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• Why do I get error, Invalid command 'PythonHandler'?

  - by nbolton

  I'm trying to deploy a Django application, but I've hit a brick wall. On Debian (latest), I've run these commands so far: apt-get install apache2 apache2-doc apache2-mpm-prefork apache2-utils libexpat1 ssl-cert libapache2-mod-python python-django I've tried adding the module manually in the Apache 2 config files, but to be honest I'm totally lost. It's totally different to Apache version 1 which I used years ago. Syntax error on line 7 of /etc/apache2/sites-enabled/000-default: Invalid command 'PythonHandler', perhaps misspelled or defined by a module not included in the server configuration I've added the following to my sites-available/default file, between the tags. <Location "/"> SetHandler python-program PythonHandler django.core.handlers.modpython SetEnv DJANGO_SETTINGS_MODULE hellodjango1.settings PythonDebug Off </Location> Here's what tutorials I've used so far, without much luck: Django | How to use Django with Apache and mod_python | Django Documentation How To Install Django On Debian Etch (Apache2/mod_python)

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• How to remove package from apt-get autoremove "queue"

  - by Darth

  I just installed Calibre for ebook management via apt-get on Ubuntu 10.04, however I found out that it's one major version behind the current release, so I decided to reinstall it directly from sources. When I uninstalled the packaged version, apt added bunch of dependencies to the autoremove queue, and as I installed newer version of Calibre from sources, it has no knowledge of it being dependent on those packages. Now I basically have all libraries that I want, but they are still in the autoremove queue. The following packages were automatically installed and are no longer required: libqt4-script libqt4-designer libqt4-dbus python-lxml python-cherrypy3 python-encutils libqt4-xmlpatterns libqt4-help python-qt4 python-clientform python-sip python-django python-mechanize libqt4-svg python-django-tagging libphonon4 libqt4-xml libqt4-assistant libqt4-webkit libqt4-scripttools python-beautifulsoup python-pypdf python-dateutil python-cssutils Use 'apt-get autoremove' to remove them. How do I tell apt that I want to keep these packages installed, without reinstalling them manually?

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• Vim */dyn support

  - by galymzhan

  What does mean the plus sign before */dyn in the :version command's output, e.g.: +python/dyn +python3/dyn +ruby/dyn +tcl/dyn I didn't find any useful documentation on it. When I run :echo has('python3') Vim returns 0. When I run :python3 print('hi') it says E370: Could not load library python31.dll meaning I should install python (as I understand). So I just can't see the difference between -*/dyn and +*/dyn. What does plus sign give to us? Also what's the difference from dyn-less feature, e.g. +python?

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• installing Gevent on OSX

  - by Dev9281

  >>> import gevent Traceback (most recent call last): File "<stdin>", line 1, in <module> File "build/bdist.macosx-10.6-universal/egg/gevent/__init__.py", line 41, in <module> File "build/bdist.macosx-10.6-universal/egg/gevent/core.py", line 7, in <module> File "build/bdist.macosx-10.6-universal/egg/gevent/core.py", line 6, in __bootstrap__ ImportError: dlopen(/Users/admin/.python-eggs/gevent-0.13.6-py2.6-macosx-10.6-universal.egg-tmp/gevent/core.so, 2): Symbol not found: _event_global_current_base_ Referenced from: /Users/admin/.python-eggs/gevent-0.13.6-py2.6-macosx-10.6-universal.egg-tmp/gevent/core.so Expected in: flat namespace in /Users/admin/.python-eggs/gevent-0.13.6-py2.6-macosx-10.6-universal.egg-tmp/gevent/core.so What's this about? I did not get any errors during the installation

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• Is there any way to isolate the python2.7 , mod_wsgi installation from main environment

  - by user31

  I have many local virtual machines for building the django websites. I find it very hard to configure all the machines with mod_wsgi , python and all that installation issues. Is there any way that i can install even python 2.7 , mod_wsgi etc and all that inside the virtual environment folder so that i can just copy paste that folder in my live server and i don't need to mess with mos_wsgi , python 2.7 and other issues. Is it possible or even any close variation of that so that puting the site to live servers is very easy and everything which is needed by site should be included locally I also face many problems when i need to move the django sites across servers

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• How do I prevent rpmbuild form injecting requirements into RPM package?

  - by Basilevs

  I'm creating an RPM package from native Python 2.5 one. Out corporate policy is to use python2.4 by default, so I'm adding a string Requires: python25 to a .spec file. When I look at created RPM file though, i see the following dependencies: rpm -qR -p ZSI-2.1_a1-py25.noarch.rpm /usr/bin/python2.5 python(abi) = 2.5 python25 rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Dependency added by me is present, but other dependencies are also here. I'm unable to provide python(abi) = 2.5 dependency, because of dumb python25 package generated by our IT department where provides tag is incorrect. How do I remove automatically added dependencies from generated RPM?

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• Apache: Use Specific Applicaion for CGI scripts

  - by RandomInsano

  I have two servers, one in production and one for development. The production server is Solaris, dev is FreeBSD. Because of this, python is installed in different directories. I'm using Python right now for making CGI scripts, and needing to remember to swap my hashbangs when I copy from dev to production is a little annoying (Same issue for SVN updates depending on which server I'm comitting from). Is there a way to configure apache so that I no longer need to hashbangs? Like, if it would lauch python and supply the CGI script for it? Might be a bit of a stretch, but no harm in asking

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• Dropbox.py on RHEL 6

  - by Timothy R. Butler

  I'm trying to run a headless install of Dropbox on RHEL 6. The daemon seems to be running, but when I try to use Dropbox's associated dropbox.py tool to control the daemon, it fails to run with the following error: Traceback (most recent call last): File "./dropbox.py", line 26, in <module> import locale File "/usr/lib64/python2.6/locale.py", line 202, in <module> import re, operator ImportError: /home/dropbox/.dropbox-dist/operator.so: undefined symbol: _PyUnicodeUCS2_AsDefaultEncodedString I'm running the current RHEL build of Python 2.6: root@cedar [/home/dropbox/.dropbox-dist]# rpm -qv python python-2.6.6-29.el6_3.3.x86_64 (I'm not sure if this would be better suited to Stack Overflow since it is on the verge of being a programming issue, but since I'm trying to use a program straight from Dropbox, I placed it here.)

