Anaconda Runtime Error: Python is not installed as a framework?

Anaconda Runtime Error: Python is not installed as a framework? - python

I've installed Anaconda with the pkg installer:
Python 2.7.10 |Continuum Analytics, Inc.| (default, May 28 2015, 17:04:42)
[GCC 4.2.1 (Apple Inc. build 5577)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://binstar.org
but when I attempt to use anything from matplotlib, i.e.:
from matplotlib import pyplot as plt
I get
RuntimeError: Python is not installed as a framework.
The Mac OS X backend will not be able to function correctly if Python is not installed
as a framework. See the Python documentation for more information on installing Python
as a framework on Mac OS X. Please either reinstall Python as a framework,
or try one of the other backends.
I'm really not sure what this means, or how to go about fixing it.

Posting since I just had this issue and this was a quick fix:
If you used pip to install:
Create ~/.matplotlib/matplotlibrc
Add "backend: TkAgg" (without the quotations) to the file.

I was having the same problem with anaconda 2 & matplotlib 1.5.3.
Running a simple conda install matplotlib to reinstall matplotlib did the trick for me.

If the problem is only matplotlib, is worth try to change the backend:
import matplotlib
matplotlib.use('TkAgg')
import matplotlib.pyplot as plt
plt.plot([1, 2, 3], [4, 5, 6])
plt.show()
If it works you can change the backend permanently from the matplotlibrc file.

I was having the same problem. Installing an older version of matplotlib did the trick for me. Try this command in your terminal while in your virtual environment:
pip install matplotlib==1.4.3

Run the file using pythonw instead of python.
This happens because python is not installed as a framework.
Therefore use pythonw myScript.py instead of python myScript.py
I am sure this will fix it.
I had a similar error.
RuntimeError: Python is not installed as a framework. The Mac OS X backend will not be able to function correctly if Python is not installed as a framework. See the Python documentation for more information on installing Python as a framework on Mac OS X. Please either reinstall Python as a framework, or try one of the other backends. If you are using (Ana)Conda please install python.app and replace the use of 'python' with 'pythonw'. See 'Working with Matplotlib on OSX' in the Matplotlib FAQ for more information.

From the matplotlib documentation;
$ conda install python.app
You need a framwork build of Python for matplotlib, but
The default python provided in (Ana)conda is not a framework build. However, a framework build can easily be installed, both in the main environment and in conda envs: install python.app (conda install python.app) and use pythonw rather than python
NB I had to add the conda-forge channel as python.app isn't included in the default miniconda channels
$ conda config --add channels conda-forge

If you experience this error, don't forget to check your bash_profile.
You can do this in terminal by:
cd
then
nano .bash_profile
check the contents. Macports and Homebrew add their own headings for things they've done here. You can remove the declarations they make to $PATH. Just leave the one Anaconda has made. I had a If you would like, you can:
cp .bash_profile ./bash_profile_backup_yyyy_mm_dd
and have a backup of the file, with filename indexing to the date you changed it. That is, provided you actually put in the date in instead of just the formatting characters I'm suggesting.
source ~/.bash_profile
will refresh your system's reference to the bash_profile and you should be good to go in importing and using matplotlib

if using inside a virtualenv, I recommend following the instructions here:
http://matplotlib.org/faq/virtualenv_faq.html

A reinstall of matplotlib should fix the issue for you as it did for me with
conda install matplotlib

Quickfix: Run your file using pythonw, instead of python.
e.g pythonw testFile.py.

Related

Unexpected behavior after conda force reinstall

After downgrading numpy from version 1.22.4 to 1.19.5 with the following command-
conda install numpy==1.19.5 --force-reinstall
Python behaves unexpectedly. For example, pip list and conda list both show that the version of numpy remains 1.22.4, yet when starting a shell, the numpy version shows up as 1.19.5:
(tensorflow) demo % python
Python 3.9.12 | packaged by conda-forge | (main, Mar 24 2022, 23:24:38)
[Clang 12.0.1 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as np
>>> np.__version__
'1.19.5'
I have tried deactivating and activating the conda environment. There are no PYTHONPATH environmental variables set, nor is there a module called numpy.py in my directory. What could explain how the numpy version imported in the shell does not correspond to the version displayed by conda list / pip list in the terminal?

