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• Distribute pre-compiled python extension module with distutils

  - by Toji

  Quick one today: I'm learning the in's and out's of Pythons distutils library, and I would like to include a python extension module (.pyd) with my package. I know of course that the recommended way is to have distutils compile the extension at the time the package is created, but this is a fairly complex extension spanning many source files and referencing several external libs so it's going to take some significant playing to get everything working right. In the meantime I have a known working build of the extension coming out of Visual Studio, and would like to use it in the installer as a temporary solution to allow me to focus on other issues. I can't specify it as a module, however, since those apparently must have an explicit .py extension. How could I indicate in my setup.py that I want to include a pre-compiled extension module? (Python 3.1, if it matters)

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• Importing a function/class from a Python module of the same name

  - by Brendan

  I have a Python package mymodule with a sub-package utils (i.e. a subdirectory which contains modules each with a function). The functions have the same name as the file/module in which they live. I would like to be able to access the functions as follows, from mymodule.utils import a_function Strangely however, sometimes I can import functions using the above notation, however other times I cannot. I have not been able to work out why though (recently, for example, I renamed a function and the file it was in and reflected this rename in the utils.__init__.py file but it no longer imported as a functions (rather as a module) in one of my scripts. The utils.__init__.py reads something like, __all__ = ['a_function', 'b_function' ...] from a_function import a_function from b_function import b_function ... mymodule.__init__.py has no reference to utils Ideas?

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• Import python module NOT on path

  - by Vort3x

  I have read all the questions I could find on it on SO, but none answers my question. I have a module foo, containing util.py and bar.py. I want to import it in IDLE or python session. How do I go about this? I could find no documentation on how to import modules not in the current directory or the default python PATH. After trying import "<full path>/foo/util.py", and from "<full path>" import util The closest I could get was import imp imp.load_source('foo.util','C:/.../dir/dir2/foo') Which gave me Permission denied on windows 7.

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• File/module structure in Python

  - by keithjgrant

  So I'm just getting started with Python, and currently working my way through diveintopython.org. The code examples are nice, but the vast majority of them are little four-line snippets, and I want to see a little more of the big picture. As I understand it--and correct me if I'm wrong--each '.py' file becomes a "module", and a group of modules in a directory becomes a "package" (at least, it does if I create a __init__.py file in that directory). What is it if I don't have a __init__.py file? So what does each "module" file look like? Do I generally define only one class in the file? Does anything else go in that file besides the class definition and maybe a handful of import commands?

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• Reinterpret a CGImageRef using PyObjC in Python

  - by Michael Rondinelli

  Hi, I'm doing something that's a little complicated to sum up in the title, so please bear with me. I'm writing a Python module that provides an interface to my C++ library, which provides some specialized image manipulation functionality. It would be most convenient to be able to access image buffers as CGImageRefs from Python, so they could be manipulated further using Quartz (using PyObjC, which works well). So I have a C++ function that provides a CGImageRef representation from my own image buffers, like this: CGImageRef CreateCGImageRefForImageBuffer(shared_ptr<ImageBuffer> buffer); I'm using Boost::Python to create my Python bridge. What is the easiest way for me to export this function so that I can use the CGImageRef from Python? Problems: The CGImageRef type can't be exported directly because it is a pointer to an undefined struct. So I could make a wrapper function that wraps it in a PyCObject or something to get it to send the pointer to Python. But then how do I "cast" this object to a CGImageRef from Python? Is there a better way to go about this?

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• Blank Screen at boot Ubuntu 12.04 - nvidia-current - Macbook Air 3,2