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• Where is OS X's $PATH set?

  - by thepurplepixel

  I have a little $PATH problem: I just reinstalled MacPorts, and my path contains the MacPorts directories as it should at the beginning of $PATH. However, despite me having no such setting in my ~/.bashrc, ~/.bash_profile or ~/.profile, /Library/Frameworks/Python.framework/Versions/2.6/bin is somehow getting appended to the beginning of my $PATH: 0 07:15:11pm ~ $ echo $PATH /Library/Frameworks/Python.framework/Versions/2.6/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin I'd like to remove it as the MacPorts version of Python is newer. This must be appended after all the above-listed files are read, but I can't think of where. There is no mention of this in /etc/profile, /etc/bashrc or /etc/paths. Any assistance would be greatly appreciated. Thanks!

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• SSL in tomcat with apr and Centos 6

  - by Jonathan

  I'm facing a problem setting up my tomcat with apr native lib, I have the following: Tomcat: 7.0.42 Java: 1.7.0_40-b43 OS: Centos 6.4 (2.6.32-358.18.1.el6.i686) APR: 1.3.9 Native lib: 1.1.27 OpenSSL: openssl-1.0.0-27.el6_4.2.i686 My server.xml looks like: ... <Listener className="org.apache.catalina.core.AprLifecycleListener" SSLEngine="on" /> ... <Connector port="8443" protocol="HTTP/1.1" SSLEnabled="true" maxThreads="150" scheme="https" secure="true" clientAuth="false" sslProtocol="TLS" SSLCertificateFile="/tmp/monitoringPortalCert.pem" SSLCertificateKeyFile="/tmp/monitoringPortalKey.pem" SSLPassword="hide" /> ... I compiled the native lib as follow: ./configure --with-apr=/usr/bin/apr-1-config --with-ssl=yes --prefix=$CATALINA_HOME make && make install The APR is loaded ok: Oct 06, 2013 7:55:14 PM org.apache.catalina.core.AprLifecycleListener init INFO: Loaded APR based Apache Tomcat Native library 1.1.27 using APR version 1.3.9. But I'm still having this error: SEVERE: Failed to initialize the SSLEngine. org.apache.tomcat.jni.Error: 70023: This function has not been implemented on this platform ./configure outcome [root@localhost native]# ./configure --with-apr=/usr/bin/apr-1-config --with-ssl=yes -- prefix=$CATALINA_HOME && make && make install checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking target system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking for working mkdir -p... yes Tomcat Native Version: 1.1.27 checking for chosen layout... tcnative checking for APR... yes setting CC to "gcc" setting CPP to "gcc -E" checking for JDK location (please wait)... /usr/java/jdk1.7.0_40 from environment checking Java platform... checking Java platform... checking for sablevm... NONE adding "-I/usr/java/jdk1.7.0_40/include" to TCNATIVE_PRIV_INCLUDES checking os_type directory... linux adding "-I/usr/java/jdk1.7.0_40/include/linux" to TCNATIVE_PRIV_INCLUDES checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for OpenSSL library... using openssl from /usr/lib and /usr/include checking OpenSSL library version... ok checking for OpenSSL DSA support... yes setting TCNATIVE_LDFLAGS to "-lssl -lcrypto" adding "-DHAVE_OPENSSL" to CFLAGS setting TCNATIVE_LIBS to "" setting TCNATIVE_LIBS to " /usr/lib/libapr-1.la -lpthread" configure: creating ./config.status config.status: creating tcnative.pc config.status: creating Makefile config.status: executing default commands make[1]: Entering directory `/usr/apache-tomcat-7.0.42/bin/tomcat-native-1.1.27- src/jni/native' make[1]: Nothing to be done for `local-all'. make[1]: Leaving directory `/usr/apache-tomcat-7.0.42/bin/tomcat-native-1.1.27- src/jni/native' make[1]: Entering directory `/usr/apache-tomcat-7.0.42/bin/tomcat-native-1.1.27- src/jni/native' make[1]: Nothing to be done for `local-all'. make[1]: Leaving directory `/usr/apache-tomcat-7.0.42/bin/tomcat-native-1.1.27- src/jni/native' /usr/lib/apr-1/build/mkdir.sh /usr/apache-tomcat-7.0.42/include/apr-1 /usr/apache- tomcat-7.0.42/lib/pkgconfig \ /usr/apache-tomcat-7.0.42/lib /usr/apache-tomcat-7.0.42/bin /usr/bin/install -c -m 644 tcnative.pc /usr/apache-tomcat-7.0.42/lib/pkgconfig/tcnative- 1.pc list=''; for i in $list; do \ ( cd $i ; make DESTDIR= install ); \ done /bin/sh /usr/lib/apr-1/build/libtool --mode=install /usr/bin/install -c -m 755 libtcnative-1.la /usr/apache-tomcat-7.0.42/lib libtool: install: /usr/bin/install -c -m 755 .libs/libtcnative-1.so.0.1.27 /usr/apache- tomcat-7.0.42/lib/libtcnative-1.so.0.1.27 libtool: install: (cd /usr/apache-tomcat-7.0.42/lib && { ln -s -f libtcnative- 1.so.0.1.27 libtcnative-1.so.0 || { rm -f libtcnative-1.so.0 && ln -s libtcnative- 1.so.0.1.27 libtcnative-1.so.0; }; }) libtool: install: (cd /usr/apache-tomcat-7.0.42/lib && { ln -s -f libtcnative- 1.so.0.1.27 libtcnative-1.so || { rm -f libtcnative-1.so && ln -s libtcnative-1.so.0.1.27 libtcnative-1.so; }; }) libtool: install: /usr/bin/install -c -m 755 .libs/libtcnative-1.lai /usr/apache-tomcat- 7.0.42/lib/libtcnative-1.la libtool: install: /usr/bin/install -c -m 755 .libs/libtcnative-1.a /usr/apache-tomcat- 7.0.42/lib/libtcnative-1.a libtool: install: chmod 644 /usr/apache-tomcat-7.0.42/lib/libtcnative-1.a libtool: install: ranlib /usr/apache-tomcat-7.0.42/lib/libtcnative-1.a libtool: install: warning: remember to run `libtool --finish /usr/local/apr/lib' make && make install outcome: make[1]: Entering directory `/usr/apache-tomcat-7.0.42/bin/tomcat-native-1.1.27- src/jni/native' make[1]: Nothing to be done for `local-all'. make[1]: Leaving directory `/usr/apache-tomcat-7.0.42/bin/tomcat-native-1.1.27- src/jni/native' make[1]: Entering directory `/usr/apache-tomcat-7.0.42/bin/tomcat-native-1.1.27- src/jni/native' make[1]: Nothing to be done for `local-all'. make[1]: Leaving directory `/usr/apache-tomcat-7.0.42/bin/tomcat-native-1.1.27- src/jni/native' /usr/lib/apr-1/build/mkdir.sh /usr/apache-tomcat-7.0.42/include/apr-1 /usr/apache- tomcat-7.0.42/lib/pkgconfig \ /usr/apache-tomcat-7.0.42/lib /usr/apache-tomcat-7.0.42/bin /usr/bin/install -c -m 644 tcnative.pc /usr/apache-tomcat-7.0.42/lib/pkgconfig/tcnative- 1.pc list=''; for i in $list; do \ ( cd $i ; make DESTDIR= install ); \ done /bin/sh /usr/lib/apr-1/build/libtool --mode=install /usr/bin/install -c -m 755 libtcnative-1.la /usr/apache-tomcat-7.0.42/lib libtool: install: /usr/bin/install -c -m 755 .libs/libtcnative-1.so.0.1.27 /usr/apache- tomcat-7.0.42/lib/libtcnative-1.so.0.1.27 libtool: install: (cd /usr/apache-tomcat-7.0.42/lib && { ln -s -f libtcnative- 1.so.0.1.27 libtcnative-1.so.0 || { rm -f libtcnative-1.so.0 && ln -s libtcnative- 1.so.0.1.27 libtcnative-1.so.0; }; }) libtool: install: (cd /usr/apache-tomcat-7.0.42/lib && { ln -s -f libtcnative- 1.so.0.1.27 libtcnative-1.so || { rm -f libtcnative-1.so && ln -s libtcnative-1.so.0.1.27 libtcnative-1.so; }; }) libtool: install: /usr/bin/install -c -m 755 .libs/libtcnative-1.lai /usr/apache-tomcat- 7.0.42/lib/libtcnative-1.la libtool: install: /usr/bin/install -c -m 755 .libs/libtcnative-1.a /usr/apache-tomcat- 7.0.42/lib/libtcnative-1.a libtool: install: chmod 644 /usr/apache-tomcat-7.0.42/lib/libtcnative-1.a libtool: install: ranlib /usr/apache-tomcat-7.0.42/lib/libtcnative-1.a libtool: install: warning: remember to run `libtool --finish /usr/local/apr/lib' It seems everything is fine, but the error is not self-explanatory Could you guys help to understand where my error is? What am I missing? Thanks in advance for your support.

