Fix FAH project builder in msmb2.8 branch

[kyleabeauchamp]

======================================================================
FAIL: Failure: AssertionError ()
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/kyleb/opt/lib/python2.7/site-packages/nose/loader.py", line 413, in loadTestsFromName
    addr.filename, addr.module)
  File "/home/kyleb/opt/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/home/kyleb/opt/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/home/kyleb/src/msmbuilder/tests/test_project.py", line 60, in <module>
    test_FahProjectBuilder1()
  File "/home/kyleb/src/msmbuilder/tests/test_project.py", line 55, in test_FahProjectBuilder1
    assert project == project_ref
AssertionError

----------------------------------------------------------------------
Ran 109 tests in 15.116s

FAILED (SKIP=6, failures=1)

[kyleabeauchamp]

The second bug, IMHO, is that the FAH-style builder is allowing trajectories with "gaps":

- converted_from: [./fah_style_data/RUN2/CLONE0/frame0.xtc, ./fah_style_data/RUN2/CLONE0/frame2.xtc]

I believe this was present even before the msmb2.8 branch.

[kyleabeauchamp]

Another (IMHO) bug is that no sorting by clone is happening. IMHO, we should try to preserve the clone order in the project as much as possible.

[kyleabeauchamp]

Another question: do we want the FAH-style loader to read in XTCs that are not of the form frame%d.xtc? Because right now it's just globbing things.

[rmcgibbo]

What is left before we merge 2.8 onto master?

[kyleabeauchamp]

No idea maybe we got them all. On Jan 21, 2014 9:17 PM, "Robert McGibbon" notifications@github.com wrote:

What is left before we merge 2.8 onto master?

— Reply to this email directly or view it on GitHubhttps://github.com/SimTk/msmbuilder/issues/290#issuecomment-32987572 .

[rmcgibbo]

Okay. I opened #292

[kyleabeauchamp]

This is mostly fixed. I'm going to open an new issue for the FAH project globbing stuff.