Update master to 2.8

[rmcgibbo]

Big merge.

This PR introduces the mdtraj dependency, and removes lots of cruft.

[rmcgibbo]

I'm going to tag a release of the current master as 2.7.0 before this merge happens.

[rmcgibbo]

https://github.com/SimTk/msmbuilder/releases/tag/2.7.0

[kyleabeauchamp]

Good On Jan 21, 2014 9:40 PM, "Robert McGibbon" notifications@github.com wrote:

I'm going to tag a release of the current master as 2.7.0 before this merge happens.

— Reply to this email directly or view it on GitHubhttps://github.com/SimTk/msmbuilder/pull/292#issuecomment-32988586 .

[rmcgibbo]

Let's get some comment on this from a quorum of @tjlane, @schwancr, @mpharrigan, etc before merging this. There's no rush.

[tjlane]

A quick scan looks good to me, but I admit I didn't delve into many details. Anything in particular you want reviewed @rmcgibbo since I'm not really working with MSMb right now?

+1 to getting mdtraj in

[kyleabeauchamp]

Here's my suggestion of what to look for (without having to invest 10 hours):

1. Just glance at the code so you have an idea of how things will be working after the merge.
2. Point out (here or as separate issues) any possible complications / subtle bugs that you foresee after glancing at the code.

[kyleabeauchamp]

So Danny and I will be doing some MSM-building, so we'll be working with this pretty extensively once it's merged. I think we should be able to find and patch any bugs that are still hidden.

[kyleabeauchamp]

OK so I've merged all my "minor" fixes and enhancements into the msmb2.8 branch. If people want to see what th changes are, they can look at the various merged Pull Requests.

[rmcgibbo]

It seems like testAssign just hangs sometimes? https://travis-ci.org/SimTk/msmbuilder/builds/17891035#L1451

[rmcgibbo]

There are a couple of sporatic problems with the travis build system, but this PR is in a working state now. We should merge. I will do it tomorrow afternoon.

[schwancr]

mdtraj uses simtk.units, is there some way to install just the units module? Or do I need to install all of openmm?

[kyleabeauchamp]

I think Robert has a way to install just the units part.

git+git://github.com/rmcgibbo/simtk.unit

[schwancr]

cool, thanks

[schwancr]

is it possible to install that with pip? It would be nice to have that dependency installed automatically

[schwancr]

I'm using this branch now, so I can be the guinea pig if there are bugs

[rmcgibbo]

I'm not sure exactly why simtk.units is required by msmbuilder2.8. In general, most of mdtraj should be okay without it.

Or maybe I should just bundle a copy of simtk.units inside mdtraj.

-Robert

On Jan 30, 2014, at 3:43 PM, Christian Schwantes notifications@github.com wrote:

I'm using this branch now, so I can be the guinea pig if there are bugs

— Reply to this email directly or view it on GitHub.

[schwancr]

here's the traceback:

In [2]: md.load('Trajectories/trj0.h5')

############################################################################

The code at unit.py:147 requires the simtk.unit module,
which is a python package for unit conversion.

simtk.unit is installed with OpenMM, which is available at http://openmm.org
It's also installable as a separate standalone package from
https://github.com/rmcgibbo/simtk.unit, and can be installed with the python
"pip" package mangers using:

pip install git+git://github.com/rmcgibbo/simtk.unit

############################################################################
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
/home/schwancr/vspm24_vol/vspm24_HD2/protG/fah_nug2/p7812/<ipython-input-2-f2dfa16a7d2d> in <module>()
----> 1 md.load('Trajectories/trj0.h5')

/home/schwancr/Installed/epd/lib/python2.7/site-packages/mdtraj-0.6.0-py2.7-linux-x86_64.egg/mdtraj/trajectory.pyc in load(filename_or_filenames, discard_overlapping_frames, **kwargs)
    282         kwargs.pop('top', None)
    283 
--> 284     return loader(filename, **kwargs)
    285 
    286 

/home/schwancr/Installed/epd/lib/python2.7/site-packages/mdtraj-0.6.0-py2.7-linux-x86_64.egg/mdtraj/hdf5.pyc in load_hdf5(filename, stride, atom_indices, frame)
    149             data = f.read(n_frames=1, atom_indices=atom_indices)
    150         else:
--> 151             data = f.read(stride=stride, atom_indices=atom_indices)
    152 
    153         topology = f.topology

/home/schwancr/Installed/epd/lib/python2.7/site-packages/mdtraj-0.6.0-py2.7-linux-x86_64.egg/mdtraj/hdf5.pyc in wrapper(*args, **kwargs)
     84             # args[0] is self on the method

     85             if args[0].mode in m:
---> 86                 return f(*args, **kwargs)
     87             raise ValueError('This operation is only available when a file '
     88                              'is open in mode="%s".' % args[0].mode)

/home/schwancr/Installed/epd/lib/python2.7/site-packages/mdtraj-0.6.0-py2.7-linux-x86_64.egg/mdtraj/hdf5.pyc in read(self, n_frames, stride, atom_indices)
    604         frames = Frames(
    605             coordinates = get_field('coordinates', (frame_slice, atom_slice, slice(None)),
--> 606                                     out_units='nanometers', can_be_none=False),
    607             time = get_field('time', frame_slice, out_units='picoseconds'),
    608             cell_lengths = get_field('cell_lengths', (frame_slice, slice(None)), out_units='nanometers'),

/home/schwancr/Installed/epd/lib/python2.7/site-packages/mdtraj-0.6.0-py2.7-linux-x86_64.egg/mdtraj/hdf5.pyc in get_field(name, slice, out_units, can_be_none)
    595                 if not isinstance(in_units, str):
    596                     in_units = in_units.decode()
--> 597                 data =  in_units_of(data, out_units, in_units)
    598                 return data
    599             except self.tables.NoSuchNodeError:

/home/schwancr/Installed/epd/lib/python2.7/site-packages/mdtraj-0.6.0-py2.7-linux-x86_64.egg/mdtraj/utils/unit.pyc in in_units_of(quantity, units_out, units_in)
    145     1000000.0
    146     """
--> 147     units = import_('simtk.unit')
    148 
    149     if quantity is None:

/home/schwancr/Installed/epd/lib/python2.7/site-packages/mdtraj-0.6.0-py2.7-linux-x86_64.egg/mdtraj/utils/delay_import.pyc in import_(module)
    191         print(m, file=sys.stderr)
    192         print(bar, file=sys.stderr)
--> 193         raise e

ImportError: No module named simtk.unit

[schwancr]

I'm not all that familiar with mdtraj to know if it needs to do that conversion step

[rmcgibbo]

You can now install simtk.unit with

pip install simtk.unit

[kyleabeauchamp]

Sweet, let me know if there's anything else we need to do before we merge this.

[rmcgibbo]

Okay. I'm starting the merge now.

[kyleabeauchamp]

Nice