  - by soulnafein

  I've installed nvidia-current using the Additional Drivers application in Ubuntu 12.04. I need those drivers so I can use accelerated WebGL. After installing the drivers, and rebooting X fails to start and I have a frozen system/dark screen. Below is the content of Xorg.0.log How can I fix this problem? [ 4.666] X.Org X Server 1.11.3 Release Date: 2011-12-16 [ 4.666] X Protocol Version 11, Revision 0 [ 4.666] Build Operating System: Linux 2.6.42-23-generic x86_64 Ubuntu [ 4.666] Current Operating System: Linux david-macbook-air 3.2.0-34-generic #53-Ubuntu SMP Thu Nov 15 10:48:16 UTC 2012 x86_64 [ 4.666] Kernel command line: BOOT_IMAGE=/boot/vmlinuz-3.2.0-34-generic root=UUID=b3d5ae2a-72af-4ef9-b775-0d40b5f80f9b ro quiet splash vt.handoff=7 [ 4.666] Build Date: 29 August 2012 12:12:33AM [ 4.666] xorg-server 2:1.11.4-0ubuntu10.8 (For technical support please see http://www.ubuntu.com/support) [ 4.666] Current version of pixman: 0.24.4 [ 4.666] Before reporting problems, check http://wiki.x.org to make sure that you have the latest version. [ 4.666] Markers: (--) probed, (**) from config file, (==) default setting, (++) from command line, (!!) notice, (II) informational, (WW) warning, (EE) error, (NI) not implemented, (??) unknown. [ 4.666] (==) Log file: "/var/log/Xorg.0.log", Time: Thu Dec 13 10:18:02 2012 [ 4.668] (==) Using system config directory "/usr/share/X11/xorg.conf.d" [ 4.668] (==) No Layout section. Using the first Screen section. [ 4.668] (==) No screen section available. Using defaults. [ 4.668] (**) |-->Screen "Default Screen Section" (0) [ 4.668] (**) | |-->Monitor "<default monitor>" [ 4.668] (==) No monitor specified for screen "Default Screen Section". Using a default monitor configuration. [ 4.668] (==) Automatically adding devices [ 4.668] (==) Automatically enabling devices [ 4.668] (WW) The directory "/usr/share/fonts/X11/cyrillic" does not exist. [ 4.668] Entry deleted from font path. [ 4.668] (WW) The directory "/usr/share/fonts/X11/100dpi/" does not exist. [ 4.668] Entry deleted from font path. [ 4.669] (WW) The directory "/usr/share/fonts/X11/75dpi/" does not exist. [ 4.669] Entry deleted from font path. [ 4.669] (WW) The directory "/usr/share/fonts/X11/100dpi" does not exist. [ 4.669] Entry deleted from font path. [ 4.669] (WW) The directory "/usr/share/fonts/X11/75dpi" does not exist. [ 4.669] Entry deleted from font path. [ 4.669] (WW) The directory "/var/lib/defoma/x-ttcidfont-conf.d/dirs/TrueType" does not exist. [ 4.669] Entry deleted from font path. [ 4.669] (==) FontPath set to: /usr/share/fonts/X11/misc, /usr/share/fonts/X11/Type1, built-ins [ 4.669] (==) ModulePath set to "/usr/lib/x86_64-linux-gnu/xorg/extra-modules,/usr/lib/xorg/extra-modules,/usr/lib/xorg/modules" [ 4.669] (II) The server relies on udev to provide the list of input devices. If no devices become available, reconfigure udev or disable AutoAddDevices. [ 4.669] (II) Loader magic: 0x7f6222467b00 [ 4.669] (II) Module ABI versions: [ 4.669] X.Org ANSI C Emulation: 0.4 [ 4.669] X.Org Video Driver: 11.0 [ 4.669] X.Org XInput driver : 16.0 [ 4.669] X.Org Server Extension : 6.0 [ 4.670] (--) PCI:*(0:2:0:0) 10de:08a3:106b:00d3 rev 162, Mem @ 0x92000000/16777216, 0x80000000/268435456, 0x90000000/33554432, I/O @ 0x00001000/128, BIOS @ 0x????????