Using ISIS in other Conda Environments

The ISIS conda package pins some of its requirements, which may clash with other packages.

Therefore, if you want to use ISIS in conjunction with other conda packages, we recommend that you avoid adding other packages to the environment you create when you install ISIS. This is similar to the best-practice of keeping your base conda environment free of extra conda packages.

Instead, when you need to run ISIS programs in other conda environments, try Stacking. Or, for some more complex scenarios, you can try editing the activation script.

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Stacking (Easy)

Create a working environment (we call ours working in this tutorial) and add the conda packages you need.

To stack environments, first activate your isis environment. Then activate your working env on top of your isis env with the --stack argument.

conda activate isis
conda activate --stack working

That's it, your working env is now stacked on top of your isis env.

Exiting stacked environments: run conda deactivate twice

You'll have to run conda deactivate two times to exit your conda environments: once to get out of working, and then once more to get out of isis.

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Editing the Activation Script (Hard)

Stacking might not work if you have a complex set of packages/dependencies, so here's one alternative: editing the activation script.

Warning

If you aren't comfortable following these steps for editing the activation script, contact your system administrator.

In theory, all you really need in your working env are the ISIS environmental variables and the path to the ISIS apps. You can set those up by customizing your conda env's activate.d/ and deactivate.d/ directories.

1. Working Env
   Create your working conda env and add the packages you need.
   
   

2. Base Conda Prefix
   Locate the path to your base conda environment.

   echo $CONDA_PREFIX
   

   Our Result: ~/miniconda3.
   You should use your own result from the above command.
   
   

3. ISIS Conda Prefix
   Locate the path to your ISIS conda environment:

   conda activate isis
   echo $CONDA_PREFIX
   

   Our Result: ~/miniconda3/envs/isis.

   You can do the same thing to find the path to your working environment, our result being ~/miniconda3/envs/working.
   
   

4. Copy Scripts
   Copy the ISIS activation and deactivation scripts to your new environment.

   Don't just copy & paste our commands, use your own system details.

   For steps 4-6, use your own env names and folder names, don't just copy and paste. If your shell doesn't use bash, you may need to use a different env_vars.* file, and/or different command syntax.

   # Go to your conda envs folder
   cd ~/miniconda3/envs/
   
   # create activate.d and deactivate.d folders in your 'working' env
   mkdir -p working/etc/conda/activate.d/
   mkdir -p working/etc/conda/deactivate.d/
   
   # Copy activation and deactivation scripts
   # from your 'isis' env to your 'working' env.
   cp isis/etc/conda/activate.d/env_vars.sh working/etc/conda/activate.d/env_vars.sh
   cp isis/etc/conda/deactivate.d/env_vars.sh working/etc/conda/deactivate.d/env_vars.sh
   

   
   

5. Add /bin to path at Activation
   Edit the copied activation file in ~/miniconda3/envs/working/etc/conda/activate.d/ to add the ISIS executable directory to the path, by adding this line at the end:

   export PATH=$PATH:$ISISROOT/bin
   

   It's important to add $ISISROOT/bin to the end of the path in your working environment, not the beginning.
   
   

6. Remove /bin from path at Deactivation
   Edit the copied deactivation file in $HOME/anaconda3/envs/working/etc/conda/deactivate.d/ to remove the path, by adding this line at the end:

   export PATH=`echo -n $PATH | awk -v RS=: -v ORS=: '/isis/ {next} {print}' | sed 's/:$//'`;`
   

   (isis here being the name of your isis env. You can look in the activate.d/env_vars.sh file to see what it should be.)