How can I run atom and hydrogen within a conda env using bash script?

Question

I used to have a simple bash script that I was using to activate a conda env and then run atom. Then, I could run python code using hydrogen which could automatically see the packages inside myenv.

The previous bash scrip was sth like this:

#!/bin/bash

source activate myenv && 
atom

Since conda > 4.4 that 'source activate' does not exist anymore, I had to revise the script to:

#!/bin/bash

source /home/ubuntu/miniconda3/etc/profile.d/conda.sh &&
conda activate myenv &&
atom

However, hydrogen does not detect myenv anymore and runs the code from the base env which results into error due to packages missing from the base env.

When I replace atom with spyder, the above script works fine and spyder kernel does see myenv.

Any idea how I can get this fixed?

Update 1:

I did some more debugging. It seems that my ipykernel is not assigned to the kernel installed within the activated environment but assigned to the default ipykernel.

When I try jupyter kernelspec list in my activate env, I get:

python3    /home/ubuntu/.local/share/jupyter/kernels/python3

But on another system, I get

/home/ubuntu/miniconda3/envs/myenv/share/jupyter/kernels/python3

which seems to be the right kernel.

Any idea on how to fix this?

Update 2:

It seems that this resolves the issue in Update 1. Then, I was able to use the accepted answer to load atom within the desired env and have hydrogen run from the ipykernel in that env.

Answer 1

source activate still works as before, although it is no longer the preferred way to activate an environment.

If you're only running a single command, try

conda run -n <envname> <command>

possibly with sourcing the profile first.

I haven't tried, but a potential problem is that you're using && after sourcing the profile. I assume that the line continuation characters ( \\ ) got lost there when you wrote the question. Just write the commands into separate lines, so that the profile is loaded before bash processes the next command.