via conda if needed: conda install git)
  3. Julia installation (see Installation guide)
  4. ~20 GB of disk space
  5. ~30 minutes of your time (mostly waiting)

miniforge and HDF5/NetCDF conflicts

There is currently a known conflict between Julia and Conda versions of HDF5 and/or NetCDF libraries when using miniforge. If you encounter issues, try using miniconda instead.

Steps

  1. git clone https://github.com/FormingWorlds/PROTEUS.git
  2. cd PROTEUS
  3. conda env create -f environment.yml
  4. conda activate proteus
  5. pip install -e .
  6. proteus install-all --export-env

macOS: PETSc compilation on Apple Silicon

If proteus install-all fails during the PETSc step on Apple Silicon (M1/M2/M3/Ultra), see the Troubleshooting page.

Before running PROTEUS

If you want to start running PROTEUS right away (from the same shell that you used to install PROTEUS), reload your environment variables:

source ~/.bashrc
conda activate proteus

source ~/.zshrc
conda activate proteus

If you chose proteus install-all without --export-env, you will need to set your PATH, FWL_DATA, Julia, and RAD_DIR environment variables manually.

When you log into the machine where you installed PROTEUS through proteus install-all --export-env, the environment variables FWL_DATA and RAD_DIR will already be set (because your shell config file was updated during installation). You still need to run conda activate proteus.

Updating PROTEUS

  1. conda activate proteus (if not already activated)
  2. proteus update-all