isaac2lord | 21 Oct 18:56 2015
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Problem installing PyMCMC/PySSM

Hi

I have been trying to install PyMCMC module in python(x,y) using pip install but got the following errors:

Windows 7 Enterprise; 64-Bit OS




Code (pip):

C:\Windows\system32>pip install C:\Users\...\Downloads\pymcmc-master.zip

Result:

Processing c:\users\...\downloads\pymcmc-master.zip
Installing collected packages: pymcmc
  Running setup.py install for pymcmc
    Complete output from command C:\...\python.exe -c "import setuptools, t
okenize;__file__='c:\\users\\...\\appdata\\local\\temp\\pip-r926zj-build\\set
up.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r
\n', '\n'), __file__, 'exec'))" install --record c:\users\...\appdata\local\t
emp\pip-xwg7_c-record\install-record.txt --single-version-externally-managed --c
ompile:
    running install
    running build
    running config_cc
    unifing config_cc, config, build_clib, build_ext, build commands --compiler
options
    running config_fc
    unifing config_fc, config, build_clib, build_ext, build commands --fcompiler
 options
    running build_src
    build_src
    building extension "stochsearch" sources
    f2py options: []
      adding 'build\src.win-amd64-2.7\fortranobject.c' to sources.
      adding 'build\src.win-amd64-2.7' to include_dirs.
      adding 'build\src.win-amd64-2.7\stochsearch-f2pywrappers.f' to sources.
    building extension "timeseriesfunc" sources
    f2py options: []
      adding 'build\src.win-amd64-2.7\fortranobject.c' to sources.
      adding 'build\src.win-amd64-2.7' to include_dirs.
    building extension "wishart" sources
    f2py options: []
      adding 'build\src.win-amd64-2.7\fortranobject.c' to sources.
      adding 'build\src.win-amd64-2.7' to include_dirs.
    building data_files sources
    Not existing data file: examples/ex_loglinear_loop.py
    Not existing data file: examples/ex_loglinear_f2py.py
    Not existing data file: examples/ex_loglinear_weave.py
    Not existing data file: doc/PyMCMC.lyx
    Not existing data file: doc/PyMCMC.pdf
    build_src: building npy-pkg config files
    running build_py
    creating build\lib.win-amd64-2.7
    creating build\lib.win-amd64-2.7\pymcmc
    copying Lib\mcmc.py -> build\lib.win-amd64-2.7\pymcmc
    copying Lib\mcmcplots.py -> build\lib.win-amd64-2.7\pymcmc
    copying Lib\mcmc_utilities.py -> build\lib.win-amd64-2.7\pymcmc
    copying Lib\regtools.py -> build\lib.win-amd64-2.7\pymcmc
    copying Lib\__init__.py -> build\lib.win-amd64-2.7\pymcmc
    running build_ext
    No module named msvccompiler in numpy.distutils; trying from distutils
    customize MSVCCompiler
    customize MSVCCompiler using build_ext
    customize GnuFCompiler
    Could not locate executable g77
    Could not locate executable f77
    customize IntelVisualFCompiler
    Could not locate executable ifort
    Could not locate executable ifl
    customize AbsoftFCompiler
    Could not locate executable f90
    customize CompaqVisualFCompiler
    Could not locate executable DF
    customize IntelItaniumVisualFCompiler
    Could not locate executable efl
    customize Gnu95FCompiler
    Could not locate executable gfortran
    Could not locate executable f95
    customize G95FCompiler
    Could not locate executable g95
    customize IntelEM64VisualFCompiler
    customize IntelEM64TFCompiler
    Could not locate executable efort
    Could not locate executable efc
    don't know how to compile Fortran code on platform 'nt'
    warning: build_ext: f77_compiler=None is not available.

    building 'stochsearch' extension
    error: extension 'stochsearch' has Fortran sources but no Fortran compiler f
ound

    ----------------------------------------
Command "C:\...\python.exe -c "import setuptools, tokenize;__file__='c:\\us
ers\\...\\appdata\\local\\temp\\pip-r926zj-build\\setup.py';exec(compile(geta
ttr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'e
xec'))" install --record c:\users\...\appdata\local\temp\pip-xwg7_c-record\in
stall-record.txt --single-version-externally-managed --compile" failed with erro
r code 1 in c:\users\...\appdata\local\temp\pip-r926zj-build


*****************************************

Also have tried installing binary version from this address, but when I run  

from pymcmc.mcmc import MCMC

it gives me the following error

ImportError: DLL load failed: %1 is not a valid Win32 application


which I think is related to the fact that I am running on a 64-Bit machine but the binary version is 32-bit. 

