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xia2 / screen19

Screening program for small-molecule single-crystal X-ray diffraction data
https://pypi.org/project/screen19/
BSD 3-Clause "New" or "Revised" License
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Compatibility fixes for procrunner 2.1.0 #38

Closed Anthchirp closed 4 years ago

Anthchirp commented 4 years ago

the procrunner.run() return object is no longer a native dictionary (https://github.com/DiamondLightSource/python-procrunner/pull/60). While dictionary access still works (and raises DeprecationWarnings) there is no implementation of .items().

I ran the tests locally but two tests failed due to matplotlib 3.0.3 being either to new or to old. (would this be problem with a CCP4 installation? 7.1.3 currently has 2.2.3):

screen19/screen.py:1139: in run
    self._wilson_calculation()
screen19/screen.py:841: in _wilson_calculation
    suggest_minimum_exposure(self.expts, self.refls, self.params.minimum_exposure)
screen19/minimum_exposure.py:410: in suggest_minimum_exposure
    output=params.output.wilson_plot,
screen19/minimum_exposure.py:252: in wilson_plot_image
    plt.yscale("log", nonpositive="clip")
../../conda_base/lib/python3.6/site-packages/matplotlib/pyplot.py:3084: in yscale
    return gca().set_yscale(value, **kwargs)
../../conda_base/lib/python3.6/site-packages/matplotlib/axes/_base.py:3704: in set_yscale
    ax.yaxis._set_scale(value, **kwargs)
../../conda_base/lib/python3.6/site-packages/matplotlib/axis.py:767: in _set_scale
    self._scale = mscale.scale_factory(value, self, **kwargs)
../../conda_base/lib/python3.6/site-packages/matplotlib/scale.py:569: in scale_factory
    return _scale_mapping[scale](axis, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
E           ValueError: provided too many kwargs, can only pass {'basex', 'subsx', nonposx'} or {'basey', 'subsy', nonposy'}.  You passed {'nonpositive': 'clip'}
../../conda_base/lib/python3.6/site-packages/matplotlib/scale.py:249: ValueError