Handle passing/initialization of reference to matchms environment

[hechth]

At first I also wanted to drop it - but then I realized:
this allows also to use import("matchms", convert = FALSE) to disable automatic conversion of python to R and vice versa, maybe not wrong to disable to speed up things?
Also, in a loop, you can define this reference once, and then in the loop re-use it. Speeds up things.
I would thus keep it (it's anyway for the advanced user).

I think having a function that populates a global variable might be the best way?

I don't think that passing the reference to the imported matchms is a good thing - this implies you could use different versions of matchms in a single session etc., which is not very clean.

But we can figure out how to do this properly in another issue.

Originally posted by @hechth in #10 (comment)

[jorainer]

What I've seen so far in other packages is that they call the import within each function. It's just not very efficient if you repeatedly do that in a loop. At present the conversion is done on each spectrum individually in such a loop (which is also not that efficient).

I totally agree that using different versions of matchms would be problematic - but here I trust the user - these function should only be for the advanced user, and they, hopefully, know what they are doing.

I am not in favour of a global variable, because that might prevent us from using parallel processing (well, question is also if we would really want to do that...).

[hechth]

Well we can export the variable to the compute cluster, right? Or is that one of the things the biocparallel package can't do? I have the vague memory that there was something like that.

[jorainer]

it depends on the cluster setup - if it has shared memory or not (on Windows, i.e. with socket-based clustering, there is no shared memory).