PyCont examples are broken

[z2v]

After PyCont update (commit 42b8acd) these PyCont examples are broken:

• PyCont_Catalytic.py
• PyCont_DiscPredPrey.py
• PyCont_Hopfield.py
• PyCont_Logistic.py
• PyCont_MorrisLecar_TypeI.py
• PyCont_MorrisLecar_TypeII.py
• PyCont_LPNeuron.py
• PyCont_HindmarshRose.py
• PyCont_ABReaction.py
• PyCont_Hamiltonian.py
• PyCont_Lorenz.py
• PyCont_vanDerPol.py

[robclewley]

I was aware that LPNeuron, Logistic, Hopfield, PredPrey, no longer work but I've asked Drew to fix those. Should be minor. The others run on my system from my git repo so I don't know what happened. I'll investigate soon.

[z2v]

Ok, I've rechecked in my environment (numpy==1.8.1, scipy==0.13.3, gcc-4.8.1):

• PyCont_Catalytic.py: OK
• PyCont_DiscPredPrey.py, PyCont_Hopfield.py: FAILURE

Traceback (most recent call last):
  File "PyCont_DiscPredPrey.py", line 80, in <module>
    PyCont['FP4'].forward()
  File "/home/vovka/projects/science/PyDSTool/PyDSTool/PyCont/Continuation.py", line 1243, in forward
    self._compute(v0=self.initdirec)
  File "/home/vovka/projects/science/PyDSTool/PyDSTool/PyCont/Continuation.py", line 1192, in _compute
    if self.BifPoints != {} and self._checkForBifPoints():
  File "/home/vovka/projects/science/PyDSTool/PyDSTool/PyCont/Continuation.py", line 532, in _checkForBifPoints
    found = bfinfo.process(Xval, Vval, self)
  File "/home/vovka/projects/science/PyDSTool/PyDSTool/PyCont/BifPoint.py", line 219, in process
    V1 = real(VR[:,W0[0]])
IndexError: list index out of range

• PyCont_Logistic.py: FAILURE

File "PyCont_Logistic.py", line 45, in <module>
    assert len(s.bylabel('SP-r-0')) == 1
TypeError: object of type 'NoneType' has no len()

• PyCont_MorrisLecar_TypeI.py, PyCont_MorrisLecar_TypeII.py, PyCont_LPNeuron.py, PyCont_HindmarshRose.py, PyCont_ABReaction.py, PyCont_Hamiltonian.py, PyCont_Lorenz.py : FAILURE

/home/vovka/projects/science/PyDSTool/examples/auto_temp/auto_MorrisLecar_vf.i:8: Error: Unable to find 'numpy.i'

• PyCont_vanDerPol.py: FAILURE

/home/vovka/projects/science/PyDSTool/examples/auto_temp/auto_vanderPol_vf.i:8: Error: Unable to find 'numpy.i'
Traceback (most recent call last):
  File "PyCont_vanDerPol.py", line 308, in <module>
    continuation(C, cycle=cycle, compute=True, disp=False)
  File "PyCont_vanDerPol.py", line 85, in continuation
    PyCont['LC_eps'].initcycle = cycle
  File "/home/vovka/projects/science/PyDSTool/PyDSTool/PyCont/ContClass.py", line 97, in __getitem__
    raise KeyError('No curve named ' + str(name))
KeyError: 'No curve named LC_eps'

There is no numpy.i file in the repo.

[robclewley]

Added the file. Should be OK now except for the known failures I mentioned above. Will try to track those down soon but they are probably requiring changes in operating parameters in the example problem rather than core PyCont code. Will leave this open until those are fixed too.

[z2v]

Confirm. Examples, that are still broken in my environment (just for the record):

• PyCont_DiscPredPrey.py
• PyCont_Hopfield.py
• PyCont_Logistic.py

[mdlama]

Fixed PyCont_Logistic.py. On to the others...

[jckegelman]

Also just for the record, these examples are broken in my environment:

• PyCont_Hopfield.py
• PyCont_Logistic.py

which produce the following errors:

Traceback (most recent call last):
  File "PyCont_Logistic.py", line 58, in <module>
    PCargs.initdirec = PyCont['FP2'].getSpecialPoint('PD1').labels['PD']['data'].branch
AttributeError: 'NoneType' object has no attribute 'labels'

Traceback (most recent call last):
  File "PyCont_Hopfield.py", line 89, in <module>
    PyCont['FO1'].backward()
  File "/home/kegelman/repos/pydstool/PyDSTool/PyCont/Continuation.py", line 1435, in backward
    for k, v in pt.labels[ctype]['data'].V.items():
KeyError: 'LP'

[z2v]

Current examples problems are collected in #101.