Occasionally, I have found that Python can conflict with packages, especially with bigger frameworks, as fully uninstalling it can be difficult. That's the beauty of virtual Python environments, you are able to just create a new one for specific versions, and not have to deal with multiple versions on your native Python install.
It might be worth using another package manager, such as Mamba (https://github.com/mamba-org/mamba), which I have had better experiences with. It also has the benefit of being multi-threaded, and more efficient.
Otherwise, your best bet would probably be to create a new virtual environment, which you can do via (be sure to change the python version if you have a specific use-case, or just get rid of the flag to have the latest version all the time):
conda create --name your-name-here python=3.9 -y
If you are using Mamba, you can replace any instance of 'conda' that you would otherwise use, for example to install your specific package:
mamba install numpy==1.19.5
Also, I would recommend using 'Miniconda', as I have had a much better experience with it, just make sure to 'activate' your specific virtual python environment.

cannot use pyperclip module in python shell after successful download [duplicate]

During the past years, I have installed many Python libraries with various Python versions. To make them ready to work immediately, I installed them blindly without control. Currently they're causing problems when I tried to install pynest which invokes numpy, scipy and matplotlib. After struggling, I am going to clean and reinstall Python and the libraries.
After investigation, I found Python 2.5/2.6/2.7/3.2 on my system, and each of them has some copies or other things at: (my OS == Mac OS X 10.7.5 Lion)
/Library/Frameworks/
/opt/local/Library/Frameworks/
/opt/local/bin/
/Applications/
/usr/local/bin/
/usr/bin/
/System/Library/Frameworks/
I know I'm crazy to have these. Now I have removed all these except the things in /System/Libarary/Frameworks (I never remove any thing from /System/Library/). After the clean work, which python now gives /usr/bin/python which links to /System/Library/Frameworks.
Now, is it a clear environment for me to reinstall python? How to double check that there's no other versions existing? How should I reinstall them to guarantee that they and their libraries won't be everywhere and have many copies again?
I want to install a clean Python 2.7 onto a proper location, and make my system know exactly where it is and never install any libraries somewhere else. Please give me some advice that how to manage it like in a professional way.
For your information, here is my current $PATH, I think it should be modified:
/opt/local/bin:/opt/local/sbin:/opt/nest/lib/python2.7/site-packages:/usr/local/lib/python2.7/site-packages:/Library/Frameworks/Python.framework/Versions/2.7/bin:/usr/texbin:/Library/Frameworks/Python.framework/Versions/3.2/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/site-packages/django/bin:/usr/X11/bin:/opt/local/bin:/opt/local/sbin:/usr/local/lib/python2.7/site-packages:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Library/Frameworks/Python.framework/Versions/3.2/bin
Please let me know If you need more information. Thank you!
UPDATE:
I'm rethinking profoudly why it becomes so crazy. I believe it's because I installed things via:
easy_install / macports / homebrew / fink / pip sometimes;
.dmg sometimes;
.pkg sometimes;
compile source code sometimes;
and they made things at different locations. I wonder what's the mechanism behind these ways? How do they choose target location? How to prevent them from messing things up?

Why did it get messed up?
There're a couples of different way to install Python, as the update of OP says, and they locate files in different locations. For example, macports puts things into /opt/local/, while homebrew puts things into /usr/local/. Also, Mac OS X brings a few python versions with itself. So, if you install python many times via different ways, you will get many python versions existing independently on your system.
What problem does it cause?
I don't know exactly. I guess the problem is that if you have many versions of python, then which one to use and where to find packages will be determined by the path order in your system PATH and the PYTHONPATH respectively. So you may lose control of where to install python modules. Consider that if you run sudo python setup.py install to install a module (it finds python by the root's PATH) and then try to import the module by python -c "import it" (this time it finds python by your PATH), maybe something will go wrong. This is my guess, I didn't validate it. But in my own case, something did go wrong.
How to avoid this?
I think the principle would be that be aware of that different ways and tools install things independently to different locations, so use them mindfully.
Unless you intend to, don't install the same thing twice via different
ways. (If you intend to do it for python, you might want to check out virtualenv)
Keep an eye on the path order in your PATH and consider if it's
correct.
When installing modules, be clear which python (or pip) is
running and where the module is installed.
So, how did I solve my own case?
Since it had been messing up already and seemed to be very hard to cure, so finally I solved this question by a full OS re-installation, and started to follow the DOs-and-DONTs above. For the installation of the scientific environment with python (numpy/scipy/matplotlib, which had shown problems to make me ask this question), I found this tutorial was extremely helpful. So, problem solved finally.

