Improvements on progress output - #676

This PR fixes a few minor annoyances with the progress output during a path sampling simulation. In particular, it includes the following:

• Switch the speed reporting from "steps per second" to "seconds per step": TPS simulations of large systems have less than 0.01 steps per second, so the old version was uninformative; even our fast systems are around 0.1-0.2 seconds per step
• Convert times (elapsed and remaining) from seconds to days, hours, minutes, seconds (easier to interpret once you get to tens of thousands of seconds remaining)
• Move the whole progress string generation into paths.tools, so that it can be re-used by other objects. Just needs the time elapsed, the steps completed, and the total number of steps
• Unit tests for new code

New output looks something like this:

Working on Monte Carlo cycle number 215
Running for 1 minute 44 seconds -  0.91 seconds per step
Estimated time remaining: 5 hours 2.52 minutes

The time elapsed is always the full string (1 day 2 hours 3 minutes 4 seconds). The time remaining always contains the first two (occupied) "levels" (day, hour, minute, second) with the remainder to 2 decimal places in the last. So (1 day 2.05 hours, or as above, 5 hours 2.52 minutes). I thought this would be the most readable (and it acknowledges that the time elapsed is exact, whereas the time remaining is a rough estimate).