Develop Reference

Python3 and 'code' CLI not working after updating to MacOS Monterey

I updated to MacOS Monterey and now python is not working:
➜ ~ python3 --version
dyld[6578]: dyld cache '/System/Library/dyld/dyld_shared_cache_x86_64h' not loaded: syscall to map cache into shared region failed
dyld[6578]: Library not loaded: /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
Referenced from: /Library/Frameworks/Python.framework/Versions/3.6/Resources/Python.app/Contents/MacOS/Python
Reason: tried: '/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation' (no such file), '/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation' (no such file)
[1] 6578 abort python3 --version
But if I run:
➜ ~ /usr/bin/python3 --version
Python 3.8.9
I am able to run it. But when running code . for opening a project in vs code it gives the same error:
dyld[6683]: dyld cache '/System/Library/dyld/dyld_shared_cache_x86_64h' not loaded: syscall to map cache into shared region failed
dyld[6683]: Library not loaded: /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
Referenced from: /Library/Frameworks/Python.framework/Versions/3.6/Resources/Python.app/Contents/MacOS/Python
Reason: tried: '/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation' (no such file), '/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation' (no such file)
/usr/local/bin/code: line 10: ./MacOS/Electron: No such file or directory
I am not sure what to do so that it runs commands like code . successfully.

This is 100% a version conflict/PATH problem.
First, open up terminal and try running echo $PATH. It should print something like this:
/opt/homebrew/bin:/opt/homebrew/sbin:/Library/Frameworks/Python.framework/Versions/3.10/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/Apple/usr/bin
As you can see, it says 3.10 for me, while yours says 3.6
#guest_fish makes a good suggestion with deleting outdated versions of Python, but another way you can try is by checking the following:
vim $HOME/.zprofile ---> this is the zsh analogue to .bash_profile, here's what mine looks like:
# Setting PATH for Python 3.10
# The original version is saved in .zprofile.pysave
PATH="/Library/Frameworks/Python.framework/Versions/3.10/bin:${PATH}"
export PATH
eval "$(/opt/homebrew/bin/brew shellenv)"
Note how it matches the first part of the path I echo'd above
vim /etc/paths ---> this should match the middle parts of your PATH, mine looks like this:
/usr/local/bin
/usr/bin
/bin
/usr/sbin
/sbin
vim /etc/paths.d/<your_unique_id> (just press tab to complete it when you're in paths.d, you generally have only one option). Mine looks like this:
/Library/Apple/usr/bin
Note how it matches the end of the path
When you visit each of these files, you can modify them (password protected obv) to put /usr/bin/python3 first, meaning that will be the first place that it looks for python build files and will (hopefully) use the correct version
Now, to fix the code thing, you could try going into VSCode and hitting SHIFT + ⌘ + P, then select Shell Command: Install 'code' command in PATH - this should update it for you automatically.
Lmk how it goes!

Your python3 is 3.8.9 but the error message is for 3.6. It looks like you have clashing python versions. I fixed this error on my machine by uninstalling 3.6 and all of its syslinks like seen here under "Uninstalling Python 3 Using Terminal", except I used homebrew commands brew doctor and then brew cleanup for steps 4. and 5.

How do I use libsvm in Python without modifying sys.path?

I installed libsvm in Ubuntu. All I want to do is call from svmutil import * in Python without it giving me an error. However, I see no good documentation on how to configure libsvm to work with python. "Adding libsvm to a path" tells me nothing.
And I don't want to use a package manager. What do I need to do to make libsvm found when running python outside of the original libsvm install folder?
(ykp) yannik#yannik-Inspiron-7580:~/Projects/libsvm$ ls
COPYRIGHT java python svm.o svm-toy
description-pak libsvm.so.2 README svm-predict svm-train
doc-pak Makefile svm.cpp svm-predict.c svm-train.c
FAQ.html Makefile.win svm.def svm-scale tools
heart_scale matlab svm.h svm-scale.c windows
(ykp) yannik#yannik-Inspiron-7580:~/Projects/libsvm$ ls python
commonutil.py Makefile README svmutil.py
description-pak __pycache__ svm.py
I tried doing sudo ln -s libsvm.so.2 /usr/local/lib and adding ~/Projects/libsvm to my PYTHONPATH with no success. Please help!