*****************************************


Since it's my first time trying to install a non-python(x,y) package that needs Fortran compilation, I'm a bit confused where to start looking for a solution. In the attached document Chapter 25.4.1 (Page 35), and in the github repo (here), a list of packages referred to install for windows compilation which I did not do yet (I am a bit unsure if I'm gonna need all of those packages later).

Appreciate any comments!
Thanks

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Attachment (PyMCMC.pdf): application/pdf, 511 KiB
Hans.Koch | 18 Oct 18:55 2015
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itk SCIFIO error

Hi,

When running some itk programs, which worked a year ago, e.g. the first few lines of the itk test:  MeanImageFilter.py:

import itk
dim = 2
IType = itk.Image[itk.F, dim]
imageFileName='BrainProtonDensitySliceBorder20.png'
reader = itk.ImageFileReader[IType].New()
reader.SetFileName(imageFileName)
reader.Update()

I now receive the following output and error message when running it with Spyder (Python 2.7) :

Python 2.7.10 (default, May 23 2015, 09:40:32) [MSC v.1500 32 bit (Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> runfile('C:/Users/koch05/Documents/WS_14_15/Book/py_mybook/codes/ch11/my_Filter.py', wdir='C:/Users/koch05/Documents/WS_14_15/Book/py_mybook/codes/ch11')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Python27\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py", line 688, in runfile
    execfile(filename, namespace)
  File "C:\Python27\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py", line 72, in execfile
    exec(compile(scripttext, filename, 'exec'), glob, loc)
  File "C:/Users/koch05/Documents/WS_14_15/Book/py_mybook/codes/ch11/my_Filter.py", line 30, in <module>
    reader.Update()
RuntimeError: C:\u\itk-git\_b\Modules\Remote\SCIFIO\src\itkSCIFIOImageIO.cxx:274:
itk::ERROR: SCIFIOImageIO(103ADF70): SCIFIO_PATH is not set. This environment variable must point to the directory containing the SCIFIO JAR files
>>>

Additional remark: in the Python27 site-package, inside the itk folder are the files SCIFIO.py and SCIFIOPython.py and in the Configuration folder: SCIFIOConfig.py

How can I fix this problem? Any help is highly appreciated.

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Pedro Cardoso | 14 Oct 10:33 2015
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Plot window not responding

Hi,
I have a problem when plotting in Spyder.

When using a the code below, the figure window opens but says "not responding". The weird thing is that if I insert a "pause" statement it plots correctly.


Using this code the plot window will freeze
import matplotlib.pyplot as plt plt.plot([1,2,3,4]) plt.ylabel('some numbers') plt.show()


Using this code the plot window will display normally the graph
import matplotlib.pyplot as plt plt.plot([1,2,3,4]) plt.ylabel('some numbers') plt.show()
plt.pause(10)

I tried to change the backend with no positive results. Any guess ?
Best Regards,
Pedro

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Thomas Strand | 2 Oct 20:06 2015
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Scaling on 4k screen

Hello!

When using python(x, y) on my Dell XPS 15, the home menu gets garbled (see picture). 

The screen resolution is 3840 x 2160 but reducing to 1920 x 1080 does not help. I still think this is related to the screen resolution somehow.


A workaround might be right-clicking on the taskbar icon, but I don't know if all the options are available from there.


Anyone got a tip on this? I surely have missed something obvious?


Best Regards,

Thomas


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Feng Zhu | 6 Oct 15:04 2015

Problem in QString API version 2, is it possible to use QString version 1 in pythonxy?

Hello All,

I got a problem of using QString api version 2. 

Basically, I have a software which was developed using python 2.5.  I am now trying to the code work with python 2.7. I chose the pythonxy 2.7.9 package since it has almost all libraries I need. 

First, I found I need to setup set QT_API=pyqt in system environment first. Otherwise it tries to use Pyside which is not working for my code. I don't know why there are to Qt inside. 

Then, the real problem is my software was developed in python 2.5 which used QString version 1. 

So in QString API version 1, I can do something like.

from PyQt4.QtCore import QString

However, in pythonxy 2.7.9, it force to set api to version 2 at low level code __init__.py in qt. So I got the following error:

    ValueError: API 'QString' has already been set to version 1

So I manually add the follow code at very beginning of my software to setup api to version 2

        import sip
        sip.setapi('QString', 2)
        sip.setapi('QVariant', 2)


However, I then cannot import QString from QtCore. 

I read some posts from other website. It says the QString is eliminated from API version 2. I should use python string as replacement. The problem is I have thousands of lines have QString. It would take ages to change it to python string. And I also don't know if my code will work after change all QString to python string. 