/131072 [ 4.670] (II) Open ACPI successful (/var/run/acpid.socket) [ 4.670] (II) LoadModule: "extmod" [ 4.671] (II) Loading /usr/lib/xorg/modules/extensions/libextmod.so [ 4.671] (II) Module extmod: vendor="X.Org Foundation" [ 4.671] compiled for 1.11.3, module version = 1.0.0 [ 4.671] Module class: X.Org Server Extension [ 4.671] ABI class: X.Org Server Extension, version 6.0 [ 4.671] (II) Loading extension MIT-SCREEN-SAVER [ 4.671] (II) Loading extension XFree86-VidModeExtension [ 4.671] (II) Loading extension XFree86-DGA [ 4.671] (II) Loading extension DPMS [ 4.671] (II) Loading extension XVideo [ 4.671] (II) Loading extension XVideo-MotionCompensation [ 4.671] (II) Loading extension X-Resource [ 4.671] (II) LoadModule: "dbe" [ 4.671] (II) Loading /usr/lib/xorg/modules/extensions/libdbe.so [ 4.671] (II) Module dbe: vendor="X.Org Foundation" [ 4.671] compiled for 1.11.3, module version = 1.0.0 [ 4.671] Module class: X.Org Server Extension [ 4.671] ABI class: X.Org Server Extension, version 6.0 [ 4.671] (II) Loading extension DOUBLE-BUFFER [ 4.671] (II) LoadModule: "glx" [ 4.671] (II) Loading /usr/lib/x86_64-linux-gnu/xorg/extra-modules/libglx.so [ 4.869] (II) Module glx: vendor="NVIDIA Corporation" [ 4.869] compiled for 4.0.2, module version = 1.0.0 [ 4.869] Module class: X.Org Server Extension [ 4.869] (II) NVIDIA GLX Module 295.40 Thu Apr 5 21:57:38 PDT 2012 [ 4.869] (II) Loading extension GLX [ 4.869] (II) LoadModule: "record" [ 4.870] (II) Loading /usr/lib/xorg/modules/extensions/librecord.so [ 4.870] (II) Module record: vendor="X.Org Foundation" [ 4.870] compiled for 1.11.3, module version = 1.13.0 [ 4.870] Module class: X.Org Server Extension [ 4.870] ABI class: X.Org Server Extension, version 6.0 [ 4.870] (II) Loading extension RECORD [ 4.870] (II) LoadModule: "dri" [ 4.870] (II) Loading /usr/lib/xorg/modules/extensions/libdri.so [ 4.870] (II) Module dri: vendor="X.Org Foundation" [ 4.870] compiled for 1.11.3, module version = 1.0.0 [ 4.870] ABI class: X.Org Server Extension, version 6.0 [ 4.870] (II) Loading extension XFree86-DRI [ 4.870] (II) LoadModule: "dri2" [ 4.871] (II) Loading /usr/lib/xorg/modules/extensions/libdri2.so [ 4.871] (II) Module dri2: vendor="X.Org Foundation" [ 4.871] compiled for 1.11.3, module version = 1.2.0 [ 4.871] ABI class: X.Org Server Extension, version 6.0 [ 4.871] (II) Loading extension DRI2 [ 4.871] (==) Matched nvidia as autoconfigured driver 0 [ 4.871] (==) Matched nouveau as autoconfigured driver 1 [ 4.871] (==) Matched nv as autoconfigured driver 2 [ 4.871] (==) Matched vesa as autoconfigured driver 3 [ 4.871] (==) Matched fbdev as autoconfigured driver 4 [ 4.871] (==) Assigned the driver to the xf86ConfigLayout [ 4.871] (II) LoadModule: "nvidia" [ 4.871] (II) Loading /usr/lib/x86_64-linux-gnu/xorg/extra-modules/nvidia_drv.so [ 4.887] (II) Module nvidia: vendor="NVIDIA Corporation" [ 4.887] compiled for 4.0.2, module version = 1.0.0 [ 4.887] Module class: X.Org Video Driver [ 4.892] (II) LoadModule: "nouveau" [ 4.894] (II) Loading /usr/lib/xorg/modules/drivers/nouveau_drv.so [ 4.894] (II) Module nouveau: vendor="X.Org