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Fix Miscellaneous ipynbs #446

Merged
merged 5 commits into from
Mar 15, 2016
Merged

Fix Miscellaneous ipynbs #446

merged 5 commits into from
Mar 15, 2016

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dwhswenson
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Several of the example ipynbs (that aren’t part of regular testing) have been broken by recent (and some not-so-recent) updates to the code. I’m fixing them so they run correctly.

  • langevin_integrator_check.ipynb
  • move_strategies_and_schemes.ipynb
  • sequential_ensembles.ipynb
  • sliced_sequential_ensemble.ipynb
  • tutorial_visualization.ipynb (partial: see More ipynb cleanup #447)
  • storage_mem_test.ipynb (partial: see More ipynb cleanup #447)
  • which_network.ipynb (incomplete notebook: removed from localtest.sh)

Just a bit of code rot we’ve had over time. We should remember to do this occasionally (and certainly before release!)

@dwhswenson
Fix langevin_integrator_check
d6f22f9
@dwhswenson
Fix move_strategies_and_schemes.
49fb302 
Also, remove non-existent test notebook from localtest.
@dwhswenson
Fixes for sliced_sequential and sequential
a10fb71 
Also sort-of fix for which_network: that one cannot pass right now
@dwhswenson
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@jhprinz : storage_mem_test.ipynb uses OpenMMRandomEngine. I don't see OpenMMRandomEngine (or any kind of RandomEngine) anywhere in the code. What should I do with that?

@dwhswenson
Remove which_network from localtest.
235ae1d 
Also some starts on storage_mem_test and tutorial_visualization: these need
input from JHP before they'll get fixed (might actually need him to handle
them).
@jhprinz
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jhprinz commented Mar 14, 2016

It is called RandomMDEngine and is part of test_helpers.py now. I renamed it at some point since it is not OpenMM specific. It used to use the Snapshots.

@dwhswenson
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Thanks. I'm going to parts of tutorial_visualization.ipynb and storage_mem_test.ipynb unfixed: there didn't seem to be an easy fix, and since I'm not sure what your intent was at the point that the bug occurs, I think it makes more sense for you to fix. Posting an issue on that in just a moment.

I suspect those will be easy for you: at least, the rest of this wasn't too bad for me to fix.

@dwhswenson dwhswenson mentioned this pull request Mar 15, 2016
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@dwhswenson
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Passed tests: ready to merge.

@jhprinz
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jhprinz commented Mar 15, 2016

Very good! Merging...

jhprinz added a commit that referenced this pull request Mar 15, 2016
@jhprinz
Merge pull request #446 from dwhswenson/fix_ipynbs
eaa334f 
Fix Miscellaneous ipynbs
@jhprinz jhprinz merged commit eaa334f into openpathsampling:master Mar 15, 2016
@dwhswenson dwhswenson deleted the fix_ipynbs branch April 7, 2016 11:49
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