If ~/Projects/libsvm/python/ is where the module you want to import exists, then you have to add ~/Projects/libsvm/python/ to your PYTHONPATH not ~/Projects/libsvm/. The PYTHONPATH doesn't just automatically recursively search down for python files if that is what you were expecting.

Windows command line, "python3" pointing to the wrong python3.exe

So, I have Anaconda, OSGeo and Python2.7 installed on my computer.
I'm also using Spyder. In Spyder :
>>> import sys
>>> sys.executable
'C:\\ProgramData\\Anaconda3\\pythonw.exe'
Which is what I want.
However, in the windows command line and powershell :
$ python3
>>> import sys
>>> sys.executable
'C:\\Progra~1\\OSGeo4W\\bin\\python3.exe'
Which is not what I want. I want to use 'C:\\ProgramData\\Anaconda3\\pythonw.exe' (or python.exe, not sure) when using python3 in the command line.
Also :
$ pip3
Fatal error in launcher: Unable to create process using '"'
I don't get why python3 in the windows command line points to OSGeo's version of Python3. Here is my path :
C:\Python27\;C:\Python27\Scripts;C:\ProgramData\Anaconda3;C:\ProgramData\Oracle\Java\javapath;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\Git\cmd;C:\Program Files\PuTTY\;C:\Progra~1\OSGeo4W\bin\;C:\Program Files\Microsoft\R Open\R-3.4.0\bin
I also have an environment variable called PYTHONHOME
C:\ProgramData\Anaconda3
Moreover (for completeness of information), I have python 2 installed :
$ python
File "C:\ProgramData\Anaconda3\lib\site.py", line 177
file=sys.stderr)
^
SyntaxError: invalid syntax
($ pip outputs the same thing).
Having python3 and python2.7 both work when using python3 and python (respectively) in the windows command line would be a nice bonus, but it's not really my priority.

There are probably several things you have to take care of:
In general the search order of the Windows PATH is from left to right starting with the system PATH. The first matching element wins. In your case this is correct because the system will search C:\ProgramData\Anaconda3\ first. However in that folder is no executable called python3 by default. On my system I created a simlink pointing to python.exe. On your system you can do it in PowerShell like this:
New-Item -Path C:\ProgramData\Anaconda3\python3.exe -ItemType SymbolicLink -Value C:\ProgramData\Anaconda3\python.exe
pip is located in Scripts\ folder so in your case you have to add C:\ProgramData\Anaconda3\Scripts to your PATH and create the corresponding simlinks again. In this case you have to create two of them because pip.exe is appending its name to the script that is trying to call (i.e. if your exe file is called foo.exe it will try to call foo-script.exe which does not exist) you can create the simlinks in PowerShell with those two commands:
New-Item -Path C:\ProgramData\Anaconda3\Scripts\pip3.exe -ItemType SymbolicLink -Value C:\ProgramData\Anaconda3\Scripts\pip.exe
and
New-Item -Path C:\ProgramData\Anaconda3\Scripts\pip3-script.py -ItemType SymbolicLink -Value C:\ProgramData\Anaconda3\Scripts\pip-script.py
Like this you will be able to use python3 and pip3 from your cmd line. Please check for similar problems with your python2 installation folder.
Hope it helps.