Foundation" [ 4.894] compiled for 1.11.3, module version = 1.0.2 [ 4.894] Module class: X.Org Video Driver [ 4.894] ABI class: X.Org Video Driver, version 11.0 [ 4.894] (II) LoadModule: "nv" [ 4.895] (WW) Warning, couldn't open module nv [ 4.895] (II) UnloadModule: "nv" [ 4.895] (II) Unloading nv [ 4.895] (EE) Failed to load module "nv" (module does not exist, 0) [ 4.895] (II) LoadModule: "vesa" [ 4.895] (II) Loading /usr/lib/xorg/modules/drivers/vesa_drv.so [ 4.896] (II) Module vesa: vendor="X.Org Foundation" [ 4.896] compiled for 1.11.3, module version = 2.3.0 [ 4.896] Module class: X.Org Video Driver [ 4.896] ABI class: X.Org Video Driver, version 11.0 [ 4.896] (II) LoadModule: "fbdev" [ 4.896] (II) Loading /usr/lib/xorg/modules/drivers/fbdev_drv.so [ 4.896] (II) Module fbdev: vendor="X.Org Foundation" [ 4.896] compiled for 1.11.3, module version = 0.4.2 [ 4.896] ABI class: X.Org Video Driver, version 11.0 [ 4.896] (==) Matched nvidia as autoconfigured driver 0 [ 4.896] (==) Matched nouveau as autoconfigured driver 1 [ 4.896] (==) Matched nv as autoconfigured driver 2 [ 4.896] (==) Matched vesa as autoconfigured driver 3 [ 4.896] (==) Matched fbdev as autoconfigured driver 4 [ 4.896] (==) Assigned the driver to the xf86ConfigLayout [ 4.896] (II) LoadModule: "nvidia" [ 4.896] (II) Loading /usr/lib/x86_64-linux-gnu/xorg/extra-modules/nvidia_drv.so [ 4.896] (II) Module nvidia: vendor="NVIDIA Corporation" [ 4.896] compiled for 4.0.2, module version = 1.0.0 [ 4.896] Module class: X.Org Video Driver [ 4.896] (II) UnloadModule: "nvidia" [ 4.896] (II) Unloading nvidia [ 4.896] (II) Failed to load module "nvidia" (already loaded, 32610) [ 4.896] (II) LoadModule: "nouveau" [ 4.897] (II) Loading /usr/lib/xorg/modules/drivers/nouveau_drv.so [ 4.897] (II) Module nouveau: vendor="X.Org Foundation" [ 4.897] compiled for 1.11.3, module version = 1.0.2 [ 4.897] Module class: X.Org Video Driver [ 4.897] ABI class: X.Org Video Driver, version 11.0 [ 4.897] (II) UnloadModule: "nouveau" [ 4.897] (II) Unloading nouveau [ 4.897] (II) Failed to load module "nouveau" (already loaded, 32610) [ 4.897] (II) LoadModule: "nv" [ 4.897] (WW) Warning, couldn't open module nv [ 4.897] (II) UnloadModule: "nv" [ 4.897] (II) Unloading nv [ 4.897] (EE) Failed to load module "nv" (module does not exist, 0) [ 4.897] (II) LoadModule: "vesa" [ 4.898] (II) Loading /usr/lib/xorg/modules/drivers/vesa_drv.so [ 4.898] (II) Module vesa: vendor="X.Org Foundation" [ 4.898] compiled for 1.11.3, module version = 2.3.0 [ 4.898] Module class: X.Org Video Driver [ 4.898] ABI class: X.Org Video Driver, version 11.0 [ 4.898] (II) UnloadModule: "vesa" [ 4.898] (II) Unloading vesa [ 4.898] (II) Failed to load module "vesa" (already loaded, 0) [ 4.898] (II) LoadModule: "fbdev" [ 4.898] (II) Loading /usr/lib/xorg/modules/drivers/fbdev_drv.so [ 4.898] (II) Module fbdev: vendor="X.Org Foundation" [ 4.898] compiled for 1.11.3, module version = 0.4.2 [ 4.898] ABI class: X.Org Video Driver, version 11.0 [ 4.898] (II) UnloadModule: "fbdev" [ 4.898] (II) Unloading fbdev [ 4.899] (II) Failed to load module "fbdev" (already loaded, 0) [ 4.899] (II) NVIDIA dlloader X Driver 295.40 Thu Apr 5 21:38:35 PDT 2012 [ 4.899] (II) NVIDIA