Library conflict and missing file in linux dev package

[Drakker]

Hi,

I already wrote an how to on working around these problems, I posted it on the Google Group: https://groups.google.com/forum/?hl=en#!topic/circuitscape/kHIcqX8FfYo

I'm also posting it here as prof. McRae suggested.

The problem occurs on Linux, on Ubuntu versions 14.04 to 15.10, but I also had the same problem running it on a CentOS cluster.

The first problem is that other system packages (notably the GZip wrappers for python) also use a library named "io". The fix is very simple, I renamed the "io.py" file in /circuitscape to "cs_io.py" and changed the import lines in "compute.py" and "compute_base.py".

The second problem is a bit more insidious and affect the GUI. It is an error returned by PythonCards:

~/circuitscape$ python circuitscape/gui.py
Traceback (most recent call last):
File "circuitscape/gui.py", line 856, in
show_gui()
File "circuitscape/gui.py", line 850, in show_gui
app = model.Application(GUI, rsrc=GUI_RSRC)
File "/usr/lib/python2.7/dist-packages/PythonCard/model.py", line 393, in init
wx.App.init(self, 0)
File "/usr/lib/python2.7/dist-packages/wx-3.0-gtk2/wx/_core.py", line 8628, in init
self._BootstrapApp()
File "/usr/lib/python2.7/dist-packages/wx-3.0-gtk2/wx/_core.py", line 8196, in _BootstrapApp
return core.PyApp__BootstrapApp(_args, *_kwargs)
File "/usr/lib/python2.7/dist-packages/PythonCard/model.py", line 445, in OnInit
self._initBackgrounds(self.resource)
File "/usr/lib/python2.7/dist-packages/PythonCard/model.py", line 438, in _initBackgrounds
bg = self.frameClass(None, bgRsrc)
File "/usr/lib/python2.7/dist-packages/PythonCard/model.py", line 685, in init
self._initLayout(aBgRsrc.components)
File "/usr/lib/python2.7/dist-packages/PythonCard/model.py", line 999, in _initLayout
self.components[rsrc.name] = rsrc
File "/usr/lib/python2.7/dist-packages/PythonCard/model.py", line 98, in setitem
control = component.ComponentFactory().createComponent(self.parent, self.parent.panel, item)
File "/usr/lib/python2.7/dist-packages/PythonCard/component.py", line 347, in createComponent
component = clazz(aParent, aResource)
File "/usr/lib/python2.7/dist-packages/PythonCard/components/image.py", line 70, in init
widget.Widget.init( self, aParent, aResource )
File "/usr/lib/python2.7/dist-packages/PythonCard/widget.py", line 68, in init
self._setBackgroundColor(self._resource.backgroundColor)
File "/usr/lib/python2.7/dist-packages/PythonCard/components/image.py", line 135, in _setBackgroundColor
bmp = self._bitmap.getBits()
AttributeError: 'Bitmap' object has no attribute 'getBits'

It seems to be related to the missing "cs_logo.jpg" file (did a find in the circuitscape folder and couldn't find it, didn't investigate any further). As I wrote in the groups, I know I fixed it a different way in the past, but I can't remember what it was and I was in a hurry to get Circuitscape to run today and ended up modifying the PythonCards library, which is a big no-no, but allowed me to launch my computations without having to create a config file from scratch.

Both these bugs have been reported in the past in the group but it seems they were never submitted here.

[lionel68]

The fix you mentioned in the googlegroups (messing up PythonCards) worked for me (Ubuntu 16.04). It is however a rather lengthy process to get Circuitscape to run using python ...