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• I am getting this error on using matplotlib

  - by Arun Abraham

  I get this error on typing this in python command prompt: import matplotlib.pyplot as plt Traceback (most recent call last): File "<pyshell#1>", line 1, in <module> import matplotlib.pyplot as plt File "/Library/Python/2.7/site-packages/matplotlib-1.3.x-py2.7-macosx-10.8-intel.egg/matplotlib/pyplot.py", line 97, in <module> _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup() File "/Library/Python/2.7/site-packages/matplotlib-1.3.x-py2.7-macosx-10.8-intel.egg/matplotlib/backends/__init__.py", line 25, in pylab_setup globals(),locals(),[backend_name]) File "/Library/Python/2.7/site-packages/matplotlib-1.3.x-py2.7-macosx-10.8-intel.egg/matplotlib/backends/backend_macosx.py", line 21, in <module> from matplotlib.backends import _macosx ImportError: dlopen(/Library/Python/2.7/site-packages/matplotlib-1.3.x-py2.7-macosx-10.8-intel.egg/matplotlib/backends/_macosx.so, 2): Library not loaded: /System/Library/Frameworks/CoreText.framework/Versions/A/CoreText Referenced from: /Library/Python/2.7/site-packages/matplotlib-1.3.x-py2.7-macosx-10.8-intel.egg/matplotlib/backends/_macosx.so Reason: image not found Can someone suggest me, how i can fix this ? I had installed all the packages with this shell script https://github.com/fonnesbeck/ScipySuperpack Is there anything that i am missing ? Any additional configuration ?

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• error when plotting log'd array in matplotlib/scipy/numpy

  - by user248237

  I have two arrays and I take their logs. When I do that and try to plot their scatter plot, I get this error: File "/Library/Python/2.6/site-packages/matplotlib-1.0.svn_r7892-py2.6-macosx-10.6-universal.egg/matplotlib/pyplot.py", line 2192, in scatter ret = ax.scatter(x, y, s, c, marker, cmap, norm, vmin, vmax, alpha, linewidths, faceted, verts, **kwargs) File "/Library/Python/2.6/site-packages/matplotlib-1.0.svn_r7892-py2.6-macosx-10.6-universal.egg/matplotlib/axes.py", line 5384, in scatter self.add_collection(collection) File "/Library/Python/2.6/site-packages/matplotlib-1.0.svn_r7892-py2.6-macosx-10.6-universal.egg/matplotlib/axes.py", line 1391, in add_collection self.update_datalim(collection.get_datalim(self.transData)) File "/Library/Python/2.6/site-packages/matplotlib-1.0.svn_r7892-py2.6-macosx-10.6-universal.egg/matplotlib/collections.py", line 153, in get_datalim offsets = transOffset.transform_non_affine(offsets) File "/Library/Python/2.6/site-packages/matplotlib-1.0.svn_r7892-py2.6-macosx-10.6-universal.egg/matplotlib/transforms.py", line 1924, in transform_non_affine self._a.transform(points)) File "/Library/Python/2.6/site-packages/matplotlib-1.0.svn_r7892-py2.6-macosx-10.6-universal.egg/matplotlib/transforms.py", line 1420, in transform return affine_transform(points, mtx) ValueError: Invalid vertices array. the code is simply: myarray_x = log(my_array[:, 0]) myarray_y = log(my_array[:, 1]) plt.scatter(myarray_x, myarray_y) any idea what could be causing this? thanks.