Unified Driver for all Supported NVIDIA GPUs [ 4.899] (II) NOUVEAU driver Date: Wed Sep 12 13:42:43 2012 +0200 [ 4.899] (II) NOUVEAU driver for NVIDIA chipset families : [ 4.899] RIVA TNT (NV04) [ 4.899] RIVA TNT2 (NV05) [ 4.899] GeForce 256 (NV10) [ 4.899] GeForce 2 (NV11, NV15) [ 4.899] GeForce 4MX (NV17, NV18) [ 4.899] GeForce 3 (NV20) [ 4.900] GeForce 4Ti (NV25, NV28) [ 4.900] GeForce FX (NV3x) [ 4.900] GeForce 6 (NV4x) [ 4.900] GeForce 7 (G7x) [ 4.900] GeForce 8 (G8x) [ 4.900] GeForce GTX 200 (NVA0) [ 4.900] GeForce GTX 400 (NVC0) [ 4.900] (II) VESA: driver for VESA chipsets: vesa [ 4.900] (II) FBDEV: driver for framebuffer: fbdev [ 4.900] (++) using VT number 7 [ 4.902] (II) Loading sub module "fb" [ 4.902] (II) LoadModule: "fb" [ 4.902] (II) Loading /usr/lib/xorg/modules/libfb.so [ 4.902] (II) Module fb: vendor="X.Org Foundation" [ 4.902] compiled for 1.11.3, module version = 1.0.0 [ 4.902] ABI class: X.Org ANSI C Emulation, version 0.4 [ 4.902] (II) Loading sub module "wfb" [ 4.902] (II) LoadModule: "wfb" [ 4.903] (II) Loading /usr/lib/xorg/modules/libwfb.so [ 4.905] (II) Module wfb: vendor="X.Org Foundation" [ 4.905] compiled for 1.11.3, module version = 1.0.0 [ 4.905] ABI class: X.Org ANSI C Emulation, version 0.4 [ 4.905] (II) Loading sub module "ramdac" [ 4.905] (II) LoadModule: "ramdac" [ 4.905] (II) Module "ramdac" already built-in [ 4.907] (II) Loading /usr/lib/x86_64-linux-gnu/xorg/extra-modules/nvidia_drv.so [ 4.907] (II) Loading /usr/lib/xorg/modules/libwfb.so [ 4.907] (II) Loading /usr/lib/xorg/modules/libfb.so [ 4.912] (WW) Falling back to old probe method for vesa [ 4.912] (WW) Falling back to old probe method for fbdev [ 4.912] (II) Loading sub module "fbdevhw" [ 4.912] (II) LoadModule: "fbdevhw" [ 4.912] (II) Loading /usr/lib/xorg/modules/libfbdevhw.so [ 4.912] (II) Module fbdevhw: vendor="X.Org Foundation" [ 4.912] compiled for 1.11.3, module version = 0.0.2 [ 4.912] ABI class: X.Org Video Driver, version 11.0 [ 4.912] (II) NVIDIA(0): Creating default Display subsection in Screen section "Default Screen Section" for depth/fbbpp 24/32 [ 4.912] (==) NVIDIA(0): Depth 24, (==) framebuffer bpp 32 [ 4.912] (==) NVIDIA(0): RGB weight 888 [ 4.912] (==) NVIDIA(0): Default visual is TrueColor [ 4.912] (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) [ 4.912] (**) NVIDIA(0): Enabling 2D acceleration [ 5.442] (EE) NVIDIA(0): Failed to initialize the display subsystem for the NVIDIA [ 5.442] (EE) NVIDIA(0): graphics device! [ 5.442] (EE) NVIDIA(0): Failed to get supported display device(s) [ 5.442] (EE) NVIDIA(0): Failed to initialize dac HAL [ 5.442] (II) UnloadModule: "nvidia" [ 5.442] (II) Unloading nvidia [ 5.442] (II) UnloadModule: "wfb" [ 5.442] (II) Unloading wfb [ 5.442] (II) UnloadModule: "fb" [ 5.443] (II) Unloading fb [ 5.443] (EE) Screen(s) found, but none have a usable configuration. [ 5.443] Fatal server error: [ 5.443] no screens found [ 5.443] Please consult the The X.Org Foundation support at http://wiki.x.org for help. [ 5.443] Please also check the log file at "/var/log/Xorg.0.log" for additional information. [ 5.443] [ 5.447] ddxSigGiveUp: Closing log [ 5.447] Server terminated with error (1). Closing log file.

