Many python packages have build dependencies on non-Python packages. I'm specifically thinking of lxml and cffi, but this dilemma applies to a lot of packages on PyPI. Both of these packages have unadvertised build dependencies on non-Python packages like libxml2-dev, libxslt-dev, zlib1g-dev, and libffi-dev. The websites for lxml and cffi declare some of these dependencies, but it appears that there is no way to do figure this out from a command line.
As a result, there are hundreds of questions on SO that take this general form:
pip install foo fails with an error: "fatal error: bar.h: No such file or directory". How do I fix it?
Is this a misuse of pip or is this how it is intended to work? Is there a sane way to know what build dependencies to install before running pip? My current approach is:
I want to install a package called foo.
pip install foo
foo has a dependency on a Python package bar.
If bar build fails, then look at error message and guess/google what non-Python dependency I need to install.
sudo apt-get install libbaz-dev
sudo pip install bar
Repeat until bar succeeds.
sudo pip uninstall foo
Repeat entire process until no error messages.
Step #4 is particularly annoying. Apparently pip (version 1.5.4) installs the requested package first, before any dependencies. So if any dependencies fail, you can't just ask pip to install it again, because it thinks its already installed. There's also no option to install just the dependencies, so you must uninstall the package and then reinstall it.
Is there some more intelligent process for using pip?
This is actually a comment about the answer suggesting using apt-get but I don't have enough reputation points to leave one.
If you use virtualenv a lot, then installing the python-packages through apt-get can become a pain, as you can get mysterious errors when the python packages installed system-wide and the python packages installed in your virtualenv try to interact with each other. One thing that I have found that does help is to use the build-dep feature. To build the matplotlib dependencies, for example:
sudo apt-get build-dep python-matplotlib
And then activate your virtual environment and do pip install matplotlib. It will still go through the build process but many of the dependencies will be taken care of for you.
This is sort what the cran repositories suggest when installing R packages in ubuntu.
For most popular packages, There is a workaround for recent ubuntu systems. For example, I want to install matplotlib. When you order pip install matplotlib, it usually fails because of a missing dependency.
You can use apt-get install python-matplotlib instead. For python3, you can use apt-get install python3-matplotlib
Related
I am wondering if there is a way to uninstall packages in PIP including those that are not listed in the requirements.txt but which were installed as dependencies of those that are.
For example, suppose I have Django==2.1 line in requirements.txt. When running pip install -r requirements.txt, the above will instruct PIP to install many extra packages on which Django depends.
However, if I then execute pip uninstall -r requirements.txt, the Django package will be uninstalled, but PIP will retain many of its now unused dependencies.
My question is how to go about cleaning those up nicely. Is there a way to make PIP preserve and consider history explicitly? If the thing which forced PIP to install a package is being uninstalled, it appears that we should also be able to flag it to wipe its now defunct dependencies.
Take a look at pipdeptree Python package and pipdeptree --reverse some_package command in particular.
The easiest option is to use pip-autoremove. After installing it via pip, you can simply call the following from the command line:
pip-autoremove Django
Which uninstalls Django and its unused dependencies including those not listed in requirements.txt.
Pretty new to linux/suse and python so excuse me if I cause some simple questions.
I've search through stackoverflow and haven't gotten a result for my question.
I'm running on Windows with a Virtual machine using SUSE. I'm trying to install py.test, but to install it, it needs either pip or easy_install. I've heard pip is preferred over easy_install, so I tried installing that with get-pip.py.
I run it with
python get-pip.py
and it tells me it has been installed, this is what it ouputs
Collecting pip
Using cached pip-6.1.1-py2.py3-none-any.whl
Collecting setuptools
Using cached setuptools-15.1-py2.py3-none-any.whl
Installing collected packages: pip, setuptools
Successfully installed pip-6.1.1 setuptools-15.1
I tried running
pip install -U pytest
however the command pip has not been found. I also looked into python-pip package via openSUSE, though I'm not sure how to open a .ymp file through a VM.
Would I have to add a path for it to work? Pointers would be appreciated.
It looks like pip was unstalled by a regular user, so it was installed under the user's homedir, thus needs to be explicitly added to the path.
On openSUSE I'd suggest installing it using YaST (as root) and it'll end up in /usr/bin/pip, shareable by all users. Here's how it looks like on openSUSE 13.2:
$> which pip
/usr/bin/pip
$> rpm -qf /usr/bin/pip
python3-pip-1.5.6-2.1.3.noarch
Just search for pip in the software management tool.
Also many additional python packages/modules come prepackaged as openSUSE RPMs, better check the software management tool 1st.
I'm trying to upgrade Scipy from 0.9.0 to 0.12.0. I use the command:
sudo pip install --upgrade scipy
and I get all sorts of errors which can be seen in the pip.log file here and I'm unfortunately not python-savvy enough to understand what's wrong. Any help will be appreciated.