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• ‘Empty’ results from MQL Query. Freebase Schema: /film/film/starring & /film/actor/film

  - by user1879631

  First post here, so I hope this is enough detail. I started using freebase-python today to get film information for a program that I’m working on. One thing that I need to grab is a list of actors that starred in a film. I’ve followed some tutorials and guides on the way to do this, and can get a list of films for a director or the director of a film, but when I try to do the same with an actor or a film’s cast, I get ‘null’ results. I have the same problem in both Python and the Freebase MQL Query Editor, and you can see what I've tried below. Links to all of the examples below written in the editor can be found here, as Stack Overflow wouldn't let me post links underneath each example on my first post! Working director query in Python: import freebase fb = freebase.mqlread q = {'type':'/film/film', 'name':'Inception', 'directed_by':[]} fb(q) Working director's filmography query in Python: import freebase fb = freebase.mqlread q = {'type':'/film/director', 'name': 'Christopher Nolan', 'film':[]} fb(q) Based on these tests, I tried to do the same with actors, but with odd results: Not working cast list query in Python: import freebase fb = freebase.mqlread q = {'type':'/film/film', 'name':'Inception', 'starring':[]} fb(q) Not working actor's filmography query in Python: import freebase fb = freebase.mqlread q = {'type':'/film/actor', 'name':'Leonardo DiCaprio', 'film':[]} fb(q) Strangely, I get an accurate number of actors/films back, but no names. Does anyone have any idea what the problem might be? Thanks a lot, I'd appreciate any advice.

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• Distutils - Where Am I going wrong?

  - by RJBrady

  I wanted to learn how to create python packages, so I visited http://docs.python.org/distutils/index.html. For this exercise I'm using Python 2.6.2 on Windows XP. I followed along with the simple example and created a small test project: person/ setup.py person/ __init__.py person.py My person.py file is simple: class Person(object): def __init__(self, name="", age=0): self.name = name self.age = age def sound_off(self): print "%s %d" % (self.name, self.age) And my setup.py file is: from distutils.core import setup setup(name='person', version='0.1', packages=['person'], ) I ran python setup.py sdist and it created MANIFEST, dist/ and build/. Next I ran python setup.py install and it installed it to my site packages directory. I run the python console and can import the person module, but I cannot import the Person class. >>>import person >>>from person import Person Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: cannot import name Person I checked the files added to site-packages and checked the sys.path in the console, they seem ok. Why can't I import the Person class. Where did I go wrong?

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• lightweight webserver to integrate on client end.

  - by Gopal

  Hi ,... I need to create a python module that will be installed on end-user machines. One of the scripts in that module should be able to receive http POSTS (usually with some JSON formatted data in the body) and then pass on that data to an appropriate python script. I can think of two ways to do this: a) Open a listening server socket on port 80, wait for that http request to come in, parse it and then pass that data to another python script depending on the url that arrived. This method will not require the end-user to install a webserver. End user only has to install the python module. b) Have a mini-webserver installed along with the python module. The webserver will do the same job as [a] via CGI without me requiring to write the CGI functionality. But then the user will have to install the web-server (ie., the hassle of yet another install). Would like to avoid that if possible. IF [b] is the easier option, what is the smallest simplest webserver there is (preferably one that can be packaged as part of the python module itself so that it does not have to be separately installed). Must be opensource of course. regards Gopal

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• Directly call distutils' or setuptools' setup() function with command name/options, without parsing

  - by Ryan B. Lynch

  I'd like to call Python's distutils' or setuptools' setup() function in a slightly unconventional way, but I'm not sure whether distutils is meant for this kind of usage. As an example, let's say I currently have a 'setup.py' file, which looks like this (lifted verbatim from the distutils docs--the setuptools usage is almost identical): from distutils.core import setup setup(name='Distutils', version='1.0', description='Python Distribution Utilities', author='Greg Ward', author_email='[email protected]', url='http://www.python.org/sigs/distutils-sig/', packages=['distutils', 'distutils.command'], ) Normally, to build just the .spec file for an RPM of this module, I could run python setup.py bdist_rpm --spec-only, which parses the command line and calls the 'bdist_rpm' code to handle the RPM-specific stuff. The .spec file ends up in './dist'. How can I change my setup() invocation so that it runs the 'bdist_rpm' command with the '--spec-only' option, WITHOUT parsing command-line parameters? Can I pass the command name and options as parameters to setup()? Or can I manually construct a command line, and pass that as a parameter, instead? NOTE: I already know that I could call the script in a separate process, with an actual command line, using os.system() or the subprocess module or something similar. I'm trying to avoid using any kind of external command invocations. I'm looking specifically for a solution that runs setup() in the current interpreter. For background, I'm converting some release-management shell scripts into a single Python program. One of the tasks is running 'setup.py' to generate a .spec file for further pre-release testing. Running 'setup.py' as an external command, with its own command line options, seems like an awkward method, and it complicates the rest of the program. I feel like there may be a more Pythonic way.

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• Add Keyboard Binding To Existing Emacs Mode

  - by Sean M

  I'm attempting my first modification of emacs. I recorded a little keyboard macro and had emacs spit it out as elisp, resulting in: (setq add-docstring "\C-rdef\C-n\C-a\C-m\C-p\C-i\C-u6\"\C-u3\C-b") (global-set-key "\C-c\C-d" 'add-docstring) Searching the emacs reference, though, revealed that C-c C-d is already bound in diff mode. I don't plan on using diff mode, but the future is unknowable and I'd like to not lay a trap for myself. So I'd like this keybinding to only operate in python mode, where it tries to help me add docstrings. In my /usr/share/emacs/23.whatever/list/progmodes, I found python.elc and python.el.gz. I unzipped python.el.gz and got a readable version of the elisp file. Now, though, the documentation becomes opaque to me. How can I add my key binding to the python mode, instead of globally? Is it possible, for bonus points, to apply the changes to python mode without restarting emacs or closing open files? It's the self-modifying editor, I figure there's a good chance that it's possible.

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• BeautifulSoup HTMLParseError. What's wrong with this?

