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trouble with "import neuron"
Posted: Tue Apr 15, 2008 2:16 am
by davidlmorton
With your help from before, nrniv -python loads okay but now when I
import neuron I have some strange behavior. After the import, the command line interpreter stops processing arrow command movement
keys and anything I type gets echoed back in an odd way. Here is an
example:
Code: Select all
[1:08am]@Sakurai:~>nrniv -python
NEURON -- VERSION 6.0.pygetsetcall.23 (35) 2007-05-23
by John W. Moore, Michael Hines, and Ted Carnevale
Duke and Yale University -- Copyright 1984-2007
>>> import neuron
>>> neuron.h("create soma")
neuron.h("create soma")
euron.h("create soma")
uron.h("create soma")
ron.h("create soma")
on.h("create soma")
n.h("create soma")
.h("create soma")
h("create soma")
("create soma")
"create soma")
create soma")
reate soma")
eate soma")
ate soma")
te soma")
e soma")
soma")
soma")
oma")
ma")
a")
")
)
1
>>> neuron.h("soma.v")
neuron.h("soma.v")
euron.h("soma.v")
uron.h("soma.v")
ron.h("soma.v")
on.h("soma.v")
n.h("soma.v")
.h("soma.v")
h("soma.v")
("soma.v")
"soma.v")
soma.v")
oma.v")
ma.v")
a.v")
.v")
v")
")
)
-65
1
Any ideas?
As an asside, I tried to get the nrnpython/setup.py to install and it tries to use a -R/path/to/something switch which mac gcc can't handle.
Thanks in advance,
David Morton[/code]
Posted: Tue Apr 15, 2008 9:52 am
by ted
Reminds me of walking in total darkness in an unfamiliar room. Suggest that you work
your way through Andrew Davison's tutorials, specifically
Accessing hoc from Python
and
Modelling single cells in NEURON with the Python interpreter
You'll find them on the Documentation page:
http://www.neuron.yale.edu/neuron/docs
Tutorials have the same issue
Posted: Tue Apr 15, 2008 2:09 pm
by davidlmorton
I tried running through the tutorial and here is the result:
Code: Select all
[1:03pm]@Sakurai:~>nrniv -python
NEURON -- VERSION 6.0.pygetsetcall.23 (35) 2007-05-23
by John W. Moore, Michael Hines, and Ted Carnevale
Duke and Yale University -- Copyright 1984-2007
>>> from neuron import h
>>> h
h
TopLevelHocInterpreter
>>> h.dt
h.dt
.dt
dt
t
0.025000000000000001
>>> h.finitialize()
h.finitialize()
.finitialize()
finitialize()
initialize()
nitialize()
itialize()
tialize()
ialize()
alize()
lize()
ize()
ze()
e()
()
)
1.0
>>> h('x = 2')
h('x = 2')
('x = 2')
'x = 2')
x = 2')
= 2')
= 2')
2')
2')
')
)
first instance of x
1
As soon as I import the neuron module it messes up the CLI and I can't even ctrl-D to exit I have to import sys and sys.exit(). If I import some other module it does not have this issue.
Code: Select all
[1:04pm]@Sakurai:~>nrniv -python
NEURON -- VERSION 6.0.pygetsetcall.23 (35) 2007-05-23
by John W. Moore, Michael Hines, and Ted Carnevale
Duke and Yale University -- Copyright 1984-2007
>>> import numpy
>>> numpy.test()
Found 5 tests for numpy.distutils.misc_util
Found 3 tests for numpy.lib.getlimits
Found 31 tests for numpy.core.numerictypes
Found 32 tests for numpy.linalg
Found 13 tests for numpy.core.umath
Found 4 tests for numpy.core.scalarmath
Found 9 tests for numpy.lib.arraysetops
Found 42 tests for numpy.lib.type_check
Found 188 tests for numpy.core.multiarray
Found 3 tests for numpy.fft.helper
Found 36 tests for numpy.core.ma
Found 1 tests for numpy.fft.fftpack
Found 12 tests for numpy.lib.twodim_base
Found 10 tests for numpy.core.defmatrix
Found 1 tests for numpy.lib.ufunclike
Found 4 tests for numpy.ctypeslib
Found 41 tests for numpy.lib.function_base
Found 2 tests for numpy.lib.polynomial
Found 9 tests for numpy.core.records
Found 26 tests for numpy.core.numeric
Found 4 tests for numpy.lib.index_tricks
Found 47 tests for numpy.lib.shape_base
Found 0 tests for __main__
......................................................................................................
......................................................................................................
......................................................................................................
......................................................................................................
......................................................................................................
.............
----------------------------------------------------------------------
Ran 523 tests in 1.737s
OK
<unittest.TextTestRunner object at 0x348dbb0>
>>>
[1:08pm]@Sakurai:~>
Posted: Tue Apr 15, 2008 3:01 pm
by hines
NEURON -- VERSION 6.0.pygetsetcall.23 (35) 2007-05-23
You are using an old development branch that is very far out of date. Try the latest
alpha version at
http://www.neuron.yale.edu/ftp/neuron/versions/alpha/
Thanks again
Posted: Tue Apr 15, 2008 7:31 pm
by davidlmorton
I guess I followed some bad advice about getting the latest svn version (or I got a developement branch instead of a release branch). Thanks again for the information. I couldn't get it to compile universal and then had troubles running it, but the .dmg for 10.4 seems to be working great.
I really appreciate that you are responsive and that you make binaries for the mac available.