bash – Python – Activate conda env through shell script

The error message is rather helpful – its telling you that conda is not properly set up from within the subshell that your script is running in. To be able to use conda within a script, you will need to (as the error message says) run conda init bash (or whatever your shell is) first. The behaviour of conda and how its set up depends on your conda version, but the reason for the version 4.4+ behaviour is that conda is dependent on certain environment variables that are normally set up by the conda shell itself. Most importantly, this changelog entry explains why your conda activate and deactivate commands no longer behave as you expect in versions 4.4 and above.

For more discussion of this, see the official conda issue on GitHub.

Edit: Some more research tells me that the conda init function mentioned in the error message is actually a new v4.6.0 feature that allows a quick environment setup so that you can use conda activate instead of the old source activate. However, the reason why this works is that it adds/changes several environment variables of your current shell and also makes changes to your RC file (e.g.: .bashrc), and RC file changes are never picked up in the current shell – only in newly created shells. (Unless of course you source .bashrc again). In fact, conda init --help says as much:

IMPORTANT: After running conda init, most shells will need to be closed and restarted for changes to take effect

However, youve clearly already run conda init, because you are able to use conda activate interactively. In fact, if you open up your .bashrc, you should be able to see a few lines added by conda teaching your shell where to look for conda commands. The problem with your script, though, lies in the fact that the .bashrc is not sourced by the subshell that runs shell scripts (see this answer for more info). This means that even though your non-login interactive shell sees the conda commands, your non-interactive script subshells wont – no matter how many times you call conda init.

This leads to a conjecture (I dont have conda on Linux myself, so I cant test it) that by running your script like so:

bash -i shell_script.sh

you should see conda activate work correctly. Why? -i is a bash flag that tells the shell youre starting to run in interactive mode, which means it will automatically source your .bashrc. This should be enough to enable you to use conda within your script as if you were using it normally.

I use source command to run the shell script, it works:

source shell_script.sh

bash – Python – Activate conda env through shell script

Quick solution for bash: prepend the following init script into your Bash scripts.

eval $(command conda shell.bash hook 2> /dev/null)

Done.

For other shells, check the init conf of your shell, copy the following content within the shell conf and prepend it into your scripts.

# >>> conda initialize >>>
...
# <<< conda initialize <<<

You can also use

conda init --all --dry-run --verbose

to get the init script you need in your scripts.

Explanation

This is related with the introduction of conda init in conda 4.6.

Quote from conda 4.6 release log

Conda 4.4 allowed “conda activate envname”. The problem was that setting up your shell to use this new feature was not always straightforward. Conda 4.6 adds extensive initialization support so that more shells than ever before can use the new “conda activate” command. For more information, read the output from “conda init –help”

After conda init is introduced in conda 4.6, conda only expose command
conda into the PATH but not all the binaries from base. And environment switch is unified by conda activate env-name and conda deactivate on all platforms.

But to make these new commands work, you have to do an additional initialization with conda init.

The problem is that your script file is run in a sub-shell, and conda is not initialized in this sub-shell.

bash – Python – Activate conda env through shell script