Deactivate Conda Env In HPC Init Script

[TimothyWillard]

Describe your changes.

This is to address a bug where a currently active env would cause the HPC init script to uncleanly load the flepiMoP env. Simplest solution is to always deactivate before activating. Redundant in the case that the flepiMoP env is already active, but easier than trying to determine the current env. No downside if no env is active.

What does your pull request address? Tag relevant issues.

No issue to tag, just noticed this issue while working on GH-365. Before this change (notice the flepimop-env is active):

(flepimop-env) [twillard@longleaf-login1 flepiMoP]$ source batch/hpc_init.sh longleaf
An explicit $FLEPI_PATH was not provided, please set one (or press enter to use '/work/users/t/w/twillard/flepiMoP'):
Using '/work/users/t/w/twillard/flepiMoP' for $FLEPI_PATH.
An explicit $FLEPI_CONDA was not provided, please set one (or press enter to use 'flepimop-env'):
Using 'flepimop-env' for $FLEPI_CONDA.
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pyarrow'
Connection to longleaf.unc.edu closed.

and after:

(flepimop-env) [twillard@longleaf-login6 flepiMoP]$ source batch/hpc_init.sh longleaf
An explicit $FLEPI_PATH was not provided, please set one (or press enter to use '/work/users/t/w/twillard/flepiMoP'):
Using '/work/users/t/w/twillard/flepiMoP' for $FLEPI_PATH.
An explicit $FLEPI_CONDA was not provided, please set one (or press enter to use 'flepimop-env'):
Using 'flepimop-env' for $FLEPI_CONDA.
Please set a project path (relative to '/work/users/t/w/twillard'):
...

Tag relevant team members.

@anjalika-nande, @emprzy, @fang19911030, @jcblemai, @pearsonca, @saraloo

[pearsonca]

I think this is likely fine.

I would prefer to be a bit more user-friendly, by issuing some kind of warning maybe (probably only if environment name != flepimop-env)? Like some stderr text along the lines of "Detected an active conda environment $X; this will be deactivated and the flepimop-env will be activated".

I don't think it needs to be a "proceed [Y/n]" situation, but my concern here is that we're introducing a subtle side-effect.

Marking this as approved - open to addressing the above in this PR (either fix or convincing me wontfix) or as own issue.

[TimothyWillard]

@pearsonca I've incorporated a message now if the active environment does not match the one being activated. The new after is:

(test-env) [twillard@longleaf-login6 flepiMoP]$ source batch/hpc_init.sh longleaf
An explicit $FLEPI_PATH was not provided, please set one (or press enter to use '/work/users/t/w/twillard/flepiMoP'):
Using '/work/users/t/w/twillard/flepiMoP' for $FLEPI_PATH.
An explicit $FLEPI_CONDA was not provided, please set one (or press enter to use 'flepimop-env'):
Using 'flepimop-env' for $FLEPI_CONDA.
Detected an active conda environment 'test-env'. This will be deactivated and the 'flepimop-env' environment will be activated.
Please set a project path (relative to '/work/users/t/w/twillard'):
...

[pearsonca]

looks good to merge to me; @TimothyWillard feel free to trigger unless you have some additional tweaks in mind.

[TimothyWillard]

looks good to merge to me; @TimothyWillard feel free to trigger unless you have some additional tweaks in mind.

I'm still testing/modifying the changes requested. I shouldn't have requested a re-review yet and this is not ready to merge.

[TimothyWillard]

I apologize for the confusion. This is now tested and ready for review. The three cases look like:

1. When a different conda env is already loaded:

[twillard@longleaf-login4 flepiMoP]$ conda activate test-env
(test-env) [twillard@longleaf-login4 flepiMoP]$ source batch/hpc_init.sh longleaf
An explicit $FLEPI_PATH was not provided, please set one (or press enter to use '/work/users/t/w/twillard/flepiMoP'):
Using '/work/users/t/w/twillard/flepiMoP' for $FLEPI_PATH.
An explicit $FLEPI_CONDA was not provided, please set one (or press enter to use 'flepimop-env'):
Using 'flepimop-env' for $FLEPI_CONDA.
Detected an active conda environment 'test-env'. This will be deactivated and the 'flepimop-env' environment wil be activated.
Please set a project path (relative to '/work/users/t/w/twillard'): ^C

2. When the flepiMoP conda env is already loaded (flepimop-env in my case):

(flepimop-env) [twillard@longleaf-login4 flepiMoP]$ source batch/hpc_init.sh longleaf
An explicit $FLEPI_PATH was not provided, please set one (or press enter to use '/work/users/t/w/twillard/flepiMoP'):
Using '/work/users/t/w/twillard/flepiMoP' for $FLEPI_PATH.
An explicit $FLEPI_CONDA was not provided, please set one (or press enter to use 'flepimop-env'):
Using 'flepimop-env' for $FLEPI_CONDA.
Detected the activate conda environment is 'flepimop-env' already, but will refresh.
Please set a project path (relative to '/work/users/t/w/twillard'): ^C

3. Probably the most common case, when no conda env is loaded:

[twillard@longleaf-login4 flepiMoP]$ source batch/hpc_init.sh longleaf
An explicit $FLEPI_PATH was not provided, please set one (or press enter to use '/work/users/t/w/twillard/flepiMoP'):
Using '/work/users/t/w/twillard/flepiMoP' for $FLEPI_PATH.
An explicit $FLEPI_CONDA was not provided, please set one (or press enter to use 'flepimop-env'):
Using 'flepimop-env' for $FLEPI_CONDA.
Please set a project path (relative to '/work/users/t/w/twillard'): ^C

As always feedback from ops is greatly appreciated, especially since this script is designed for ops use.

[anjalika-nande]

I think this is very clear!

[saraloo]

Thanks, this is great :)