I also tried to change the API version to 1 at version low level code __init__.py in qt.

    def prepare_pyqt4():
        # Set PySide compatible APIs.
        import sip
        sip.setapi('QString', 1)
        sip.setapi('QVariant', 1)

I then got hundreds strange error when I launch my software, for example:

****) FlightPad: Unhandled exception
Traceback (most recent call last):
  File "C:\python27\lib\site-packages\pyface\ui\qt4\workbench\split_tab_widget.py", line 310, in _focus_changed
    ntw, ntidx = self._tab_widget_of(new)
  File "C:\python27\lib\site-packages\pyface\ui\qt4\workbench\split_tab_widget.py", line 331, in _tab_widget_of
    for tw in self.findChildren(_TabWidget, None):
TypeError: arguments did not match any overloaded call:
  QObject.findChildren(type, QString name=QString()): argument 2 has unexpected type 'NoneType'
  QObject.findChildren(tuple, QString name=QString()): argument 1 has unexpected type 'PyQt4.QtCore.pyqtWrapperType'
  QObject.findChildren(type, QRegExp): argument 2 has unexpected type 'NoneType'
  QObject.findChildren(tuple, QRegExp): argument 1 has unexpected type 'PyQt4.QtCore.pyqtWrapperType'
An unexpected error has occurred:
 arguments did not match any overloaded call:
  QObject.findChildren(type, QString name=QString()): argument 2 has unexpected type 'NoneType'
  QObject.findChildren(tuple, QString name=QString()): argument 1 has unexpected type 'PyQt4.QtCore.pyqtWrapperType'
  QObject.findChildren(type, QRegExp): argument 2 has unexpected type 'NoneType'
  QObject.findChildren(tuple, QRegExp): argument 1 has unexpected type 'PyQt4.QtCore.pyqtWrapperType'(<type 'exceptions.TypeError'>)

It looks like pythonxy at low level doesn't like QString API version to be set 1. 

Could anyone please advise me what I should do to fit my code? Should I replace python string of QString in my code thousands lines? Or if there is any official way to keep use QString version 1 in pythonxy?

Thanks very much! Looking forward to your reply.

Best Regards,







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Feng Zhu | 7 Oct 01:00 2015

Problem to use QString API version 1 or 2.

Hello,

 

I got some problem to use QString API version 2.

 

Basically, I have a software which is developed by python 2.5. I am now trying to make it work with python 2.7. I chose the pythonxy 2.7.9 since it has almost all libraries I need.

 

The first thing I realise is that I need to set QT_API=pyqt in system environment. Otherwise, it will pythonxy will try to use PySide Qt, which is not working with my code.

 

Then, the real problem is my code was developed with python 2.5, so it used QString version 1.

 

So in QString API version 1, I can do:

 

from PyQt4.QtCore import QString

 

However, I found that pythonxy 2.7.9 forced to set QString API version to 2, at low level code __init__.py in qt.

 

So I have to add the following code at very beginning of my code:

 

import sip

sip.setapi('QString'2)

sip.setapi('QVariant'2)

 

However, after I set it to API 2. I cannot import QString from QtCore anymore.

 

I read some posts from other website. It says QString is eliminated from API version 2. It suggests to use python string replace all QString. However, I have thousands of lines have QString. It will take long time to replace. And I also don’t know if python string will work.

 

I also tried to force set QString API to 1 at low level code, __init__.py in qt by:

 

 

def prepare_pyqt4():

    Set PySide compatible APIs.

    import sip

    sip.setapi('QString'1)

    sip.setapi('QVariant'1)

 

Then, I will get hundreds of strange erros, for example:

 

 

****) FlightPad: Unhandled exception

Traceback (most recent call last):

  File "C:\python27\lib\site-packages\pyface\ui\qt4\workbench\split_tab_widget.py", line 310, in _focus_changed

    ntw, ntidx = self._tab_widget_of(new)

  File "C:\python27\lib\site-packages\pyface\ui\qt4\workbench\split_tab_widget.py", line 331, in _tab_widget_of

    for tw in self.findChildren(_TabWidget, None):

TypeError: arguments did not match any overloaded call:

  QObject.findChildren(type, QString name=QString()): argument 2 has unexpected type 'NoneType'

  QObject.findChildren(tuple, QString name=QString()): argument 1 has unexpected type 'PyQt4.QtCore.pyqtWrapperType'

  QObject.findChildren(type, QRegExp): argument 2 has unexpected type 'NoneType'

  QObject.findChildren(tuple, QRegExp): argument 1 has unexpected type 'PyQt4.QtCore.pyqtWrapperType'

QWidget::create: Failed to create window ()

*) pyface.workbench.workbench: window <psi.workbench.workbench_window.WorkbenchWindow object at 0x05D56630> activated