  - by user1915496

  This is my code: from bs4 import BeautifulSoup as BS import urllib2 url = "http://services.runescape.com/m=news/recruit-a-friend-for-free-membership-and-xp" res = urllib2.urlopen(url) soup = BS(res.read()) other_content = soup.find_all('div',{'class':'Content'})[0] print other_content Yet an error comes up: /Library/Python/2.7/site-packages/bs4/builder/_htmlparser.py:149: RuntimeWarning: Python's built-in HTMLParser cannot parse the given document. This is not a bug in Beautiful Soup. The best solution is to install an external parser (lxml or html5lib), and use Beautiful Soup with that parser. See http://www.crummy.com/software/BeautifulSoup/bs4/doc/#installing-a-parser for help. "Python's built-in HTMLParser cannot parse the given document. This is not a bug in Beautiful Soup. The best solution is to install an external parser (lxml or html5lib), and use Beautiful Soup with that parser. See http://www.crummy.com/software/BeautifulSoup/bs4/doc/#installing-a-parser for help.")) Traceback (most recent call last): File "web.py", line 5, in <module> soup = BS(res.read()) File "/Library/Python/2.7/site-packages/bs4/__init__.py", line 172, in __init__ self._feed() File "/Library/Python/2.7/site-packages/bs4/__init__.py", line 185, in _feed self.builder.feed(self.markup) File "/Library/Python/2.7/site-packages/bs4/builder/_htmlparser.py", line 150, in feed raise e I've let two other people use this code, and it works for them perfectly fine. Why is it not working for me? I have bs4 installed...

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• What could cause xmlrpclib.ResponseError: ResponseError() ?

  - by Tom

  Hi, I am experimenting with XML-RPC. I have the following server script (python): from SimpleXMLRPCServer import SimpleXMLRPCServer server = SimpleXMLRPCServer(('localhost', 9000)) def return_input(someinput): return someinput server.register_function(return_input) try: print 'ctrl-c to stop server' server.serve_forever() except KeyboardInterrupt: print 'stopping' and the following client script: import xmlrpclib server = xmlrpclib.ServerProxy('http://www.example.com/pathto/xmlrpcTester2.py') print server.return_input('some input') I have tested this locally and it works fine. All it does it spit out the input fron the client script, which is right. However, when I try to do it on a remote server I get the following error: Traceback (most recent call last): File "client.py", line 4, in <module> print server.return_input('some input') File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/xmlrpclib.py", line 1199, in __call__ return self.__send(self.__name, args) File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/xmlrpclib.py", line 1489, in __request verbose=self.__verbose File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/xmlrpclib.py", line 1253, in request return self._parse_response(h.getfile(), sock) File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/xmlrpclib.py", line 1392, in _parse_response return u.close() File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/xmlrpclib.py", line 836, in close raise ResponseError() xmlrpclib.ResponseError: ResponseError() Any ideas what could cause this? Thanks in advance for your help.

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• Python 3.4 adds re.fullmatch()

  - by Jan Goyvaerts

  Python 3.4 does not bring any changes to its regular expression syntax compared to previous 3.x releases. It does add one new function to the re module called fullmatch(). This function takes a regular expression and a subject string as its parameters. It returns True if the regular expression can match the string entirely. It returns False if the string cannot be matched or if it can only be matched partially. This is useful when using a regular expression to validate user input. Do note that fullmatch() will return True if the subject string is the empty string and the regular expression can find zero-length matches. A zero-length match of a zero-length string is a complete match. So if you want to check whether the user entered a sequence of digits, use \d+ rather than \d* as the regex.

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• usb wifi dongle on ubuntu server, cannot install realtek driver RTL 8188cus

