How to re-install lxml?

Question

Python version and Device used

• Python 2,7.5
• Mac 10.7.5
• BeautifulSoup 4.2.1.

I'm following the BeautifulSoup tutorial but when I try to parse a xml page using the lxml library I get the following error:

bs4.FeatureNotFound: Couldn't find a tree builder with the features you requested: lxml,xml. Do you need to install a parser library? 

I am sure that I already installed lxml by all methods: easy_install, pip, port, etc. I tried to add a line to my code to see if lxml is installed or not:

import lxml 

Then python can just successfully go through this code and display the previous error message again, occurring at the same line.

So I am quite sure that lxml was installed, but not installed correctly. So I decided to uninstall lxml, and then re-install using a 'correct' method. But when I type in

easy_install -m  lxml 

I get the following error:

Searching for lxml Best match: lxml 3.2.1 Processing lxml-3.2.1-py2.7-macosx-10.6-intel.egg  Using /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/lxml- 3.2.1-py2.7-macosx-10.6-intel.egg  Because this distribution was installed --multi-version, before you can import modules from this package in an application, you will need to 'import pkg_resources' and then use a 'require()' call similar to one of these examples, in order to select the desired version:  pkg_resources.require("lxml")  # latest installed version pkg_resources.require("lxml==3.2.1")  # this exact version pkg_resources.require("lxml>=3.2.1")  # this version or higher  Processing dependencies for lxml Finished processing dependencies for lxml 

So I don't know how to continue my uninstall, I looked up many posts about this issue on google but still I can't find any useful info.

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Here is my Source code

import mechanize from bs4 import BeautifulSoup import lxml  class count:     def __init__(self,protein):         self.proteinCode = protein         self.br = mechanize.Browser()      def first_search(self):         #Test 0         soup = BeautifulSoup(self.br.open("http://www.ncbi.nlm.nih.gov/protein/21225921?report=genbank&log$=prottop&blast_rank=1&RID=YGJHMSET015"), ['lxml','xml'])         return  if __name__=='__main__':     proteinCode = sys.argv[1]     gogogo = count(proteinCode) 

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Questions

1. How can I uninstall lxml?
2. How can I install lxml 'correctly'? How do I know that it is correctly installed?

Answer 1

I am using BeautifulSoup 4.3.2 and OS X 10.6.8. I also have a problem with improperly installed lxml. Here are some things that I found out:

First of all, check this related question: Removed MacPorts, now Python is broken

Now, in order to check which builders for BeautifulSoup 4 are installed, try

>>> import bs4 >>> bs4.builder.builder_registry.builders 

If you don't see your favorite builder, then it is not installed, and you will see an error as above ("Couldn't find a tree builder...").

Also, just because you can import lxml, doesn't mean that everything is perfect.

Try

>>> import lxml >>> import lxml.etree 

To understand what's going on, go to the bs4 installation and open the egg (tar -xvzf). Notice the modules bs4.builder. Inside it you should see files such as _lxml.py and _html5lib.py. So you can also try

>>> import bs4.builder.htmlparser >>> import bs4.builder._lxml >>> import bs4.builder._html5lib 

If there is a problem, you will see, why a parricular module cannot be loaded. You can notice how at the end of builder/__init__.py it loads all those modules and ignores whatever was not loaded:

# Builders are registered in reverse order of priority, so that custom # builder registrations will take precedence. In general, we want lxml # to take precedence over html5lib, because it's faster. And we only # want to use HTMLParser as a last result. from . import _htmlparser register_treebuilders_from(_htmlparser) try:     from . import _html5lib     register_treebuilders_from(_html5lib) except ImportError:     # They don't have html5lib installed.     pass try:     from . import _lxml     register_treebuilders_from(_lxml) except ImportError:     # They don't have lxml installed.     pass 

Answer 2

If you are using Python2.7 in Ubuntu/Debian, this worked for me:

$ sudo apt-get build-dep python-lxml $ sudo pip install lxml  

Test it like:

mona@pascal:~/computer_vision/image_retrieval$ python Python 2.7.6 (default, Jun 22 2015, 17:58:13)  [GCC 4.8.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import lxml