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• Java PlayFramework & Python Django GAE

  - by Maik Klein

  I already know Java, C# and C++. Now I want to start with web development and I saw that some really big sites are built with Python/C++. I like the coding style of Python, it looks really clean, but some other things like no errors before runtime is really strange. However, I don't know what I should learn now. I started with Python but then I saw that Google App Engine also supports Java and the PlayFramework looks amazing too. Now I am really confused. Should I go with Python or Java? I found the IDE for Python "PyCharm" really amazing for web development. Does Java have something similar, eclipse maybe? I know that this question isn't constructive, but it will help me with my decision. What are pro and cons of both languages?

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• How to familiarize myself with Python

  - by Zel

  I am Python beginner. Started Python 1.5 months back. I downloaded the Python docs and read some part of the tutorial. I have been programming on codechef.com and solving problems of projecteuler. I am thinking of reading Introduction to algorithms and following this course on MIT opencourse ware as I haven't been getting much improvement in programming and I am wasting much time thinking just what should I do when faced with any programming problem. But I think that I still don't know the correct way to learn the language itself. Should I start the library reference or continue with Python tutorial? Is learning algorithms useful for language such as C and not so much for Python as it has "batteries included"? Are there some other resources for familiarization with the language and in general for learning to solve programming problems? Or do I need to just devote some more time?

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• Typing commands into a terminal always returns "-bash: /usr/bin/python: is a directory"

  - by Artur Sapek

  I think I messed something up on my Ubuntu server while trying to upgrade to Python 2.7.2. Every time I type in a command that doesn't have a response, the default from bash is this: -bash: /usr/bin/python: is a directory Just like it would say if I typed the name of a directory. But this happens every time I enter a command that doesn't do anything. artur@SERVER:~$ dslkfjdsklfdshjk -bash: /usr/bin/python: is a directory I remember messing with the update-alternatives to point at python at some point, perhaps that could be it? Any inklings as to why this is happening? Related to this problem is also the fact that when I try using easy_install it tells me -bash: /usr/bin/easy_install: /usr/bin/python: bad interpeter: Permission denied /etc/fstab/ is set to exec. I've read that could fix the second problem but it hasn't.

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• How to make a python script run in Anacron

  - by Jeremy

  I have a python script that I would like to run daily using anacron, but I haven't been able to get it to work. The script is in my home directory, and I have put a symlink to it in /etc/cron.daily/. I saw somewhere that things here can't have dots in the filename, so the symlink has the .py extension removed (the original file still has it). The python file does have #!/usr/bin/python on the first line. This is my first experience with cron / anacron, and so I'm sure I'm making a dumb mistake - I just don't know what it is. Is a symlink a problem? Do I need the actual file there? Is the python script the problem? Do I need to run a bash script that will open the python script? Is there something else I'm not thinking of?

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• Python script as a service on Ubuntu 11.10

  - by bugs99

  I am facing the following problem. I want to run a python script as a service on Ubuntu 11.10 system (already mentioned in the following link: Python service using Upstart on Ubuntu) I followed the steps mentioned in the above mentioned link, but i got the following error message in syslog: init: script main process (21826) terminated with status 1 Jun 8 16:59:55 bilbo kernel: [263012.984531] init: script main process ended, respawning Jun 8 16:59:55 bilbo kernel: [263013.044099] init: script main process (21827) terminated with status 1 The above two lines are getting repeated all the time. On saying sudo start script, I get the following: $ sudo start script script start/running, process 21826 Following is the content of my script.conf placed in /etc/init: description "Used to start python script as a service" author "bilbo" start on runlevel [2] stop on runlevel [06] exec python /home/bilbo/scripts/webserver.py respawn Please tell me what I am doing wrong? Do I have to change my python code as well?

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• How to install Visual Python?