  - by Sandro Dzneladze

  I got cheap Ebay wifi dongle from HongKong, Im trying to set it up on my ubuntu server. Occasionally need to move server, so it cannot always be connected to router via lan. Anyhow, usb wifi came with a driver cd. I uploaded files to my home directory and tried to run install script (RTL 8188cus): sudo bash install.sh But I get error: Authentication requested [root] for make driver: make ARCH=x86_64 CROSS_COMPILE= -C /lib/modules/2.6.38-8-server/build M=/home/minime/RTL 8188cus/Linux/driver/rtl8192CU_linux_v2.0.1324.20110126 modules make[1]: Entering directory `/usr/src/linux-headers-2.6.38-8-server' make[1]: *** No rule to make target `8188cus/Linux/driver/rtl8192CU_linux_v2.0.1324.20110126'. Stop. make[1]: Leaving directory `/usr/src/linux-headers-2.6.38-8-server' make: *** [modules] Error 2 Compile make driver error: 2, Please check error Mesg Any ideas what Im doing wrong? There is another driver folder for linux called: RTL 81XX, which doesn't have install.sh at all! I tried to use make command, but I get: make: *** No targets specified and no makefile found. Stop. Any help? this is first time I'm installing driver from source. Im on Ubuntu 11.04 server. lsusb Bus 001 Device 002: ID 0bda:8176 Realtek Semiconductor Corp. lspci -nn 00:00.0 Host bridge [0600]: Intel Corporation N10 Family DMI Bridge [8086:a000] (rev 02) 00:02.0 VGA compatible controller [0300]: Intel Corporation N10 Family Integrated Graphics Controller [8086:a001] (rev 02) 00:1b.0 Audio device [0403]: Intel Corporation N10/ICH 7 Family High Definition Audio Controller [8086:27d8] (rev 02) 00:1c.0 PCI bridge [0604]: Intel Corporation N10/ICH 7 Family PCI Express Port 1 [8086:27d0] (rev 02) 00:1d.0 USB Controller [0c03]: Intel Corporation N10/ICH 7 Family USB UHCI Controller #1 [8086:27c8] (rev 02) 00:1d.1 USB Controller [0c03]: Intel Corporation N10/ICH 7 Family USB UHCI Controller #2 [8086:27c9] (rev 02) 00:1d.2 USB Controller [0c03]: Intel Corporation N10/ICH 7 Family USB UHCI Controller #3 [8086:27ca] (rev 02) 00:1d.3 USB Controller [0c03]: Intel Corporation N10/ICH 7 Family USB UHCI Controller #4 [8086:27cb] (rev 02) 00:1d.7 USB Controller [0c03]: Intel Corporation N10/ICH 7 Family USB2 EHCI Controller [8086:27cc] (rev 02) 00:1e.0 PCI bridge [0604]: Intel Corporation 82801 Mobile PCI Bridge [8086:2448] (rev e2) 00:1f.0 ISA bridge [0601]: Intel Corporation NM10 Family LPC Controller [8086:27bc] (rev 02) 00:1f.2 IDE interface [0101]: Intel Corporation N10/ICH7 Family SATA IDE Controller [8086:27c0] (rev 02) 00:1f.3 SMBus [0c05]: Intel Corporation N10/ICH 7 Family SMBus Controller [8086:27da] (rev 02) 01:00.0 Ethernet controller [0200]: Atheros Communications Device [1969:1083] (rev c0) sudo lshw description: Desktop Computer product: To Be Filled By O.E.M. (To Be Filled By O.E.M.) vendor: To Be Filled By O.E.M. version: To Be Filled By O.E.M. serial: To Be Filled By O.E.M. width: 64 bits capabilities: smbios-2.6 dmi-2.6 vsyscall64 vsyscall32 configuration: boot=normal chassis=desktop family=To Be Filled By O.E.M. sku=To Be Filled By O.E.M. uuid=00020003-0004-0005-0006-000700080009 *-core description: Motherboard product: AD525PV3 vendor: ASRock physical id: 0 *-firmware description: BIOS vendor: American Megatrends Inc. physical id: 0 version: P1.20 date: 04/01/2011 size: 64KiB capacity: 448KiB capabilities: pci upgrade shadowing cdboot bootselect socketedrom edd int13floppy1200 int13floppy720 int13floppy2880 int5printscreen int9keyboard int14serial int17printer int10video acpi usb ls120boot zipboot biosbootspecification netboot *-cpu description: CPU product: Intel(R) Atom(TM) CPU D525 @ 1.80GHz vendor: Intel Corp. physical id: 4 bus info: cpu@0 version: Intel(R) Atom(TM) CPU D525 @ 1.80GHz serial: To Be Filled By O.E.M. slot: CPUSocket size: 1800MHz capacity: 1800MHz width: 64 bits clock: 200MHz capabilities: x86-64 fpu fpu_exception wp vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx constant_tsc arch_perfmon pebs bts rep_good nopl aperfmperf pni dtes64 monitor ds_cpl tm2 ssse3 cx16 xtpr pdcm movbe lahf_lm configuration: cores=2 enabledcores=2 threads=4 *-cache:0 description: L1 cache physical id: 5 slot: L1-Cache size: 48KiB capacity: 48KiB capabilities: internal write-back data *-cache:1 description: L2 cache physical id: 6 slot: L2-Cache size: 1MiB capacity: 1MiB capabilities: internal write-back unified *-memory description: System Memory physical id: c slot: System board or motherboard size: 2GiB *-bank:0 description: SODIMM DDR2 Synchronous 800 MHz (1.2 ns) product: ModulePartNumber00 vendor: Manufacturer00 physical id: 0 serial: SerNum00 slot: DIMM0 size: 2GiB width: 64 bits clock: 800MHz (1.2ns) *-bank:1 description: DIMM [empty] product: ModulePartNumber01 vendor: Manufacturer01 physical id: 1 serial: SerNum01 slot: DIMM1 *-pci description: Host bridge product: N10 Family DMI Bridge vendor: Intel Corporation physical id: 100 bus info: pci@0000:00:00.0 version: 02 width: 32 bits clock: 33MHz configuration: driver=agpgart-intel resources: irq:0 *-display description: VGA compatible controller product: N10 Family Integrated Graphics Controller vendor: Intel Corporation physical id: 2 bus info: pci@0000:00:02.0 version: 02 width: 32 bits clock: 33MHz capabilities: msi pm vga_controller bus_master cap_list rom configuration: driver=i915 latency=0 resources: irq:41 memory:fea80000-feafffff ioport:dc00(size=8) memory:e0000000-efffffff memory:fe900000-fe9fffff *-multimedia description: Audio device product: N10/ICH 7 Family High Definition Audio Controller vendor: Intel Corporation physical id: 1b bus info: pci@0000:00:1b.0 version: 02 width: 64 bits clock: 33MHz capabilities: pm msi pciexpress bus_master cap_list configuration: driver=HDA Intel latency=0 resources: irq:43 memory:fea78000-fea7bfff *-pci:0 description: PCI bridge product: N10/ICH 7 Family PCI Express Port 1 vendor: Intel Corporation physical id: 1c bus info: pci@0000:00:1c.0 version: 02 width: 32 bits clock: 33MHz capabilities: pci pciexpress msi pm normal_decode bus_master cap_list configuration: driver=pcieport resources: irq:40 ioport:e000(size=4096) memory:feb00000-febfffff ioport:80000000(size=2097152) *-network description: Ethernet interface product: Atheros Communications vendor: Atheros Communications physical id: 0 bus info: pci@0000:01:00.0 logical name: eth0 version: c0 serial: XX size: 100Mbit/s capacity: 1Gbit/s width: 64 bits clock: 33MHz capabilities: pm msi pciexpress vpd bus_master cap_list ethernet physical