minimal changes to allow changing database path

[ilia-nikiforov-umn]

This minimal change allows changing the path of the local database. This is necessary to allow the Docker image to be exported to an operational Singularity container that is able to use the local database (since singularity uses the host filesystem and therefore cannot write to /pipeline/db/). So far, kimitems install and pipeline-run-pair is confirmed working using Singularity. All other necessary paths should be able to be set using a custom file specified with the PIPELINE_ENVIRONMENT_FILE environment variable passed into the container.

[ilia-nikiforov-umn]

@dskarls these minimal changes allow for everything the KDP does (at least in the process of pipeline-run-pair, including local dependencies) to be contained within a custom specified directory, which allows it to be run using singularity on a cluster. Also, it seems that the KIM_API_USER_COLLECTION variable wasn't doing anything, I grepped for it and it wasn't referenced anywhere.

I believe this doesn't break anything in the main branch, do you see this causing any problems?

[dskarls]

I see no problems whatsoever with the db path customization. As long as the KIM API is handling models properly, you can merge this.

[dskarls]

KIM_API_USER_COLLECTION was a special envvar that the KIM API used to inspect when figuring out where to install or load models but it may no longer use it (and it was also only one way to specify that information). As long as you've confirmed that models are installed where you need them to be and are accessible when doing things like pipeline-run-pair, this should be fine.

[ilia-nikiforov-umn]

@dskarls

Confirmed that the current version of the API doesn't know anything about this variable (both commands return nothing)

ilia@ilia-xps:~/kim-api-2.3.0$ grep KIM_API_USER_COLLECTION README.md 
ilia@ilia-xps:~/kim-api-2.3.0$ find -type f | xargs grep KIM_API_USER_COLLECTION