  - by user214152

  I'm a Linux newbie but I'm determined to get my favorite applications on my laptop running Ubuntu 12.04. I just installed Cinnamon. I'm trying to install Visual Python and it requires Python 2.7. I followed the instructions on the VPython site but the Wine application isn't extracting anything from the Python .msi file. From the first line wine start /i python-2.7.5.amd64.msi /qn TARGETDIR=~/Python27 ALLUSERS=1 it says fixme:storage:create_storagefile Storage share mode not implemented. I created that Python27 directory so I know it exists and it's empty. I know Ubuntu already has Python 2.7 so I just tried running the VPython.exe file but it says "This program can only be installed on versions of Windows designed for the following processor architectures: x64." My Toshiba satellite has a 64-bit processor. Could anybody help?

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• Can anyone tell me why these lines are not working?

  - by user343934

  I am trying to generate tree with fasta file input and Alignment with MuscleCommandline import sys,os, subprocess from Bio import AlignIO from Bio.Align.Applications import MuscleCommandline cline = MuscleCommandline(input="c:\Python26\opuntia.fasta") child= subprocess.Popen(str(cline), stdout = subprocess.PIPE, stderr=subprocess.PIPE, shell=(sys.platform!="win32")) align=AlignIO.read(child.stdout,"fasta") outfile=open('c:\Python26\opuntia.phy','w') AlignIO.write([align],outfile,'phylip') outfile.close() I always encounter with these problems Traceback (most recent call last): File "", line 244, in run_nodebug File "C:\Python26\muscleIO.py", line 11, in align=AlignIO.read(child.stdout,"fasta") File "C:\Python26\Lib\site-packages\Bio\AlignIO_init_.py", line 423, in read raise ValueError("No records found in handle") ValueError: No records found in handle

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• Python repl in python application

  - by Olorin

  Hello i am learning python(so i can use qt with python not only c++) and i'm curios if it would be possible to embed a python interpreter in my application as a repl. I would like to give users to possibility to script the app using python either loading a file (and that file to act as a plugin for the app) or by evaluating code entered in a text box or something like that. Just like you can embed the interpreter in C or C++ and script the app using python can this be done if the application is itself written in python(and made a stand-alone binary using py2exe or something similar)? something like Anders did with the C# repl or Miguel with mono. Thanks.

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• Using Python on Mac

  - by choise

  hi, i want to learn python using my mac. now i want to setup a python version = 3.1.3, because my materials for learning are using this version. typing python into terminal results version 2.6.1, using the dmg installer on python.org (http://docs.python.org/ftp/python/3.1.3/) doesn't have an effect on the python version in terminal, but it's bundled with an own shell under Applications/Python 3.1/Idle.app my question now is, should i use this shell for learing or is there a better way, updating the python version bundled with snow leopard? i already tried defaults write com.apple.versioner.python Version 3.1.3 or defaults write com.apple.versioner.python Version 3.0 without any result. thanks!

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• Until when will Python 2.5 be supported?

  - by Emilien

  Apparently Python only supports 2 minor versions (like 2.X), so that would mean Python 2.5 would get phased out when Python 2.7 comes out (in June 2010?) Is this correct? PEP 356 -- Python 2.5 Release Schedule doesn't give much answers to this question.

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• No IDLE for Python 3?

  - by NotSuper

  I installed Python 3.1 yesterday on my Windows Vista PC, and was surprised to find that the version of IDLE is 2.6.4, for "Python 2.6.4 (r264:75708, Oct 26 2009, 08:23:19) [MSC v.1500 32 bit (Intel)] on win32" I was hoping to use IDLE to investigate some of the new features of Python 3... I guess I'm stuck with the command line... Anyone know what's up with Python 3's IDLE? Thanks

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• Replacement for htmllib module in Python 3.0

  - by Abbas

  I want to use the htmllib module but it's been removed from Python 3.0. Does anyone know what's the replacement for this module?

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• Using python decorator functions from a different module

  - by user328069

  I want to use a function from another module as a decorator, but I need it to manipulate the current module's global namespace. For example, I want to be able to go from this: class SomeClass: pass root = SomeClass to this: from othermodule import decorator @decorator class Someclass: pass Any ideas?