Couldn't create working virtual environment for Python 3.4

I installed Python 3.4.2 and Virtualenv 12.0.5 in my Linux Mint 17.1
Then I tried creating:
$ virtualenv venv
And also using --clear and/or -p /usr/bin/python3.4, always getting the messages:
Using base prefix '/usr'
New python executable in venv/bin/python3
Also creating executable in venv/bin/python
ERROR: The executable venv/bin/python3 could not be run: [Errno 13] Permission denied
Another try was:
$ pyvenv-3.4 venv
It gave no errors on creation, but in the venv/bin file the python3.4 is a symbolic link to /usr/local/bin/python3.4. Then when I activate and install any lib using pip or pip3, then try to import it, I get the error:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named 'anymoduledownloaded'
I always used virtualenv in Python 2.X and never got this kind of errors. Any thoughts on what am I doing wrong?
Thanks!!
=======EDITED=======
This is the output of my partitions (fdisk -l):
Device Boot Start End Blocks Id System
/dev/sda1 2048 98707455 49352704 83 Linux
/dev/sda2 303507456 3890644991 1793568768 5 Extended
/dev/sda3 * 98707456 303507455 102400000 7 HPFS/NTFS/exFAT
/dev/sda4 3890644992 3907028991 8192000 82 Linux swap / Solaris
/dev/sda5 303509504 3890644991 1793567744 7 HPFS/NTFS/exFAT`
And also my fstab:
<file system> <mount point> <type> <options> <dump> <pass>
-> was on /dev/sda1 during installation
UUID=a38f9c6d-3cd9-4486-b896-acbc6182ec61 / ext4 errors=remount-ro 0 1
-> swap was on /dev/sda4 during installation
UUID=efad7b53-79a8-4230-8226-9ca90c68ea9d none swap sw 0 0`

Is that a shared partition that you have mounted? Does the shared partition have a different filesystem then the non-shared one you tried upon? If yes, then IMO, that will definitely cause an error since you are making and compiling binaries for python on one filesystem, and so it will not work on another filesystem.
As mentioned in this answer, adding to your /etc/fstab with an entry with exec flag might make it work for you, i.e., you might need to add another entry for the NTFS disk here to make it automount:
<file system> <mount point> <type> <options> <dump> <pass>
-> was on /dev/sdaX during installation
UUID=<uid_of_NTFS> / ntfs auto,user,exec,nodev,rw,errors=remount-ro 0 1

I struggled with this as well so I wrote an ugly bash script to help me with this. The only salient difference between what you do and what I do is on line 133:
/path/to/python/bin/python3.4 /path/to/python/bin/pyvenv /path/to/venv
That is, explicitly name the instance of python and the venv tool. Then
/path/to/venv/bin/pip install django # or whatever
Edit
I installed Linux Mint in a VM to try and build a Python 3.4 virtual environment. Based on the error messages I saw and this answer, I learned that I must do the following to get a complete Python 3.4 build:
apt-get install build-essential libssl-dev openssl
Without this, my Python 3.4 build did not contain pip. Note that you probably want to install readline and other development packages.
Unsolicited Advice
Do not do this as root, create a user dedicated to running your venv
Create a script to create your environment
Check that script into your source code repo
I deleted my python binaries and venvs multiple times and then recreated all of with this script to make sure that my script reproduced my environment and then stripped the identifying information and saved that on github to share it. I should really be using a more formal tool for this like docker/puppet/chef.

Compiling vim with specific version of Python

I'm working on several Python projects who run on various versions of Python. I'm hoping to set up my vim environment to use ropevim, pyflakes, and pylint but I've run into some issues caused by using a single vim (compiled for a specific version of Python which doesn't match the project's Python version).
I'm hoping to build vim into each of my virtualenv directories but I've run into an issue and I can't get it to work. When I try to build vim from source, despite specifying the Python config folder in my virtualenv, the system-wide Python interpreter is always used.
Currently, I have Python 2.6.2 and Python 2.7.1 installed with several virtualenvs created from each version. I'm using Ubuntu 10.04 where the system-default Python is 2.6.5. Every time I compile vim and call :python import sys; print(sys.version) it returns Python 2.6.5.
configure --prefix=/virtualenv/project --enable-pythoninterp=yes --with-python-config-dir=/virtualenv/project/lib/python2.6/config
Results in the following in config.log:
...
configure:5151: checking --enable-pythoninterp argument
configure:5160: result: yes
configure:5165: checking for python
configure:5195: result: /usr/bin/python
...
It should be /virtualenv/project/bin/python. Is there any way to specify the Python interpreter for vim to use?
NOTE: I can confirm that /virtualenv/project/bin appears at the front of PATH environment variable.

