conda

Installing conda

To install conda, we use Mambaforge. Mambaforge is a way of installing conda that sets conda-forge as the default (and only) channel, and it includes mamba, a drop-in replacement for conda that is faster and more feature-complete.

Don’t run conda init bash

Note

TL;DR: use ca to activate an environment. See below for why.

Usually, after installing conda, you would typically run conda init bash. These dotfiles are set up to explicitly avoid that here.

Why? First, because this adds lines to your .bashrc file (if on Linux) or your .bash_profile file (if on Mac). Thereafter, every single new bash session runs that code…which involves importing some Python libraries and running conda itself. Since the conda Python module loads other modules, and those modules load still others, every time a bash session is started, many files are touched.

Why is this a problem?

Reading many files on every bash session can cause I/O slowdown in a high-performance computing environment (like NIH’s Biowulf) when many jobs are kicked off simultaneously. So we want to avoid this on HPC environments. This I/O load is not an issue on a personal machine,since it’s unlikely that you’ll be starting so many bash sessions.

Second, you may find that on tmux, when you create a new pane or window, your prompt still indicates that you’re in a conda environment, but running which python returns the system Python. It turns out that this is because tmux prepends the system path to the PATH when creating a new pane or window. The solution is to run conda deactivate a bunch of times, until the prompt no longer has the (env_name) indicator in it, and then activate the environment you want.

The solution

1. To activate an environment, use ca at the time you want to use it. Use ca by itself to activate the base environment. Use ca <envname> to activate a specific environment.

   # activate named environment
   ca myenv
   
   # activate environment at path
   ca ./env
   

2. Every new tmux pane starts with everything deactivated.

How it works

These dotfiles provide a function, ca (short for “conda activate”). It’s defined in the ~/.functions file which in turn is sourced in ~/.bashrc. This function runs eval "$(conda shell.bash hook)", which is a way of running the same commands that conda init bash would add to your ~/.bashrc. But it runs it on demand, not every shell. In other words, this is wrapping the conda init bash stuff inside a function that we only call when we need it.

The file .functions also has a conda_deactivate_all function, which keeps running conda deactivate until there’s no activated environment (this idea is from this SO answer). You typically won’t run this on your own much, but theres a line in ~/.bashrc that runs conda_deactivate_all if we’re in a tmux session, so it will run on each new tmux pane. You’ll need to activate the environment again in the new pane.