How do I activate a conda env in a subshell?

Question

I've written a python program. And if I have a shebang like this one:

#!/usr/bin/python

and I make the file executable with:

$ chmod 755 program.py

I can run the program like so:

$ ./program.py

Here is the issue. I use the conda virtual environments. When I run the program like above, the system creates a subshell that does not recognize the active environment:

(my_env) $ ./program.py
ImportError: No module named pymongo

If I do it this way, however...

(my_env) $ python program.py
# blah blah... runs great

How do I specify the right environment for use in the subshell? Is it possible? I'd like to save my fingers the effort of typing the six character string that is python.

Another post, Shebangs in conda managed environments, briefly touches on this but does not provide the right answer. Instead of activating the environment in the subshell, it just says, go ahead and ignore the shebang... just use the $ python program.py syntax.

Answer 1

conda run

If you always plan to run the script from a shell session where conda is defined, then another alternative is let Conda load the env using the conda run command. In this case, the shebang would be

#!/usr/bin/env conda run -n my_env python

The advantage here is that you don't need the env to be activated when you call ./program.py and you don't have to hardcode the location of the interpreter.

Note: This command was added as a "preview" in Conda v4.6.0 (see Release Notes) to address the issue of running a command inside an env.

Answer 2

In your script, change...

#!/usr/bin/python

...to:

#!/usr/bin/env python

The python used by an activated conda environment is ${CONDA_PREFIX}/bin/python and not /usr/bin/python

Notice the difference?

(root) ~/condaexpts$ which python
/home/ubuntu/condaexpts/m3/bin/python

(root) ~/condaexpts$ /usr/bin/env python
Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> 

(root) ~/condaexpts$ source deactivate

~/condaexpts$ which python
/usr/bin/python

~/condaexpts$ /usr/bin/env python
Python 2.7.6 (default, Oct 26 2016, 20:30:19) 
[GCC 4.8.4] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 

Answer 3

You can also point directly to the environment with the shebang line so you need not depend on something setting up the parent environment prior to calling the script.

First determine your preferred python environment's path:

$ . activate mypython
$ which python
/home/username/anaconda/envs/mypython/bin/python      # for example 

Then use it in a script:

#!/home/username/anaconda/envs/mypython/bin/python
import os,sys
print sys.executable
print os.__file__

The above script would give output like this:

/home/username/anaconda/envs/mypython/bin/python
/home/username/anaconda/envs/mypython/lib/python2.7/os.pyc

Having a non-generic command in the shebang makes the script less portable, but if you depend the specific packages in a particular virtual environment, this is what you want.