An unexpected error has occurred:

arguments did not match any overloaded call:

  QObject.findChildren(type, QString name=QString()): argument 2 has unexpected type 'NoneType'

  QObject.findChildren(tuple, QString name=QString()): argument 1 has unexpected type 'PyQt4.QtCore.pyqtWrapperType'

  QObject.findChildren(type, QRegExp): argument 2 has unexpected type 'NoneType'

  QObject.findChildren(tuple, QRegExp): argument 1 has unexpected type 'PyQt4.QtCore.pyqtWrapperType'(<type 'exceptions.TypeError'>)

****) FlightPad: Unhandled exception

Traceback (most recent call last):

  File "C:\python27\lib\site-packages\pyface\ui\qt4\workbench\split_tab_widget.py", line 310, in _focus_changed

    ntw, ntidx = self._tab_widget_of(new)

  File "C:\python27\lib\site-packages\pyface\ui\qt4\workbench\split_tab_widget.py", line 331, in _tab_widget_of

    for tw in self.findChildren(_TabWidget, None):

TypeError: arguments did not match any overloaded call:

  QObject.findChildren(type, QString name=QString()): argument 2 has unexpected type 'NoneType'

  QObject.findChildren(tuple, QString name=QString()): argument 1 has unexpected type 'PyQt4.QtCore.pyqtWrapperType'

  QObject.findChildren(type, QRegExp): argument 2 has unexpected type 'NoneType'

  QObject.findChildren(tuple, QRegExp): argument 1 has unexpected type 'PyQt4.QtCore.pyqtWrapperType'

QWidget::create: Failed to create window ()

 

Could any one advise me what I should do to make pythonxy works. Shall I change thousands lines to replace python string to QString. Or if there is any officially way to keep using QString version 1 in python xy?

 

Thanks very much for the help.

 

Best Regards,

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Jonathan Schock | 14 Sep 18:21 2015

Python 3.x Version, Development?

Hi all,
I would like to contribute in the python(x,y) development, especially in making a 3.x version happen.
Can someone hint me to any developer resources? Github? SVN? Wiki? Something?
Greets
Joni

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Michael Clerx | 31 Aug 21:14 2015
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AdditionalPlugins page is missing from github

Hi all,

The new github page looks great, but the link to the additional plugins is broken (http://python-xy.github.io/p/pythonxy/wiki/AdditionalPlugins).

cheers,
  Michael

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Erick Fonseca | 22 Jul 04:42 2015
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How to reinstall packages?

So, I had a perfectly working installation of Python(x, y). Recently, though, I started messing 
around with some modules and ended up running a pip command with --upgrade, which I suppose 
upgraded scipy. 

Now, scipy and sklearn stopped working correctly. I thought to simply delete their folders from 
Lib/site-packages and running the Python (x, y) installer, but it didn't help. The installer ignored 
their absence.

Is there a simple way to reinstall just some specific missing packages? Perhaps some config file 
in the Python folder that I should change before running the installer?

Thanks,
Erick Fonseca

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Gabi Davar | 1 Jul 21:18 2015
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Gravatar

Python(x, y) 2.7.10.0 Released!

Hi All,


I'm happy to announce that Python(x, y) 2.7.10.0 is available for immediate download.from any of the mirrors. The full change log can be viewed here. Please post your comments and suggestions to the mailing list.

Work on the Python 3.x 64 bit version will resume once Visual Studio 2015 RTM is released.

What's new in general:

  • All packages have been updated to their latest versions. Numpy, Scipy etc.
  • ipython has been held back at 2.4.1 to avoid potential compatibility issues.
  • OpenCV has been help back at 2.4.11 to avoid potential compatibility issues.

New noteworthy packages:

  • yappi - Yet Another Python Profiler.
  • libnacl - A ctypes wrapper around libsodium.
Have fun!

-Gabi Davar

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Trey Suntrup | 30 May 04:23 2015
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Scipy: ImportError: cannot import name doccer

I just installed python xy 2.7.9 on Windows 7. I went to run some previously written code in Spyder which calls:

from scipy.sparse import linalg as sla

However, I get the following error:

File "C:\Python27\lib\site-packages\scipy\sparse\linalg\__init__.py", line 113, in <module> from .matfuncs import * File "C:\Python27\lib\site-packages\scipy\sparse\linalg\matfuncs.py", line 20, in <module> import scipy.misc File "C:\Python27\lib\site-packages\scipy\misc\__init__.py", line 44, in <module> from . import doccer ImportError: cannot import name doccer

Does anyone know how to fix this? I find this weird because it worked with my previous copy of Python (which I uninstalled before installing the new version).

Thanks!

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Gmane