tp 10bt 10bt-fd 100bt 100bt-fd 1000bt-fd autonegotiation configuration: autonegotiation=on broadcast=yes driver=atl1c driverversion=1.0.1.0-NAPI duplex=full firmware=N/A ip=192.168.1.99 latency=0 link=yes multicast=yes port=twisted pair speed=100Mbit/s resources: irq:42 memory:febc0000-febfffff ioport:ec00(size=128) *-usb:0 description: USB Controller product: N10/ICH 7 Family USB UHCI Controller #1 vendor: Intel Corporation physical id: 1d bus info: pci@0000:00:1d.0 version: 02 width: 32 bits clock: 33MHz capabilities: uhci bus_master configuration: driver=uhci_hcd latency=0 resources: irq:23 ioport:d880(size=32) *-usb:1 description: USB Controller product: N10/ICH 7 Family USB UHCI Controller #2 vendor: Intel Corporation physical id: 1d.1 bus info: pci@0000:00:1d.1 version: 02 width: 32 bits clock: 33MHz capabilities: uhci bus_master configuration: driver=uhci_hcd latency=0 resources: irq:19 ioport:d800(size=32) *-usb:2 description: USB Controller product: N10/ICH 7 Family USB UHCI Controller #3 vendor: Intel Corporation physical id: 1d.2 bus info: pci@0000:00:1d.2 version: 02 width: 32 bits clock: 33MHz capabilities: uhci bus_master configuration: driver=uhci_hcd latency=0 resources: irq:18 ioport:d480(size=32) *-usb:3 description: USB Controller product: N10/ICH 7 Family USB UHCI Controller #4 vendor: Intel Corporation physical id: 1d.3 bus info: pci@0000:00:1d.3 version: 02 width: 32 bits clock: 33MHz capabilities: uhci bus_master configuration: driver=uhci_hcd latency=0 resources: irq:16 ioport:d400(size=32) *-usb:4 description: USB Controller product: N10/ICH 7 Family USB2 EHCI Controller vendor: Intel Corporation physical id: 1d.7 bus info: pci@0000:00:1d.7 version: 02 width: 32 bits clock: 33MHz capabilities: pm debug ehci bus_master cap_list configuration: driver=ehci_hcd latency=0 resources: irq:23 memory:fea77c00-fea77fff *-pci:1 description: PCI bridge product: 82801 Mobile PCI Bridge vendor: Intel Corporation physical id: 1e bus info: pci@0000:00:1e.0 version: e2 width: 32 bits clock: 33MHz capabilities: pci subtractive_decode bus_master cap_list *-isa description: ISA bridge product: NM10 Family LPC Controller vendor: Intel Corporation physical id: 1f bus info: pci@0000:00:1f.0 version: 02 width: 32 bits clock: 33MHz capabilities: isa bus_master cap_list configuration: latency=0 *-ide description: IDE interface product: N10/ICH7 Family SATA IDE Controller vendor: Intel Corporation physical id: 1f.2 bus info: pci@0000:00:1f.2 logical name: scsi0 version: 02 width: 32 bits clock: 66MHz capabilities: ide pm bus_master cap_list emulated configuration: driver=ata_piix latency=0 resources: irq:19 ioport:1f0(size=8) ioport:3f6 ioport:170(size=8) ioport:376 ioport:ff90(size=16) memory:80200000-802003ff *-disk description: ATA Disk product: WDC WD10TPVT-11U vendor: Western Digital physical id: 0.0.0 bus info: scsi@0:0.0.0 logical name: /dev/sda version: 01.0 serial: WD-WXC1A80P0314 size: 931GiB (1TB) capabilities: partitioned partitioned:dos configuration: ansiversion=5 signature=00088c47 *-volume:0 description: EXT4 volume vendor: Linux physical id: 1 bus info: scsi@0:0.0.0,1 logical name: /dev/sda1 logical name: /media/private version: 1.0 serial: 042daf2d-350c-4640-a76a-4554c9d98c59 size: 300GiB capacity: 300GiB capabilities: primary journaled extended_attributes large_files huge_files dir_nlink recover extents ext4 ext2 initialized configuration: created=2011-11-06 11:05:03 filesystem=ext4 label=Private lastmountpoint=/media/private modified=2012-04-13 20:01:16 mount.fstype=ext4 mount.options=rw,relatime,barrier=1,stripe=1,data=ordered mounted=2012-04-13 20:01:16 state=mounted *-volume:1 description: Extended partition physical id: 2 bus info: scsi@0:0.0.0,2 logical name: /dev/sda2 size: 625GiB capacity: 625GiB capabilities: primary extended partitioned partitioned:extended *-logicalvolume:0 description: Linux filesystem partition physical id: 5 logical name: /dev/sda5 logical name: /media/storage capacity: 600GiB configuration: mount.fstype=ext4 mount.options=rw,relatime,barrier=1,stripe=1,data=ordered state=mounted *-logicalvolume:1 description: Linux filesystem partition physical id: 6 logical name: /dev/sda6 logical name: /media/dropbox capacity: 24GiB configuration: mount.fstype=ext4 mount.options=rw,relatime,barrier=1,stripe=1,data=ordered state=mounted *-volume:2 description: EXT4 volume vendor: Linux physical id: 3 bus info: scsi@0:0.0.0,3 logical name: /dev/sda3 logical name: /media/www version: 1.0 serial: 9b0a27b4-05d8-40d5-bfc7-4aeba198db7b size: 2570MiB capacity: 2570MiB capabilities: primary journaled extended_attributes large_files huge_files dir_nlink recover extents ext4 ext2 initialized configuration: created=2011-11-06 11:05:11 filesystem=ext4 label=www lastmountpoint=/media/www modified=2012-04-15 11:31:12 mount.fstype=ext4 mount.options=rw,relatime,barrier=1,stripe=1,data=ordered mounted=2012-04-15 11:31:12 state=mounted *-volume:3 description: Linux swap volume physical id: 4 bus info: scsi@0:0.0.0,4 logical name: /dev/sda4 version: 1 serial: 6ed1130e-3aad-4fa6-890b-77e729121e3b size: 4098MiB capacity: 4098MiB capabilities: primary nofs swap initialized configuration: filesystem=swap pagesize=4096 *-serial UNCLAIMED description: SMBus product: N10/ICH 7 Family SMBus Controller vendor: Intel Corporation physical id: 1f.3 bus info: pci@0000:00:1f.3 version: 02 width: 32 bits clock: 33MHz configuration: latency=0 resources: ioport:400(size=32) *-scsi physical id: 1 bus info: usb@1:4 logical name: scsi2 capabilities: emulated scsi-host configuration: driver=usb-storage *-disk description: SCSI Disk physical id: 0.0.0 bus info: scsi@2:0.0.0 logical name: /dev/sdb size: 3864MiB (4051MB) capabilities: partitioned partitioned:dos configuration: signature=000b4c55 *-volume description: EXT4 volume vendor: Linux physical id: 1 bus info: scsi@2:0.0.0,1 logical name: /dev/sdb1 logical name: / version: 1.0 serial: 33926e39-4685-4f63-b83c-f2a67824b69a size: 3862MiB capacity: 3862MiB capabilities: primary bootable journaled extended_attributes large_files huge_files dir_nlink recover extents ext4 ext2 initialized configuration: created=2011-10-11 14:03:46 filesystem=ext4 lastmountpoint=/ modified=2012-03-19 11:47:29 mount.fstype=ext4 mount.options=rw,noatime,errors=remount-ro,barrier=1,data=ordered mounted=2012-04-15 11:31:11 state=mounted rfkill list all Doesnt show anything! dmesg | grep -i firmware [ 0.715481] pci 0000:00:1f.0: [Firmware Bug]: TigerPoint LPC.BM_STS cleared

