Confusion over Python versions - python

I am confused about setting up the Python environment on Mac M1. I have been using the latest version of Python3 3.10.4. However when I issue the following command at the Terminal. python3 --version. I get Python 3.9.12 why? I would like to set the latest version as default and be able to install packages like numpy and matplotlib for it. Ideally I would like to get rid of all the other versions. Any help would be appreciated.

When you type a command like python in the Terminal, without specifying the full path to the python executable, the shell (normally zsh on macOS) searches in multiple places to try to find a program called python.
The places that are searched are specified by the PATH environment variable, which is a list of directories separated by :.
For example, with the following PATH settings, it would try /opt/homebrew/bin/python first, then /usr/local/bin/python, then /usr/bin/python, etc. until it finds it. The first one wins.
% echo $PATH
/opt/homebrew/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
When you activate Conda environments and other Python virtual environments, these temporarily modify the PATH during that session, so that the programs installed in these environments take priority over the system ones.
To figure out which Python would be started, you can use the which command, or command -v:
% which python3
/opt/homebrew/bin/python3
% command -v python3
/opt/homebrew/bin/python3
Finally you can ask Python directly where it is running from:
>>> import sys
>>> print(sys.executable)
/opt/homebrew/opt/python#3.9/bin/python3.9
You appear to have many Pythons installed in many places which is creating your confusion. You say you have been using 3.10.4 which is the one at /usr/local/bin/python3.
If you want to install packages on this Python, you can specify its path explicitly:
/usr/local/bin/python3 -m pip install matplotlib

Related

VS Code can't find python 3 interpreter

I am installing Python 3.7.2 for the first time, and I'm using the VS Code python extension.
When I run python -V I get Python 2.7.10 which is not correct!
When I select the usr/local/bin/python3 interpreter in VS Code I get this error when running a script:
bash: /Users/erik/Work/Python/usr/local/bin/python3: No such file or directory
But when I look in usr/local/bin I can see that Python3 is there. I'm not sure why VS Code pastes the work directory in front of usr/local/bin ?
My first thought was that Python3 should be in the PATH variable so I ran the included Update Shell Profile command, which gives this feedback:
This script will update your shell profile when
the 'bin' directory of python is not early enough
of the PATH of your shell.
All right, you're a python lover already
Now, after rebooting VS Code I get a new option for selecting an interpreter:
/Library/Frameworks/Python.framework/Versions/3.7/bin/python3
Is that different from the Python in usr/local/bin ? When I select it, I get this error:
The script isort is installed in '/Users/erik/Library/Python/3.7/bin' which is not on PATH.
I also get this sideways related error:
You are using pip version 18.1. You should consider upgrading via the 'pip install --upgrade pip' command.
But, when following these instructions I get yet another error:
bash: pip: command not found
All in all, this process and the official documentation seem less than user-friendly? Apparently I'm required to dig deep through my mac's system files in the terminal before even writing one line of code.
Am I missing an essential step here?
I suggest that you use virtual environment for your project
first
pip install virtualenv
open cmd in your project directory that you open in VS-Code (it's important that vs-code sees this virtualenv folder that we will create)
mkvirtualenv my_env
and it will activate it automatically. if not run
my_env/bin/Scripts/activate or my_env/Scripts/activate
Then go open vs-code then select my_env for python interpreter
Well, if you want to change your default Python version for the whole system, it might break some applications that are depending on Python 2.
You can alias the commands by adding this line to your ~/.bash_profile:
$ alias python='python3'
The python command will now refer to python3.
If you want to execute the original Python (which refers to python2), you can escape the alias (so \python will launch python2 without touching the alias).
Btw.
$ unlink /usr/local/bin/python
$ ln -s /usr/local/bin/python3.7 /usr/local/bin/python
could also be a workaround for you.

