I've just upgraded to OSX Yosemite. I'm running brew doctor and among the zillions of warnings it generates is:
Warning: /usr/local/share/python is not needed in PATH.
Formerly homebrew put Python scripts you installed via `pip` or `pip3`
(or `easy_install`) into that directory above but now it can be removed
from your PATH variable.
Python scripts will now install into /usr/local/bin.
You can delete anything, except 'Extras', from the /usr/local/share/python
(and /usr/local/share/python3) dir and install affected Python packages
anew with `pip install --upgrade`.
I've looked carefully everywhere, and I can't find what is adding /usr/local/share/python to my path. My .bash_profile contains no mention of python. /private/etc/paths.d contains only a file called "git". I did find an instance of /usr/local/share/python in /private/etc/paths, but I deleted that, but when I start a new terminal after that and rerun brew doctor I still get the warning. Can anyone suggest how I can stop this? It's driving me insane!
Im not able to comment, and while I don't have an answer, this might help through process of elimination, or potentially help your future problem solver.
What about etc/profile; any sign in that file?
Do you have a ~/.profile it could be in?
What do you get when you: echo $PATH, any sign of said path?
What about export, or declare (with no options)?
How are you setting/exporting your desired path now?
Probably not what you want to hear, but I always do a fresh install rather than upgrade for fear of issues like this. Doing so would most likely solve your issues; all zillion of them. I know I haven't had any issues, or even a single warning from Homebrew, since I moved to Yosemite.
Related
I keep trying to install pip in various different ways, yet everytime I try to, it does not work. I tried to investigate by going to the Python folder in C:\Users(my pc name)\AppData\Local\Programs\Python, and even after I deleted my previous Python folders, uninstalled and fixed my PATH variables. Any clue why this is happening?
Update: No solution has been found, so for now I'm going to hard-reset python by uninstalling everything, then trying to reinstall and such. I'll make a second update if what I try works.
Update 2: Got the same error, so reverted back to 3.10.9, and it was completely fixed. Not sure why 3.11.1 doesn't work with my pc, but I fixed it by updating my pip.ini file in %APPDATA%\pip\pip.ini .
Because in your case older python was installed before latest. Overlap happend in namespase, when new python took python name, but new pip dont.
That issue occurs because pip is actually separate from python. And it have new lead number versions often, which probably occured in betwin your python versions installations.
Deleting all Python versions and clean install, starting from latest version, seems easiest solution.
If you have more than one python interpreter, things may become messy.
The best way to do that is by using virtual environments.You can use native python venv, Poetry or even Conda.
Or you could call pip module using the desired interpreter:
c:\...path_to_python_3_11\python.exe -m pip install my_module
For internal reasons my group shares a conda environment with a number of different groups. This limits flexibility of the package installation, because we don't want to accidentally update dependent packages (I know we live in the past...) To get around the inflexibility my group wants install the packages we develop in a remote directory. Using pip to install the packages works fine using the --target flag to designate the new/remote install folder. We will then modify our PYTHONPATHin our .bashrc to access our newly installed packages via standard import x.
The issue I have is the packages in our setup.py defined in the install_requires=['pandas==0.24.1']are also being installed in the remote directory, even though that requirement is satisfied by the shared python site_packages. What appears to be happening is that pip is installing the dependencies only looking in the remote packages directory. Is there some way install our packages while also having pip look in multiple places for package requirement satisfaction, specifically our python installation's site-packages?
I was thinking pip would use PYTHONPATH to check if a dependency is met, but that does not seem to be the case.
Please let me know if this does not make sense, packaging is still new to me. So i am sure I used the wrong terms all over the place.
I believe using "path configuration files" might help.
Say you have some packages installed in /path/to/external-packages and the regular location for site packages in the current environment is /path/to/site-packages.
Then you could add a file /path/to/site-packages/external-packages.pth with the following content:
/path/to/external-packages
I believe this should at least work for some pip commands: check, list, show, maybe more.