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• Sending keystrokes using Python

  - by Rudi Strydom

  I am trying to build a remote control application to control media on my Ubuntu. Does anyone know a way in order to accomplish this. The media keys in particular. Thank you. EIDT: I have tried using XTE, but is seems python in truncating the input or there is a limit or something which means that you can't do Ctrl + Key key presses, which wont suit my needs. I also tried uinput, but alas you need to run it as root, which also will not quite my needs. Now I am looking at EVDEV which seems promicing, that is if I can get it working.

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• How to install SpatiaLite 3 on 12.04

  - by Terra

  1) sudo apt-get install libsqlite3-dev libgeos-dev 2) libspatialite-3.0.0-stable$ ./configure Result: configure: error: cannot find proj_api.h, bailing out checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking stdio.h usability... yes checking stdio.h presence... yes checking for stdio.h... yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking for inttypes.h... (cached) yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking sqlite3.h usability... yes checking sqlite3.h presence... yes checking for sqlite3.h... yes checking sqlite3ext.h usability... yes checking sqlite3ext.h presence... yes checking for sqlite3ext.h... yes checking for g++... no checking for c++... no checking for gpp... no checking for aCC... no checking for CC... no checking for cxx... no checking for cc++... no checking for cl.exe... no checking for FCC... no checking for KCC... no checking for RCC... no checking for xlC_r... no checking for xlC... no checking whether we are using the GNU C++ compiler... no checking whether g++ accepts -g... no checking dependency style of g++... none checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking dependency style of gcc... (cached) gcc3 checking how to run the C preprocessor... gcc -E checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop checking how to convert i686-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... dlltool checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for mt... mt checking if mt is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for an ANSI C-conforming const... yes checking for off_t... yes checking for size_t... yes checking whether time.h and sys/time.h may both be included... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for working volatile... yes checking whether lstat correctly handles trailing slash... yes checking whether lstat accepts an empty string... no checking whether lstat correctly handles trailing slash... (cached) yes checking for working memcmp... yes checking whether stat accepts an empty string... no checking for strftime... yes checking for memset... yes checking for sqrt... no checking for strcasecmp... yes checking for strerror... yes checking for strncasecmp... yes checking for strstr... yes checking for fdatasync... yes checking for ftruncate... yes checking for getcwd... yes checking for gettimeofday... yes checking for localtime_r... yes checking for memmove... yes checking for strerror... (cached) yes checking for sqlite3_prepare_v2 in -lsqlite3... yes checking for sqlite3_rtree_geometry_callback in -lsqlite3... yes checking proj_api.h usability... no checking proj_api.h presence... no checking for proj_api.h... no configure: error: cannot find proj_api.h, bailing out

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• Rendering citations and references in HTML using PHP/Perl/Python/

  - by Nick

  Is there a PHP/Perl/Python/... library for picking citations out of an HTML file and rendering a nice list of references at the bottom, like in Wikipedia? I'm developing a website with heavily-sourced content, and I'd really like to have automatically-generated lists of formatted references, like in Wikipedia. (Check out their philosophy page, and see how the superscript numbered citations interact with the references at the bottom. This is all dynamically generated, automatically ordered & linked.) They do it really well: the citations are linked to the references (which are backlinked to the citations), when you click on one of the links, the target is highlighted, etc. I'm tempted to build the site on MediaWiki just for this one feature, but it seems like overkill. Do I have any options?

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• Python - calculate multinomial probability density functions on large dataset?

  - by Seafoid

  Hi, I originally intended to use MATLAB to tackle this problem but the inbuilt functions has limitations that do not suit my goal. The same limitation occurs in NumPy. I have two tab-delimited files. The first is a file showing amino acid residue, frequency and count for an in-house database of protein structures, i.e. A 0.25 1 S 0.25 1 T 0.25 1 P 0.25 1 The second file consists of quadruplets of amino acids and the number of times they occur, i.e. ASTP 1 Note, there are 8,000 such quadruplets. Based on the background frequency of occurence of each amino acid and the count of quadruplets, I aim to calculate the multinomial probability density function for each quadruplet and subsequently use it as the expected value in a maximum likelihood calculation. The multinomial distribution is as follows: f(x|n, p) = n!/(x1!*x2!*...*xk!)*((p1^x1)*(p2^x2)*...*(pk^xk)) where x is the number of each of k outcomes in n trials with fixed probabilities p. n is 4 four in all cases in my calculation. I have created three functions to calculate this distribution. # functions for multinomial distribution def expected_quadruplets(x, y): expected = x*y return expected # calculates the probabilities of occurence raised to the number of occurrences def prod_prob(p1, a, p2, b, p3, c, p4, d): prob_prod = (pow(p1, a))*(pow(p2, b))*(pow(p3, c))*(pow(p4, d)) return prob_prod # factorial() and multinomial_coefficient() work in tandem to calculate C, the multinomial coefficient def factorial(n): if n <= 1: return 1 return n*factorial(n-1) def multinomial_coefficient(a, b, c, d): n = 24.0 multi_coeff = (n/(factorial(a) * factorial(b) * factorial(c) * factorial(d))) return multi_coeff The problem is how best to structure the data in order to tackle the calculation most efficiently, in a manner that I can read (you guys write some cryptic code :-)) and that will not create an overflow or runtime error. To data my data is represented as nested lists. amino_acids = [['A', '0.25', '1'], ['S', '0.25', '1'], ['T', '0.25', '1'], ['P', '0.25', '1']] quadruplets = [['ASTP', '1']] I initially intended calling these functions within a nested for loop but this resulted in runtime errors or overfloe errors. I know that I can reset the recursion limit but I would rather do this more elegantly. I had the following: for i in quadruplets: quad = i[0].split(' ') for j in amino_acids: for k in quadruplets: for v in k: if j[0] == v: multinomial_coefficient(int(j[2]), int(j[2]), int(j[2]), int(j[2])) I haven'te really gotten to how to incorporate the other functions yet. I think that my current nested list arrangement is sub optimal. I wish to compare the each letter within the string 'ASTP' with the first component of each sub list in amino_acids. Where a match exists, I wish to pass the appropriate numeric values to the functions using indices. Is their a better way? Can I append the appropriate numbers for each amino acid and quadruplet to a temporary data structure within a loop, pass this to the functions and clear it for the next iteration? Thanks, S :-)

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