Pip not installing Python modules to proper directory

So I downloaded a module, but when I tried to use it in a program, Python threw the error:
"ImportError: No module named markovify"
When I go to try to change my .bash_profile, it shows this:
"# Setting PATH for Python 3.5
The orginal version is saved in .bash_profile.pysave
PATH="/Library/Frameworks/Python.framework/Versions/3.5/bin:${PATH}"
export PATH"
I've been using 2.7.10 all this time, and Terminal defaults to it. (When I type in Python, that's the version it says I'm using)
I'm trying to get pip to install modules for python 2.7.10 to a different folder.
What's weird is this: I seem to have installed pyparsing with pip and it seems to work. I tried installing markovify and it throws this error message.
What am I missing?
When I go to try to change my .bash_profile, it prints this
That suggests you're using some tool to change your profile. Did you also use that tool to install markovify? You need to be clear about your environment when you have environment questions! :-)
If you installed markovify from the command line, I'd suggest opening a new terminal and running these commands, just to make sure you're working from where you think you are:
$ python --version
Python 2.7.10
$ command -v python
/usr/bin/python
The most likely problem, it seems to me, is that you got a bit tangled up and wound up doing something other than what you intended. From a fresh start, provided you're starting with the environment you want, pip should, you know, Just Work.
I'm trying to get pip to install modules for python 2.7.10 to a different folder.
That's possible to do, but are you sure that's what you want? Usually if you're using the Python interpreter you intend to, and haven't putzed with PYTHON_PATH & friends, when you run pip, it will install to its default location, which sure enough is where Python will look for it when you say to import it.
As an experiment, you might check if markovify was somehow installed for Python 3.5. Try
$ /Library/Frameworks/Python.framework/Versions/3.5/bin/python -c 'import markovify'
(You might also want to check that the Python interpreter is in fact in that folder and has that name.)
When you're working on more than one Python version, you should work on Virtual Environments:
Virtual Env on Hitchhiker's Guide