I'd recommend building vim against the 2 interpreters, then invoking it using the shell script I provided below to point it to a particular virtualenv.
I was able to build vim against Python 2.7 using the following command (2.7 is installed under $HOME/root):
% LD_LIBRARY_PATH=$HOME/root/lib PATH=$HOME/root/bin:$PATH \
./configure --enable-pythoninterp \
--with-python-config-dir=$HOME/root/lib/python2.7/config \
--prefix=$HOME/vim27
% make install
% $HOME/bin/vim27
:python import sys; print sys.path[:2]
['/home/pat/root/lib/python27.zip', '/home/pat/root/lib/python2.7']
Your virtualenv is actually a thin wrapper around the Python interpreter it was created with -- $HOME/foobar/lib/python2.6/config is a symlink to /usr/lib/python2.6/config.
So if you created it with the system interpreter, VIM will probe for this and ultimately link against the real interpreter, using the system sys.path by default, even though configure will show the virtualenv's path:
% PATH=$HOME/foobar/bin:$PATH ./configure --enable-pythoninterp \
--with-python-config-dir=$HOME/foobar/lib/python2.6/config \
--prefix=$HOME/foobar
..
checking for python... /home/pat/foobar/bin/python
checking Python's configuration directory... (cached) /home/pat/foobar/lib/python2.6/config
..
% make install
% $HOME/foobar/bin/vim
:python import sys; print sys.path[:1]
['/usr/lib/python2.6']
The workaround: Since your system vim is most likely compiled against your system python, you don't need to rebuild vim for each virtualenv: you can just drop a shell script named vim in your virtualenv's bin directory, which extends the PYTHONPATH before calling system vim:
Contents of ~/HOME/foobar/bin/vim:
#!/bin/sh
ROOT=`cd \`dirname $0\`; cd ..; pwd`
PYTHONPATH=$ROOT/lib/python2.6/site-packages /usr/bin/vim $*
When that is invoked, the virtualenv's sys.path is inserted:
% $HOME/foobar/bin/vim
:python import sys; print sys.path[:2]
['/home/pat/foobar/lib/python2.6/site-packages', '/usr/lib/python2.6']

For what it's worth, and no one seems to have answered this here, I had some luck using a command line like the following:
vi_cv_path_python=/usr/bin/python26 ./configure --includedir=/usr/include/python2.6/ --prefix=/home/bcrowder/local --with-features=huge --enable-rubyinterp --enable-pythoninterp --disable-selinux --with-python-config-dir=/usr/lib64/python2.6/config

I would like to give a similar solution to crowder's that works quite well for me.
Imagine you have Python installed in /opt/Python-2.7.5 and that the structure of that folder is
$ tree -d -L 1 /opt/Python-2.7.5/
/opt/Python-2.7.5/
├── bin
├── include
├── lib
└── share
and you would like to build vim with that version of Python. All you need to do is
$ vi_cv_path_python=/opt/Python-2.7.5/bin/python ./configure --enable-pythoninterp --prefix=/SOME/FOLDER
Thus, just by explicitly giving vi_cv_path_python variable to configure the script will deduce everything on it's own (even the config-dir).
This was tested multiple times on vim 7.4+ and lately with vim-7-4-324.

I was having this same issue with 3 different versions of python on my system.
for me the easiest thing was to change my $PATH env variable so that the folder that has the version of python I wanted was (in my case /usr/local/bin) was found before another.

During my compiling vim80, the system python is 2.6, I have another python 2.7 under ~/local/bin, I find that, to make the compiling work:
update $PATH to place my python path ahead
add a soft link, ln -s python python2 ( the configure file would try to locate python config by probing python2 )
make distclean before re-run ./configure to make sure no cached wrong value is picked.