replace custom ProgressMeter with tqdm

[jbarnoud]

EDIT (@orbeckst): Based on the discussion in this issue we decided to replace our lib.util.ProgressMeter with tqdm. Use this issue for discussion to refine this idea.

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The progress bar could give an estimate of when the calculation is going to be done. This is reassuring for the end user, and allows to plan other things during long calculation (or to know when to come back from a coffee break).

This is easily achievable by keeping track of the time elapsed between two calls of the update method as we know how many frames remain to be analyzed.

It can be misleading for analyses that need to iterate several time through the trajectory, or that have a very long _conclude method. But the current progress bar is misleading already.

[orbeckst]

Instead of calculating time between two calls I would keep track of the time since the start because that should improve your estimate for the average time per iteration and thus improve your extrapolated ETC (estimated time to completion).

[kain88-de]

Have a look in the code of pyprind. I use the package to have long verbose views and it has a good ETC estimate.

[orbeckst]

As discussed in PR #960 (#960 (comment) and following comments) we want to transition to using tqdm.

There are some caveats regarding use in Jupyter notebooks (#960 (comment)) but overall everyone is happy with the provided functionality and we would be ok adding it as a core dependency.

Note that we need to

• deprecate lib.log.ProgressMeter (for anyone who has been using it in their own code) and remove in 1.0
• replace internal use of ProgressMeter with a new version based on tqdm.tqdm().

Perhaps we can simply derive our own class from tqdm.tqdm with our default settings, like lib.log.ProgressReporter or ProgressBar

import tqdm
class ProgressBar(tqdm.tqdm):
   def __init__(self, *args, **kwargs):
          verbose = kwargs.pop('verbose', True)
          # disable: Whether to disable the entire progressbar wrapper [default: False]. 
          # If set to None, disable on non-TTY.
          kwargs['disable'] = None if verbose else True
          super(ProgressBar, self).__init__(*args, **kwargs)

and then use as

from ..lib.log import ProgressBar

for ts in ProgressBar(u.trajectory[start:stop:step], verbose=verbose):
      analyze(ts)

It should cut down on code because we don't need manual status updates such as the pm.echo().

[orbeckst]

There is probably a way to switch to the fancy GUI versions tqdm.tqdm_gui or tqdm.tqdm_notebook for notebooks but I haven't looked into this at all.