Running Jupyter with multiple Python and IPython paths

I'd like to work with Jupyter notebooks, but have had difficulty doing basic imports (such as import matplotlib). I think this was because I have several user-managed python installations. For instance:
> which -a python
/usr/bin/python
/usr/local/bin/python
> which -a ipython
/Library/Frameworks/Python.framework/Versions/3.5/bin/ipython
/usr/local/bin/ipython
> which -a jupyter
/Library/Frameworks/Python.framework/Versions/3.5/bin/jupyter
/usr/local/bin/jupyter
I used to have anaconda, but removed if from the ~/anaconda directory. Now, when I start a Jupyter Notebook, I get a Kernel Error:
File "/Library/Frameworks/Python.framework/Versions/3.5/lib/pytho‌n3.5/subprocess.py",
line 947, in init restore_signals, start_new_session)
File "/Library/Frameworks/Python.framework/Versions/3.5/lib/pytho‌n3.5/subprocess.py",
line 1551, in _execute_child raise child_exception_type(errno_num, err_msg)
FileNotFoundError: [Errno 2]
No such file or directory: '/Users/npr1/anaconda/envs/py27/bin/python'
What should I do?!
This is fairly straightforward to fix, but it involves understanding three different concepts:
How Unix/Linux/OSX use $PATH to find executables (%PATH% in Windows)
How Python installs and finds packages
How Jupyter knows what Python to use
For the sake of completeness, I'll try to do a quick ELI5 on each of these, so you'll know how to solve this issue in the best way for you.
1. Unix/Linux/OSX $PATH
When you type any command at the prompt (say, python), the system has a well-defined sequence of places that it looks for the executable. This sequence is defined in a system variable called PATH, which the user can specify. To see your PATH, you can type echo $PATH.
The result is a list of directories on your computer, which will be searched in order for the desired executable. From your output above, I assume that it contains this:
$ echo $PATH
/usr/bin/:/Library/Frameworks/Python.framework/Versions/3.5/bin/:/usr/local/bin/
In windows echo %path%
Probably with some other paths interspersed as well. What this means is that when you type python, the system will go to /usr/bin/python. When you type ipython, in this example, the system will go to /Library/Frameworks/Python.framework/Versions/3.5/bin/ipython, because there is no ipython in /usr/bin/.
It's always important to know what executable you're using, particularly when you have so many installations of the same program on your system. Changing the path is not too complicated; see e.g. How to permanently set $PATH on Linux?.
Windows - How to set environment variables in Windows 10
2. How Python finds packages
When you run python and do something like import matplotlib, Python has to play a similar game to find the package you have in mind. Similar to $PATH in unix, Python has sys.path that specifies these:
$ python
>>> import sys
>>> sys.path
['',
'/Users/jakevdp/anaconda/lib/python3.5',
'/Users/jakevdp/anaconda/lib/python3.5/site-packages',
...]
Some important things: by default, the first entry in sys.path is the current directory. Also, unless you modify this (which you shouldn't do unless you know exactly what you're doing) you'll usually find something called site-packages in the path: this is the default place that Python puts packages when you install them using python setup.py install, or pip, or conda, or a similar means.
The important thing to note is that each python installation has its own site-packages, where packages are installed for that specific Python version. In other words, if you install something for, e.g. /usr/bin/python, then ~/anaconda/bin/python can't use that package, because it was installed on a different Python! This is why in our twitter exchange I recommended you focus on one Python installation, and fix your$PATH so that you're only using the one you want to use.
There's another component to this: some Python packages come bundled with stand-alone scripts that you can run from the command line (examples are pip, ipython, jupyter, pep8, etc.) By default, these executables will be put in the same directory path as the Python used to install them, and are designed to work only with that Python installation.
That means that, as your system is set-up, when you run python, you get /usr/bin/python, but when you run ipython, you get /Library/Frameworks/Python.framework/Versions/3.5/bin/ipython which is associated with the Python version at /Library/Frameworks/Python.framework/Versions/3.5/bin/python! Further, this means that the packages you can import when running python are entirely separate from the packages you can import when running ipython or a Jupyter notebook: you're using two completely independent Python installations.
So how to fix this? Well, first make sure your $PATH variable is doing what you want it to. You likely have a startup script called something like ~/.bash_profile or ~/.bashrc that sets this $PATH variable. On Windows, you can modify the user specific environment variables. You can manually modify that if you want your system to search things in a different order. When you first install anaconda/miniconda, there will be an option to do this automatically (add Python to the PATH): say yes to that, and then python will always point to ~/anaconda/python, which is probably what you want.
3. How Jupyter knows what Python to use
We're not totally out of the water yet. You mentioned that in the Jupyter notebook, you're getting a kernel error: this indicates that Jupyter is looking for a non-existent Python version.
Jupyter is set-up to be able to use a wide range of "kernels", or execution engines for the code. These can be Python 2, Python 3, R, Julia, Ruby... there are dozens of possible kernels to use. But in order for this to happen, Jupyter needs to know where to look for the associated executable: that is, it needs to know which path the python sits in.
