[Biopython-dev] Enhancements to Phylo.draw; pyplot best practices

[Eric Talevich]

On Mon, Apr 16, 2012 at 11:20 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Hi Eric,
>
> That seems to have caused a test failure on one of our buildslaves:
>
> ======================================================================
> ERROR: Run the tree layout algorithm, but don't display it.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/home/buildslave/BuildBot/lin2664/build/Tests/test_Phylo_depend.py",
> line 51, in test_draw
>    Phylo.draw(dollo, do_show=False)
>  File "/home/buildslave/BuildBot/lin2664/build/build/lib.linux-x86_64-2.6/Bio/Phylo/_utils.py",
> line 366, in draw
>    fig = plt.figure()
>  File "/usr/local/lib/python2.6/site-packages/matplotlib/pyplot.py",
> line 270, in figure
>    **kwargs)
>  File "/usr/local/lib/python2.6/site-packages/matplotlib/backends/backend_wxagg.py",
> line 120, in new_figure_manager
>    backend_wx._create_wx_app()
>  File "/usr/local/lib/python2.6/site-packages/matplotlib/backends/backend_wx.py",
> line 1377, in _create_wx_app
>    wxapp = wx.PySimpleApp()
>  File "/usr/local/lib/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/_core.py",
> line 8078, in __init__
>    wx.App.__init__(self, redirect, filename, useBestVisual, clearSigInt)
>  File "/usr/local/lib/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/_core.py",
> line 7946, in __init__
>    raise SystemExit(msg)
> SystemExit: Unable to access the X Display, is $DISPLAY set properly?
>
> ----------------------------------------------------------------------
>
> http://testing.open-bio.org:8010/builders/Linux%2064%20-%20Python%202.6/builds/534/steps/shell/logs/stdio
> http://testing.open-bio.org:8010/builders/Linux%2064%20-%20Python%202.6/builds/535/steps/shell/logs/stdio
>
> Interestingly the same machine is passing the tests under other Python versions.
> That would seem to rule out the $DISPLAY environment variable being the cause.
> My hunch would be this is something about the Python 2.6 install, perhaps it
> is missing some library (wxPython maybe).
>
> Logged in as the buildslave on this machine I can see that both Python 2.6 & 2.7
> have the same version of matplotlib installed, but only one is failing the test:
>
> $ python2.5
> Python 2.5.5 (r255:77872, Jan 14 2011, 17:09:55)
> [GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import matplotlib
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
> ImportError: No module named matplotlib
>
> $ python2.6
> Python 2.6.6 (r266:84292, Aug 31 2010, 16:21:14)
> [GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import matplotlib
>>>> matplotlib.__version__
> '1.0.0'
>
> $ python2.7
> Python 2.7 (r27:82500, Jul 13 2010, 14:02:41)
> [GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import matplotlib
>>>> matplotlib.__version__
> '1.0.0'
>
>
> Peter


Actually, it was this commit which added new unit tests:
https://github.com/biopython/biopython/commit/a5f995bc1d9e113d88195cc7ae6f389984d762d8

On my machine with Python 2.6 and Ubuntu, the test passes, so I'm not
sure how to debug this, exactly. Do you know a way to prevent
matplotlib from attempting to launch the Wx app, beyond turn off
interactive mode as the test already does?

One idea is to specify a matplotlib backend other than wx. For
example, using this import approach in test_Phylo_depend.py might do
the trick:

try:
    import matplotlib
except ImportError:
    raise MissingExternalDependencyError(
            "Install matplotlib if you want to use Bio.Phylo._utils.")
else:
    # Don't use the Wx backend for matplotlib, b/c that depends on Wx being
    # properly set up on the build machine. Instead, use the simpler postscript
    # backend -- we're not going to display or save the plot anyway, so it
    # doesn't matter much, as long as it's not Wx. I guess.
    matplotlib.use("ps")
    from matplotlib import pyplot


Would you be able to test this on the errant buildbot machine without
having to commit this to the trunk?


Thanks,
Eric