The error messages all state the same: You lack BLAS (Basic Linear Algebra Subroutines) on your system, or scipy cannot find it. When installing packages from source in ubuntu, as you are effectively trying to do with pip, one of the easiest ways to make sure dependencies are in place is by the command
$ sudo apt-get build-dep python-scipy
which will install all packages needed to build the package python-scipy. You may in some cases run into the problem that the version of the source package you are trying to install have different dependencies than the version included with ubuntu, but in your case, I think chances are good that the above command will be sufficient to fetch BLAS for you, headers included.
I had the same problem upgrading from scipy 0.9 to 0.13.3, and I solved it using the following answer and installing:
sudo apt-get install libblas-dev
sudo apt-get install liblapack-dev
sudo apt-get install gfortran
Make sure libatlas-base-dev and libatlas-sse2-dev are installed, it seems like it can't find your atlas library. Also, see this question:
Does Python SciPy need BLAS?
I found Adam Klein's instructions for setting up scipy (and friends) in a virtual environment very useful.
One problem I ran into (which was probably my own fault): After all was said and done, I found importing scipy still loaded version 0.9.0, not 0.12.0. The problem was that my sys.path was finding the old system version before the new version.
The fix was to make
/path/to/.virtualenvs/arthur/local/lib/python2.7/site-packages
appear before
/usr/lib/python2.7/dist-packages
in sys.path. If you have virtualenvwrapper installed, then
you can add the path using
add2virtualenv /path/to/.virtualenvs/arthur/lib/python2.7/site-packages
Hi recently i installed setup tools module and google app engine gives me errors . Is there a way to uninstall setuptool? can any one tell me step by step because i tried hard
The answer depends on how it was installed.
If it was installed using the ubuntu (debian) package manager, try:
sudo apt-get remove --purge python-setuptools
[updated]
If you installed manually, probably the setuptools final location will be something like (adjust for your environment/python version):
/usr/local/lib/python2.6/dist-packages
Just delete the setuptools stuff there.
Lame, I know, but it is your burden for not using the excellent package manager provided by ubuntu: stick to dpkg unless you need bleeding edge stuff. For other python modules installed by setuptools, it provides no "uninstall" feature (but pip does, that is why there is a lot of enthusiasm around virtualenv, pip and yolk).
[2017 update]
It is 2017 and installing Python modules changed a bit:
pip is now the preferred installer program. Starting with Python 3.4, it is included by default with the Python binary installers.
venv is the standard tool for creating virtual environments (semi-isolated Python environments that allow packages to be installed for use by a particular application, rather than being installed system wide), and has been part of Python since Python 3.3. Starting with Python 3.4, it defaults to installing pip into all created virtual environments.
virtualenv is a third party alternative (and predecessor) to venv and if not official it is still very popular because it allows virtual environments to be used on versions of Python prior to 3.4, which either don’t provide venv at all, or aren’t able to automatically install pip into created environments.
easy_install pip
pip uninstall pip setuptools
(pip and setuptools both use the same package formats, but pip has uninstall support. kinda hilarious that installing something is the easiest way to uninstall.)
I was having trouble with the method below because my pip wasn't up to date.
easy_install pip
pip uninstall pip setuptools
After upgrading pip like this:
sudo -H pip install --upgrade pip
I was able to successfully uninstall setuptools like so:
pip uninstall setuptools
Seems kinda weird that they'd require a package manager to install a package manager. I'm on Windows BTW.
Pip does require setuptools. Pip is really just a wrapper around setuptools to provide a better installer than easy_install and some nicer installation behaviors, plus uninstall, requirements files, etc. Even if you somehow got pip installed without setuptools it still won't run without it.
You can use Distribute instead of setuptools: it installs a package called setuptools (it's a fork of the latter). You can install Distribute by downloading and running distribute_setup.py.
Update: As Gringo Suave says, the above is obsolete now - distribute and setuptools have now merged, and the merged project is called setuptools.
You can download setuptools package as Windows installer from pypi/setuptools and then install pip or easy_install
Solution for Windows Users
If you installed ActivePython on Windows, then you have pip by default, as well as PyPM (ActiveState's package manager). The following excerpt is from What's included in ActivePython 2.7:
Additional Packages
PyPM: Python Package Manager to download and install binary packages. Also included: virtualenv, Distribute, pip, SQLAlchemy.
Solution for OS X Users
Not sure if setuptools is required when installing pip using homebrew. You might try that.
To install homebrew:
ruby -e "$(curl -fsSL https://gist.github.com/raw/323731/install_homebrew.rb)"
Then to install pip:
brew install pip
Sure, just grab the source from http://pypi.python.org/pypi/pip/0.8.2#downloads
unpack it, cd into it, and run python setup.py install