Here is what was confusing me and how I solved it.
$ which python
/usr/bin/python
$ which python3
/usr/local/bin/python3
$ ls /usr/local/bin/python
ls: /usr/local/bin/python: No such file or directory
So notice I didn't have a HomeBrew installation of python2.7, but did have the python3 installation. The version under /usr/bin/python is using the system default. You can tell based on the module search path:
$ /usr/bin/python
Python 2.7.10 (default, Feb 7 2017, 00:08:15)
[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)] on darwin
`enter code here`Type "help", "copyright", "credits" or "license" for
more information.
>>> import sys
>>> sys.path
['', '/Library/Python/2.7/...
Notice the '/Library/Python'... that's Mac OS's version of python. But I want to stay strictly on a user installed version (i.e. HomeBrew).
So here's what I did to fix this:
$ brew install python
...
Warning: python 2.7.13 is already installed, it's just not linked.
You can use `brew link python` to link this version.
$ brew link --overwrite python
$ which python
/usr/local/bin/python
$ python
Python 2.7.10 (default, Feb 7 2017, 00:08:15)
[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.path
['', '/usr/local/Cellar/python/2.7.13...
Its no longer /Library/.. but /usr/local.
Now its finding all of my pip installed modules! Problem solved!
UPDATE:
After updating brew to version 1.5.4, it seems the symbolic links were removed. And now you have to add this to your path:
export PATH="/usr/local/opt/python/libexec/bin:$PATH"
Read the Caveats section in 'brew info python':
==> Caveats
This formula installs a python2 executable to /usr/local/bin.
If you wish to have this formula's python executable in your PATH then add
the following to ~/.bash_profile:
export PATH="/usr/local/opt/python/libexec/bin:$PATH"
Pip and setuptools have been installed. To update them
pip2 install --upgrade pip setuptools
You can install Python packages with
pip2 install <package>
They will install into the site-package directory
/usr/local/lib/python2.7/site-packages
See: https://docs.brew.sh/Homebrew-and-Python.html

In order to install a python distributions into specific folder, you can use the --prefix scheme during python installation. Using the prefix scheme, you can for example install Python 2.7 into the folder /opt/py27. Now, in order to use the new installed Python distribution you have to: cleanup you PATH and LD_LIBRARY_PATH:
Remove all 'old' Python paths and
configure (according to my example) the environment variables like this:
PATH: Add /opt/py27/bin
LD_LIBRARY_PATH: Add /opt/py27/lib
That's it.
(In case you need multiple environments of Python installed at the same time, I'd suggest to have a look at virtualenv)

tl;dr
brew install python
Symptoms
I had similar issues with python programs not finding dependencies.
My python3 version was a broken symlink.
My pip was pointing to a python 3.8
And my pip3 was pointing to 3.9
python -V was outputting some python 2.7 version
python3 -V was outputting some python3.8 version
Solution
I ran brew install python and it fixed all my problems.

pip installed module but python gives Import error [duplicate]

Here is what was confusing me and how I solved it.
$ which python
/usr/bin/python
$ which python3
/usr/local/bin/python3
$ ls /usr/local/bin/python
ls: /usr/local/bin/python: No such file or directory
So notice I didn't have a HomeBrew installation of python2.7, but did have the python3 installation. The version under /usr/bin/python is using the system default. You can tell based on the module search path:
$ /usr/bin/python
Python 2.7.10 (default, Feb 7 2017, 00:08:15)
[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)] on darwin
`enter code here`Type "help", "copyright", "credits" or "license" for
more information.
>>> import sys
>>> sys.path
['', '/Library/Python/2.7/...
Notice the '/Library/Python'... that's Mac OS's version of python. But I want to stay strictly on a user installed version (i.e. HomeBrew).
So here's what I did to fix this:
$ brew install python
...
Warning: python 2.7.13 is already installed, it's just not linked.
You can use `brew link python` to link this version.
$ brew link --overwrite python
$ which python
/usr/local/bin/python
$ python
Python 2.7.10 (default, Feb 7 2017, 00:08:15)
[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.path
['', '/usr/local/Cellar/python/2.7.13...
Its no longer /Library/.. but /usr/local.
Now its finding all of my pip installed modules! Problem solved!
UPDATE:
After updating brew to version 1.5.4, it seems the symbolic links were removed. And now you have to add this to your path:
export PATH="/usr/local/opt/python/libexec/bin:$PATH"
Read the Caveats section in 'brew info python':
==> Caveats
This formula installs a python2 executable to /usr/local/bin.
If you wish to have this formula's python executable in your PATH then add
the following to ~/.bash_profile:
export PATH="/usr/local/opt/python/libexec/bin:$PATH"
Pip and setuptools have been installed. To update them
pip2 install --upgrade pip setuptools
You can install Python packages with
pip2 install <package>
They will install into the site-package directory
/usr/local/lib/python2.7/site-packages
See: https://docs.brew.sh/Homebrew-and-Python.html

