#2 fix auto-07p for newer numpy

[Sergey Kirpichev]

Currently, if I import any data with auto-07p, like this

>>> import auto
>>> S2 = auto.load('S2', e='wf')
Runner configured
>>> S2['U(2)'][:3]
/usr/lib/auto-07p/python/Points.py:1086: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  r = rank(array_temp)
/usr/lib/auto-07p/python/Points.py:968: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  if rank(vals) == 0:
/usr/lib/auto-07p/python/Points.py:996: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  r=rank(self.indepvararray)
/usr/lib/auto-07p/python/Points.py:491: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  r = rank(array_temp)
array([-3.14145317, -3.14139868, -3.14134285])

it breaks matplotlib, for example:

>>> import matplotlib.pylab as plt
>>> plt.plot([1, 2, 3])
[...]
>>> plt.show(_)
[...]
  File "/home/sk/venv/dev/lib/python3.5/site-packages/numpy/core/numeric.py", line 868, in flatnonzero
    return np.nonzero(np.ravel(a))[0]
  File "/home/sk/venv/dev/lib/python3.5/site-packages/numpy/core/fromnumeric.py", line 1574, in ravel
    return asanyarray(a).ravel(order=order)
RecursionError: maximum recursion depth exceeded

It seems that removing numpy.nonzero override with flatnonzero - solves this problem.

[Omer Tzuk]

I have commented out the line N.nonzero = N.flatnonzero, however, I still get an error message when I try to plot something using Python 3:

$ auto
Python 3.7.0 (default, Oct  9 2018, 10:31:47) 
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
(AUTOInteractiveConsole)
AUTO> from autoutilities import plotCont
AUTO> bif,ps=plotCont()
...
Using plain TkInter for plotting. You can obtain better quality graphics
using matplotlib (http://matplotlib.sf.net).
Traceback (most recent call last):
...
File ".../auto/07p/python/AUTOCommands.py", line 1840, in plot
    handle = windowPlotter.WindowPlotter2D(root,**options)
  File ".../auto/07p/python/graphics/windowPlotter.py", line 256, in __init__
    WindowPlotter.__init__(self,plotter.plotter,parent,**kw)
  File ".../auto/07p/python/graphics/windowPlotter.py", line 55, in __init__
    grapherClass,interior)
  File ".../auto/07p/python/graphics/Pmw.py", line 560, in createcomponent
    widget = widgetClass(*widgetArgs, **kw)
  File ".../auto/07p/python/graphics/plotter.py", line 102, in __init__
    self._plotNoDraw()
  File ".../auto/07p/python/graphics/plotter.py", line 343, in _plotNoDraw
    self.__plot7(*columns)
  File ".../auto/07p/python/graphics/plotter.py", line 607, in __plot7
    self.__plot7branch(branch,xcolumns,ycolumns,zcolumns)
  File ".../auto/07p/python/graphics/plotter.py", line 554, in __plot7branch
    xy = branch.coordarray[col]
  File ".../auto/07p/python/bifDiag.py", line 229, in __getattr__
    return super(bifDiagBranch, self).__getattr__(attr)
  File ".../auto/07p/python/parseB.py", line 297, in __getattr__
    self.__parse()
  File ".../auto/07p/python/parseB.py", line 343, in __parse
    stability = self.__parsenumpy(points)
  File ".../auto/07p/python/parseB.py", line 372, in __parsenumpy
    [len(points)-1]))

ValueError: all the input arrays must have same number of dimensions
AUTO> 

[Bart Oldeman]

Please try:
https://github.com/auto-07p/auto-07p
it's fixed there and the plotter tested with Python 3, numpy and matplotlib.