Be careful to read about and experiment with this technique, as it may have undesired side effects. Additionally, if I am not mistaken, there should be no need for modification to PYTHONPATH environment variable.
I've installed anaconda, but I still want to use python as normal within a Terminal window (zsh). At the moment, running which python shows /Users/USERNAME/opt/anaconda3/bin/python.
I don't want this command to point to my anaconda installation. I want to use python as I have in the past, and for it to point to my python 2.7 installation (/usr/bin/python).
The same issue is present with pip and with python3. How do I change these paths back to their default locations?
I want to start out by saying I personally have never used Anaconda, but I have many friends who have and they always seem to wind up getting into hot water as far as configurations go. If you don't need the data-science specific tools that Anaconda offers (most of which I imagine you can get just as easily by using pip install <package_name>), then I STRONGLY urge you to not use Anaconda. I would suggest you instead use homebrew to install python 3.7 and leave the system version of python 2.7 alone... Anyways...
I recently fixed an issue similar to the one you're describing for a friend. I ended up deleted his anacaonda build and reinstalling fresh from homebrew (link: https://brew.sh/), so this is how I helped him and hopefully this will help you too.
Firstly, I would check the configuration of your ~/.bash_profile (or potentially ~/.bashrc) file. Comment out any lines you find that have to do with Anaconda by preceding with the # character. I believe when anaconda installs it puts the location of the anaconda-version-of-python higher in the PATH hierarchy, therefore you computer sees it first before it has the chance to look in /usr/bin...
Secondly, you need to move the anaconda-python to the trash... I would start by trashing the whole '/Users/USERNAME/opt/anaconda3' directory. If memory serves me correctly anaconda stores other python related things in the /MacitoshHD/Library/Frameworks directory, but don't quote me on that. I would advise looking there and trashing whatever seems to be related to the anaconda install.
After that, in a new terminal (so that your PATH refreshes), I installed homebrew, and then ran the command brew install python3 to install python3. I think perhaps I ran the command recommended in the installer output, something like "brew link python3" to symlink python3 where it needs to be linked after the installation.
Finally, everything is done python2 and python3 are installed and working with no issues. python2 is the system default version and python3 is the homebrew installed version. Feel free to ask any questions and I will try to help more, hopefully those instructions will get you started though.
I have spent days struggling to get a scientific Python environment running on Mac OS Lion. I tried the SciPack Superpack route, and also various manual installations via pip and easy_install, but still got errors trying to import or use various modules. Based on the advice in this Stackoverflow thread I set up a fresh installation using MacPorts.
However, when I run the macports Python, it is ignoring packages in the macports installation and instead trying to load incompatible packages from the old installation. I am absolutely sure that I am running the newly installed macports Python. I have checked the symlinks and have checked python_select and have launched Python by directly typing the path to the new installation. But when I try to import, say, statsmodels, it pulls in the old version from another directory.
Here are the contents of sys.path (edited for brevity):
['',
'/Library/Python/2.7/site-packages/mrjob-0.4.3_dev-py2.7.egg',
'/Library/Python/2.7/site-packages/statsmodels-0.6.0-py2.7-macosx-10.9-intel.egg',
...
'/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python',
'/Library/Python/2.7/site-packages/twilio-3.6.6-py2.7.egg',
'/Library/Python/2.7/site-packages/six-1.6.1-py2.7.egg',
'/Library/Python/2.7/site-packages/httplib2-0.9-py2.7.egg',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/readline',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyObjC',
'/Library/Python/2.7/site-packages']
The macports installation is in /opt/local, while the older installation is under /Library/Python. As you can see, the older packages are higher up in the list, which means that they have higher priority.
Environmental variable PYTHONPATH is empty. If I do put anything into PYTHONPATH, that appears in sys.path after the /Library entries but before the /opt entries. So it does not solve the problem.
If I invoke the new python with the -S option, sys.path becomes:
['',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload']
That succeeds in getting rid of the alien site packages entries, but it also nukes macports' site-packages entries so then I can't load anything.