In order to install a python distributions into specific folder, you can use the --prefix scheme during python installation. Using the prefix scheme, you can for example install Python 2.7 into the folder /opt/py27. Now, in order to use the new installed Python distribution you have to: cleanup you PATH and LD_LIBRARY_PATH:
Remove all 'old' Python paths and
configure (according to my example) the environment variables like this:
PATH: Add /opt/py27/bin
LD_LIBRARY_PATH: Add /opt/py27/lib
That's it.
(In case you need multiple environments of Python installed at the same time, I'd suggest to have a look at virtualenv)

tl;dr
brew install python
Symptoms
I had similar issues with python programs not finding dependencies.
My python3 version was a broken symlink.
My pip was pointing to a python 3.8
And my pip3 was pointing to 3.9
python -V was outputting some python 2.7 version
python3 -V was outputting some python3.8 version
Solution
I ran brew install python and it fixed all my problems.

Uninstalled IPython on Ubuntu but can still be used

I tried to install rpy2 earlier today, to use IPython Notebooks in conjunction with R. I'm using Ubuntu 12.04. However, I had issues with using the magics extension, so went off down a rathole to resolve...
I've tried to uninstall IPython via the command
sudo apt-get remove --auto-remove ipython
... which seemed to work correctly, and from looking in /usr/lib/python2.7/dist-packages, I manually can't see an IPython directory. I double checked the uninstallation method worked:
me#my_laptop:/usr/lib/python2.7/dist-packages$ sudo apt-get remove -auto-remove ipython
Reading package lists... Done
Building dependency tree
Reading state information... Done
Package ipython is not installed, so not removed
0 to upgrade, 0 to newly install, 0 to remove and 0 not to upgrade.
However, I can go into a terminal and type ipython I get the following -- note that I can import the package as well:
me#my_laptop:/usr/lib/python2.7/dist-packages$ pwd
/usr/lib/python2.7/dist-packages
me#my_laptop:/usr/lib/python2.7/dist-packages$ ipython
Python 2.7.3 (default, Dec 18 2014, 19:10:20)
Type "copyright", "credits" or "license" for more information.
IPython 3.0.0-b1 -- An enhanced Interactive Python.
? -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help -> Python's own help system.
object? -> Details about 'object', use 'object??' for extra details.
In [1]: import IPython
In [2]: IPython
Out[2]: <module 'IPython' from '/usr/local/lib/python2.7/dist-packages/IPython/__init__.pyc'>
NB I tried to use the comment by kermit666 in, butthis did not seem to help: Broken IPython notebook install Ubuntu 13.10 how to force reinstall
Does Python cache its packages somehow, like in a database, that I need to
update somehow? I don't understand how it is loading something that in theory has been deleted?

really works use "sudo pip uninstall ipython"

you just check the package where it's located
$ which ipython
May be u get the path /usr/local/bin/ and then type the command.
$ sudo rm -rf /usr/local/bin/ipython
It may be works.It's worked for me.

this should work:
> pip uninstall ipython

How to check whether I have IPython installed on my machine and what sequence to install these libraries?

I need to use python for a machine learning course and I also need to install some external libraries. I'm a bit confused as to what the correct order is for installation of everything as I've heard the paths can get messed up if done incorrectly.
Here is what I need:
Python version 2.7
IPython
The libraries available inside this package by enthought
So 1st step is to see whether I have python installed
Yes: I have this version
AM#~ >python
Python 2.7.2 (default, Jun 20 2012, 16:23:33)
[GCC 4.2.1 Compatible Apple Clang 4.0 (tags/Apple/clang-418.0.60)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Next IPython
How do I check if I have IPython?
Also whats the ideal procedure to install it? Any caveats? Any special path settings?
Can I use brew to install it?
Enthought libraries
Do I have to install these libraries in any particular order? before IPython? after IPython?
Do I have to set any specific paths?
Im trying to avoid having to install and make an error and then reinstall etc.
So any help would be much appreciated. Im running Mac OS X 10.7 (Mountain Lion).
Thanks

You can simply check the version, as we do with other software packages to check if a software package is installed properly or not.
Type in your terminal.
ipython --version
It'll print the version if ipython is installed properly.

It is so simple to get all IPython, Matplotlib, Scipy etc. now that you have Python 2.7 installed. If this is for a course, I assume you have a .edu email address with this institution? If so just go here: http://www.enthought.com/products/edudownload.php
Submit your info. Download and install it like any other program. You will then be able to call ipython from the terminal. Or to use matplotlib call ipython --pylab from the terminal.
Definitely do not go about installing the libraries one-by-one unless you are very familiar with how that works.

Develop Reference

Python is a programming language that lets you work quickly and integrate systems more effectively.