CODEWITHSUNDEEP
pythonshellunix
Igor Rivin
Igor Rivin

Reputation: 4864

conda and python shell scripts

Suppose I have a python shell script of the usual shebang kind (let's suppose it's in a file called foo.py:

#!/usr/bin/env python
print("Hello World")

with the twist that I need to run it in a given python environment Now, of course, I can write a script of the following kind:

#!/bin/sh
conda activate myenv
exec foo.py

But this is mildly unsatisfying aesthetically. Is there a way to package the environment into the script to avoid the extra level of scripting?

Upvotes: 1

Views: 3296

Answers (1)

Ollin Boer Bohan
Ollin Boer Bohan

Reputation: 2401

Option 1: explicit interpreter path

You can explicitly find the path to the python interpreter in your environment and use that in the shebang:

source activate myenv
which python

Will output something like /Users/me/anaconda/envs/myenv/bin/python. You can then write the python script's shebang using that full path:

#!/Users/me/anaconda/envs/myenv/bin/python
...

However, it's still kinda ugly.

Option 2: symlinks

#!/usr/bin/env python just looks through $PATH for something called "python" and uses that to run the script. We can use this behavior to get nicer shebangs for our conda environments.

Here's a script to add symlinks in ~/bin for each conda environment:

#!/usr/bin/env bash
conda_prefix="$HOME/anaconda" # Modify this line if your anaconda folder is somewhere else
mkdir -p "$HOME/bin" # Make ~/bin if it doesn't exist
for env_dir in "$conda_prefix/envs/"*; do
    env_name=$(basename "$env_dir")
    ln -s "$env_dir/bin/python" "$HOME/bin/$env_name"
    echo "Made symlink for environment $env_name"
done

Once you've run that once (and you've added $HOME/bin to your $PATH in .profile), you can reference conda envs directly in the shebang:

#!/usr/bin/env myenv
...

This will find myenv in the $PATH as $HOME/bin/myenv, which is a symlink to $HOME/anaconda/envs/myenv/bin/python thanks to our script above.

Upvotes: 3

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