Profiling data collection

[LourensVeen]

This implements profiling data collection, completing the existing code on the Python side, implementing it in C++, and adding functionality to send the data to the manager and save it to a SQLite database.

Some optimisation and analysis tools are still to follow, but this should allow other work to continue while that's in work.

This was rebased on top of the checkpointing and other recent additions, and the automatic merges were quite a mess at times, but it passes all the tests at least :-)...

[LourensVeen]

One general comment: can you add a flag, and/or muscle_enable_profiling special setting to specifically enable or disable profiling?

Yes, good idea, it was on my internal to-do list already. I've updated https://github.com/multiscale/muscle3/issues/78 to list it as well.

[LourensVeen]

Okay, I've

• [x] fixed most of the issues
• [x] put the remaining ones on the list for the future
• [x] argued about one other one

and also

• [x] the tests are passing, and
• [x] Codacy is complaining.

I think that means we're ready to merge!