These paths are specified in jupyter's kernelspec, and it's possible for the user to adjust them to their desires. For example, here's the list of kernels that I have on my system:
$ jupyter kernelspec list
Available kernels:
python2.7 /Users/jakevdp/.ipython/kernels/python2.7
python3.3 /Users/jakevdp/.ipython/kernels/python3.3
python3.4 /Users/jakevdp/.ipython/kernels/python3.4
python3.5 /Users/jakevdp/.ipython/kernels/python3.5
python2 /Users/jakevdp/Library/Jupyter/kernels/python2
python3 /Users/jakevdp/Library/Jupyter/kernels/python3
Each of these is a directory containing some metadata that specifies the kernel name, the path to the executable, and other relevant info.
You can adjust kernels manually, editing the metadata inside the directories listed above.
The command to install a kernel can change depending on the kernel. IPython relies on the ipykernel package which contains a command to install a python kernel: for example
$ python -m ipykernel install
It will create a kernelspec associated with the Python executable you use to run this command. You can then choose this kernel in the Jupyter notebook to run your code with that Python.
You can see other options that ipykernel provides using the help command:
$ python -m ipykernel install --help
usage: ipython-kernel-install [-h] [--user] [--name NAME]
[--display-name DISPLAY_NAME] [--prefix PREFIX]
[--sys-prefix]
Install the IPython kernel spec.
optional arguments:
-h, --help show this help message and exit
--user Install for the current user instead of system-wide
--name NAME Specify a name for the kernelspec. This is needed to
have multiple IPython kernels at the same time.
--display-name DISPLAY_NAME
Specify the display name for the kernelspec. This is
helpful when you have multiple IPython kernels.
--prefix PREFIX Specify an install prefix for the kernelspec. This is
needed to install into a non-default location, such as
a conda/virtual-env.
--sys-prefix Install to Python's sys.prefix. Shorthand for
--prefix='/Users/bussonniermatthias/anaconda'. For use
in conda/virtual-envs.
Note: the recent version of anaconda ships with an extension for the notebook that should automatically detect your various conda environments if the ipykernel package is installed in it.
Wrap-up: Fixing your Issue
So with that background, your issue is quite easy to fix:
Set your PATH so that the desired Python version is first. For example, you could run export PATH="/path/to/python/bin:$PATH" to specify (one time) which Python you'd like to use. To do this permanently, add that line to your .bash_profile/.bashrc (note that anaconda can do this automatically for you when you install it). I'd recommend using the Python that comes with anaconda or miniconda: this will allow you to conda install all the tools you need.
Make sure the packages you want to use are installed for that python. If you're using conda, you can type, e.g. conda install jupyter matplotlib scikit-learn to install those packages for anaconda/bin/python.
Make sure that your Jupyter kernels point to the Python versions you want to use. When you conda install jupyter it should set this up for anaconda/bin/python automatically. Otherwise you can use the jupyter kernelspec command or python -m ipykernel install command to adjust existing kernels or install new ones.
For installing modules into other Python Jupyter kernels not managed by Anaconda, you need to copy the path to the Python executable for the kernel and run /path/to/python -m pip install <package>
#jakevdp explained it very well.
When I updated my ubuntu I also had the same problem and I solved it by changing the kernel configuration file(kernel.json).
To list the kernel files location.
Use
jupyter kernelspec list
It will return
Available kernels:
python3 /home/user1/.local/share/jupyter/kernels/python3
python2 /usr/local/share/jupyter/kernels/python2
I was using python3 so I changed the file at
/home/user1/.local/share/jupyter/kernels/python3
by following step
nano /home/user1/.local/share/jupyter/kernels/python3/kernel.json
There inside
argv
I changed the first parameter(i.e. python3 directory path) form
"/usr/bin/python3.5"
to
"/usr/bin/python3"
and saved it with
ctr+x
and restarted jupyter-notebook.
also found not to put your virtual environment inside the git repo as it becomes non-readable to read the python packages. seems different permissions use while reading and writing (writing - installing a package - use pip), how unable to read. Hence, for me the python libraries were getting read from system installation and not virtual environment.
#jakevdp's Answer above & his blog https://jakevdp.github.io/blog/2017/12/05/installing-python-packages-from-jupyter/ gives fairly good idea about what's going wrong, however just updating path from shell was not working for me, there are 2 ways that worked for me
Either update path on notebook using magic commands, run below on cell
originalPath = %env PATH
%env PATH = [local anaconda path]/kernels/[custom_kernel]/bin/:$originalPath
Or you can even update the kernel.json & set the path in env
{
"argv": [
"[custom kernel path]/bin/python",
"-m",
"ipykernel_launcher",
"-f",
"{connection_file}"
],
"env": {
"PATH": "[custom kernel path]/bin/:[rest of the paths]"
},
"display_name": "custom_kerbel",
"language": "python"
}
If you just want to install a package into the current environment to be able to import it, you can use the %pip and %conda magicks.
As you mention anaconda, you probably should use conda to install:
# Install a conda package in the current Jupyter kernel
%conda install <dependency_name>
Alternatively, if you need to use pip:
# Install a pip package in the current Jupyter kernel
%pip install <python_package_name>