I believe that the culprit is a file called /Library/Python/2.7/site-packages/easy-install.pth , with the following contents (again edited for brevity):
import sys; sys.__plen = len(sys.path)
./mrjob-0.4.3_dev-py2.7.egg
...
./statsmodels-0.6.0-py2.7-macosx-10.9-intel.egg
...
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python
./twilio-3.6.6-py2.7.egg
./six-1.6.1-py2.7.egg
./httplib2-0.9-py2.7.egg
import sys; new=sys.path[sys.__plen:]; del sys.path[sys.__plen:]; p=getattr(sys,'__egginsert',0); sys.path[p:p]=new; sys.__egginsert = p+len(new)
If I rename that file before launching macports python, python no longer is adding these alien packages to its sys.path. Now sys.path looks a lot like it does when I use "python -S" option except it has these additional entries at the end:
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages',
'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyObjC',
'/Library/Python/2.7/site-packages'
Now I am able to load macports' own packages, say for example statsmodels. By checking statsmodels.__file__ I have confirmed that it is importing the local package and not the alien package.
However, I consider this a workaround/kludge rather than a real solution. A solution should make it behave as expected, which is: Macports' Python, launched from /opt/local/... installation, should prioritize packages installed via macports into the /opt/local/... directory tree and go looking elsewhere only if the module does not exist locally. So for example I would expect the /opt/local entries to come first in sys.path, with the /Library entries further down the list.
It seems like this should be the default behavior and I've seen a lot of comments here on Stackoverflow that just assert that this is how Macports Python behaves. So...how do I make it so?
There are at least two separate root causes for the problem you are seeing. One is that non-system OS X framework builds of Python 2.7, including MacPorts Python 2.7, deliberately include the system Python site-packages location, /Library/Python/2.7/site-packages, in sys.path, normally at the end of sys.path after that instance's own site-packages directory. This has been a debated feature in upstream Python and there is an open MacPorts issue to remove it (https://trac.macports.org/ticket/34763), the argument being that it is better to keep the system Python and the MacPorts Python totally separate.
The second root cause is the behavior of the original setuptools package and its easy_install command as supplied with OS X. As you have discovered, it does some fancy manipulation of sys.path by some magic tricks with .pth files, including easy-install.pth, to ensure that the packages that have been installed using easy_install show up first in sys.path and override other installed versions of those packages. Also as you have found, one way - and the easiest way - to remove that behavior is to delete the easy-install.pth file in /Library/Python/2.7/site-packages. That is assuming you don't want to use any of the packages installed there with the Apple-supplied system Python.
The long-term strategy to avoid this problem in the future is to make sure you do not use the Apple-supplied easy_install or easy_install-2.7 commands found in /usr/bin. They will install packages to /Library/Python for use by the system Python and will create or update easy-install.pth. In general, you should avoid use of easy_install all together. Its modern replacement is pip which provides better control and avoids tricks with .pth files. If MacPorts doesn't already provide a port for the Python package you want to install, usually of the form py27-xxxx, install and use the MacPorts py27-pip port instead of easy_install:
/opt/local/bin/pip-2.7 install xxxx
You can also use the usual MacPorts features like port select pip pip27.
If I install all packages using
python setup.py install --prefix=~/.local
how can I make Python read my packages from there and not from the system wide version? I tried editing PYTHONPATH to put ~/.local/lib/python2.x/site-packages/ first, but it does not help.
I thought that ~/.local is guaranteed to be read first in Python 2.6 and later versions. Is this true? Is something special required to make it true? That would solve the issue. Right now it seems that PYTHONPATH paths get incorporated into sys.path but are in the list after the system-wide site-packages directories, making the system wide version get used instead of the one in ~/.local.
Using pip is not an option unfortunately.
It is recommended that you use virtualenv with a proper activation script which will take care of settings up PYTHONPATH properly, without messing up system-wide Python installation in any way
http://www.virtualenv.org/en/latest/index.html