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• Python - Subprocess Popen and Thread error

  - by n0idea

  In both functions record and ftp, i have subprocess.Popen if __name__ == '__main__': try: t1 = threading.Thread(target = record) t1.daemon = True t1.start() t2 = threading.Thread(target = ftp) t2.daemon = True t2.start() except (KeyboardInterrupt, SystemExit): sys.exit() The error I'm receiving is: Exception in thread Thread-1 (most likely raised during interpreter shutdown): Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 551, in __bootstrap_inner File "/usr/lib/python2.7/threading.py", line 504, in run File "./in.py", line 20, in recordaudio File "/usr/lib/python2.7/subprocess.py", line 493, in call File "/usr/lib/python2.7/subprocess.py", line 679, in __init__ File "/usr/lib/python2.7/subprocess.py", line 1237, in _execute_child <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'close' What might the issue be ?

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• Killing a subprocess including its children from python

  - by user316664

  Hi, I'm using the subprocess module on python 2.5 to spawn a java program (the selenium server, to be precise) as follows: import os import subprocess display = 0 log_file_path = "/tmp/selenium_log.txt" selenium_port = 4455 selenium_folder_path = "/wherever/selenium/lies" env = os.environ env["DISPLAY"] = ":%d.0" % display command = ["java", "-server", "-jar", 'selenium-server.jar', "-port %d" % selenium_port] log = open(log_file_path, 'a') comm = ' '.join(command) selenium_server_process = subprocess.Popen(comm, cwd=selenium_folder_path, stdout=log, stderr=log, env=env, shell=True) This process is supposed to get killed once the automated tests are finished. I'm using os.kill to do this: os.killpg(selenium_server_process.pid, signal.SIGTERM) selenium_server_process.wait() This does not work. The reason is that the shell subprocess spawns another processfor the java program, and the pid of that process is unknown to my python code. I've tried killing the process group with os.killpg, but that kills also the python process which runs this code in the first place. Setting shell to false, thus avoiding the java program to run inside a shell environment, is also out of the question, due to other reasons. Does anyone have an idea how I can kill the shell and any other processes generated by it? Cheers, Ulas

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• How to get path to the installed GIT in Python?

  - by Vladimir Prudnikov

  I need to get a path to the GIT on Max OS X 10.6 using Python 2.6.1 into script variables. I use this code for that: r = subprocess.Popen(shlex.split("which git"), stdout=subprocess.PIPE) print r.stdout.read() but the problem is that output is empty (I tried stderr too). It works fine with another commands such as pwd or ls. Can anyone help me with that?

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• Why use Python interactive mode?

  - by mvid

  When I first started reading about Python, all of the tutorials have you use Python's Interactive Mode. It is difficult to save, write long programs, or edit your existing lines (for me at least). It seems like a far more difficult way of writing Python code than opening up a code.py file and running the interpreter on that file. python code.py I am coming from a Java background, so I have ingrained expectations of writing and compiling files for programs. I also know that a feature would not be so prominent in Python documentation if it were not somehow useful. So what am I missing?

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• Boost.Python tutorial in Ubuntu 10.04

  - by Doughy

  I downloaded the latest version of Boost and I'm trying to get the Boost.python tutorial up and running on Ubuntu 10.04: http://www.boost.org/doc/libs/1_43_0/libs/python/doc/tutorial/doc/html/python/hello.html I navigated to the correct directory, ran "bjam" and it compiled using default settings. I did not yet create a bjam config file. The compilation appears to have worked, but now I have no idea how to include the files in my python script. When I try to run the python hello world script, it gives me this error: Traceback (most recent call last): File "./hello.py", line 6, in <module> import hello_ext ImportError: libboost_python.so.1.43.0: cannot open shared object file: No such file or directory Anyone know what is going on?

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• Avoiding accidentally catching KeyboardInterrupt and SystemExit in Python 2.4

  - by jrdioko

  In Python scripts, there are many cases where a keyboard interrupt (Ctrl-C) fails to kill the process because of a bare except clause somewhere in the code: try: foo() except: bar() The standard solution in Python 2.5 or higher is to catch Exception rather than using bare except clauses: try: foo() except Exception: bar() This works because, as of Python 2.5, KeyboardInterrupt and SystemExit inherit from BaseException, not Exception. However, some installations are still running Python 2.4. How can this problem be handled in versions prior to Python 2.5? (I'm going to answer this question myself, but putting it here so people searching for it can find a solution.)

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