What version of Python is on my Mac?

I have a mac, when I do:
python --version
I got:
Python 2.7.6
but when I got to:
/System/Library/Frameworks/Python.framework/Versions/3.3
where is 2.7.6 located ?
any advice what should I do?
UPDATE:
$ which -a python python3
/usr/bin/python
/usr/local/bin/python3
$ brew list python python3
Error: No such keg: /usr/local/Cellar/python
$ locate python
WARNING: The locate database (/var/db/locate.database) does not exist.
To create the database, run the following command:
sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.locate.plist
Please be aware that the database can take some time to generate; once
the database has been created, this message will no longer appear.
in PyCharm editor, the default settings interpreter shows:
You could have multiple Python versions on your macOS.
You may check that by command, type or which command, like:
which -a python python2 python2.7 python3 python3.6
Or type python in Terminal and hit Tab few times for auto completion, which is equivalent to:
compgen -c python
By default python/pip commands points to the first binary found in PATH environment variable depending what's actually installed. So before installing Python packages with Homebrew, the default Python is installed in /usr/bin which is shipped with your macOS (e.g. Python 2.7.10 on High Sierra). Any versions found in /usr/local (such as /usr/local/bin) are provided by external packages.
It is generally advised, that when working with multiple versions, for Python 2 you may use python2/pip2 command, respectively for Python 3 you can use python3/pip3, but it depends on your configuration which commands are available.
It is also worth to mention, that since release of Homebrew 1.5.0+ (on 19 January 2018), the python formula has been upgraded to Python 3.x and a python#2 formula will be added for installing Python 2.7. Before, python formula was pointing to Python 2.
For instance, if you've installed different version via Homebrew, try the following command:
brew list python python3
or:
brew list | grep ^python
it'll show you all Python files installed with the package.
Alternatively you may use apropos or locate python command to locate more Python related files.
To check any environment variables related to Python, run:
env | grep ^PYTHON
To address your issues:
Error: No such keg: /usr/local/Cellar/python
Means you don't have Python installed via Homebrew. However double check by specifying only one package at a time (like brew list python python2 python3).
The locate database (/var/db/locate.database) does not exist.
Follow the advice and run:
sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.locate.plist
After the database is rebuild, you can use locate command.
To check third version, we can use,
python3 --version
To install python on macOS, we need to install command line developer tools. From Catalina, python is removed from OS bundle. For more information, Apple Official and Python Official.
Use below command to see all python installations :
which -a python
Use the which command. It will show you the path
which python
Take a look at the docs regarding Python on Mac.
The version at /System/Library/Frameworks/Python.framework is installed by Apple and is used by the system. It is version 3.3 in your case. You can access and use this Python interpreter, but you shouldn't try to remove it, and it may not be the one that comes up when you type "Python" in a terminal or click on an icon to launch it.
You must have installed another version of Python (2.7) on your own at some point, and now that is the one that is launched by default.
As other answers have pointed out, you can use the command which python on your terminal to find the path to this other installation.
You can use python official installer. It's very easy and interactive.
Refer https://www.python.org/downloads/release/python-2716/
Just type python and then hit tab-button You will get the list of all the python available in your os

Python ImportError while module is installed [Ubuntu]

I'd like to make a switch from Windows to Linux (Ubuntu) writing my python programs but I just can't get things to work. Here's the problem: I can see that there are quite the number of modules pre-installed (like numpy, pandas, matplotlib, etc.) in Ubuntu. They sit nicely in the /host/Python27/Lib/site-packages directory. But when I write a test python script and try to execute it, it gives me an ImportError whenever I try to import a module (for instance import numpy as np gives me ImportError: No module named numpy). When I type which python in the commandline I get the /usr/bin/python path. I think I might need to change things related to the python path, but I don't know how to do that.
You can use the following command in your terminal to see what folders are in your PYTHONPATH.
python -c "import sys, pprint; pprint.pprint(sys.path)"
I'm guessing /host/Python27/Lib/site-packages wont be in there (it doesn't sound like a normal python path. How did you install these packages?).
If you want to add folders to your PYTHONPATH then use the following:
export PYTHONPATH=$PYTHONPATH:/host/Python27/Lib/site-packages
Personally here are some recommendations for developing with Python:
Use virtualenv. It is a very powerful tool that creates sandboxed python environments so you can install modules and keep them separate from the main interpreter.
Use pip - When you've created a virtualenv, and activated it you can use pip install to install packages for you. e.g. pip install numpy will install numpy into your virtual environment and will be accessible from only this virtualenv. This means you can also install different versions for testing etc. Very powerful. I would recommend using pip to install your python packages over using ubuntu apt-get install as you are more likely to get the newer versions of modules (apt-get relies on someone packaging the latest versions of your python libraries and may not be available for as many libraries as pip).
When writing python scripts that you will make executable (chmod +x my_python_script.py) make sure you put #!/usr/bin/env python at the top as this will pick up the python interpreter in your virtual environment. If you don't (and put #!/usr/bin/python) then running ./my_python_script.py will always use the system python interpreter.
/host/Python27/Lib/site-packages is not a default python directory on linux installations as far as I am aware.
The normal python installation (and python packages) should be found under /usr/lib or /usr/lib64 depending on your processor architecture.
If you want to check where python is searching in addition to these directories you can use a terminal with the following command:
echo $PYTHONPATH
If the /host/Python27/Lib/site-packages path is not listed, attempt to use the following command and try it again:
export PYTHONPATH=$PYTHONPATH:host/Python27/Lib/site-packages
If this should work and you do not want to write this in a terminal every time you want to use these packages, simply put it into a file called .bashrc in your home folder (normally /home/<username>).
When installing other python libraries, specify the pip version you want to install it to, if it's python2 you use, then enter this syntax:
pip2 install <package>
For python3
pip3 install <package>

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