Msys2 with python 3.8: ImportError: cannot import name 'open_code' from 'io'

Asked 4/4, 2020 at 13:15 Answered 24/4, 2020 at 10:40

Solved python python-3.7 msys2 python-3.8

NOTE: There have been several EDITs to the question, as per comments. They are indicated below, and separated by lines. As of now, the only remaining issue seems to be that numpy cannot load, possibly (but not certainly) due to two alternative python 3.8 systems present.

I have updated my msys2 system a couple of months ago. That apparently included an update from python 3.7 to 3.8, but which left me with two broken pythons: I can start python when it is 3.7, but there are no associated packages, and I cannot start python when it is 3.8, which is the version holding packages. I do not know what went wrong with that, or what did I do wrong. I just noticed this now with the first time I mean to use python again after the upgrade.

I will describe here a sequence of steps I followed and what I found. I will post supporting code below for clarity.

I can start python, but pandas (e.g.) and many other packages are not found in python. Checking further, /mingw64/lib/python3.7/site-packages is essentially empty (surely emptied when upgrading to 3.8).
Looking for the pandas package, I found I have one version installed.
The pandas version is for python 3.8, surely upgraded from 3.7.
I redirected PYTHONPATH from 3.7 to 3.8
~~Now I cannot even start python.~~ EDIT Now I can start python, with some misconfiguration issues (i.e., partially fixed).

Now the question is

~~How can I fix python3.8, which gives the error below?~~

ImportError: cannot import name 'open_code' from 'io' (unknown location)

How can I fix python3.8, which gives the problems below?

New problems:

5.1. I should have python pointing to 3.8, and also fix packages.

5.2. Some modules are not found, some other are.

Note: I don't know if Msys2 upgrade breaks python2-pyqt5 has anything to do with this.

https://github.com/tox-dev/tox/issues/1334

https://github.com/yan12125/python3-android/issues/19

https://python-forum.io/Thread-Fatal-Python-error-init-sys-streams-can-t-initialize-sys-standard-streams-Attribute

TL;DR: Supporting code

pandas not found

$ python
Python 3.7.4 (default, Jul 11 2019, 10:29:54)
[GCC 9.1.0] on msys
Type "help", "copyright", "credits" or "license" for more information.
Reading /home/user1/.pythonrc
readline is in /usr/lib/python3.7/lib-dynload/readline.cpython-37m.dll
>>> import pandas
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'pandas'
>>>

pandas is actually installed

$ pacman -Sl | grep python | grep installed
mingw64 mingw-w64-x86_64-python 3.8.2-1 [installed: 3.8.1-1]
mingw64 mingw-w64-x86_64-python-apipkg 1.5-1 [installed]
...
mingw64 mingw-w64-x86_64-python-pandas 1.0.3-1 [installed: 1.0.1-1]
...
mingw64 mingw-w64-x86_64-python2-setuptools 44.1.0-1 [installed: 42.0.2-1]
msys python 3.7.4-1 [installed]
msys python2 2.7.17-1 [installed]

My pandas version is for python 3.8

$ pacman -Ql mingw-w64-x86_64-python-pandas | head -5
mingw-w64-x86_64-python-pandas /mingw64/
mingw-w64-x86_64-python-pandas /mingw64/lib/
mingw-w64-x86_64-python-pandas /mingw64/lib/python3.8/
mingw-w64-x86_64-python-pandas /mingw64/lib/python3.8/site-packages/
mingw-w64-x86_64-python-pandas /mingw64/lib/python3.8/site-packages/pandas-1.0.1-py3.8.egg-info/

I redirected PYTHONPATH from 3.7 to 3.8

Changed

export PYVERSION="3.7"
export PYTHONDIR2="${MINGW_HOME}/lib/python${PYVERSION}"
export PYTHONPATH="${PYTHONDIR2}:${PYTHONDIR2}/site-packages"

export PYVERSION="3.8"
...

~~Now I cannot even start python.~~ EDIT: Old problem:

$ python
Fatal Python error: init_sys_streams: can't initialize sys standard streams
Traceback (most recent call last):
  File "/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/io.py", line 54, in <module>
ImportError: cannot import name 'open_code' from 'io' (unknown location)
Aborted (core dumped)

New problems:

$ python --version
Python 3.7.4
$ type python
python is hashed (/usr/bin/python)
$ ls /usr/bin/python
/usr/bin/python
$ python3.8
Python 3.8.2 (default, Apr  9 2020, 13:17:39)  [GCC 9.3.0 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
Reading C:/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/home/user1/.pythonrc
Module readline not available.
Traceback (most recent call last):
  File "C:/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/home/user1/.pythonrc", line 42, in <module>
    del os, atexit, readline, rlcompleter, save_history, historyPath
NameError: name 'readline' is not defined
>>> import readline
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'readline'
>>> import zipfile
>>> import pandas
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages/pandas/__init__.py", line 16, in <module>
    raise ImportError(
ImportError: Unable to import required dependencies:
numpy: DLL load failed while importing _ctypes: No se puede encontrar el módulo especificado.
>>> import numpy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages/numpy/__init__.py", line 142, in <module>
    from . import core
  File "C:/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages/numpy/core/__init__.py", line 106, in <module>
    from . import _dtype_ctypes
  File "C:/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages/numpy/core/_dtype_ctypes.py", line 25, in <module>
    import _ctypes
ImportError: DLL load failed while importing _ctypes: No se puede encontrar el módulo especificado.
>>> exit()
Error in atexit._run_exitfuncs:
Traceback (most recent call last):
  File "<frozen importlib._bootstrap>", line 991, in _find_and_load
  File "<frozen importlib._bootstrap>", line 973, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'readline'

EDIT #2: Adding info as requested. I just noticed I don't have pip. That matches the fact that I never installed any package with pip...

$ echo $PATH
/usr/local/bin:/usr/bin:/bin:/opt/bin:/c/Windows/System32:/c/Windows:/c/Windows/System32/Wbem:/c/Windows/System32/WindowsPowerShell/v1.0/:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl:/c/Users/user1/OneDrive/Documents/soft-hard-ware/linux-ubuntu:/c/Users/user1/OneDrive/Documents/soft-hard-ware/linux-ubuntu/rsync:/c/Users/user1/Documents/appls_mydocs/science-math-visualization/gp524-win64-mingw_3/gnuplot/bin:/mingw64/bin
$ echo $PYTHONPATH
/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8:/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages
$ echo $PYTHONSTARTUP
/home/user1/.pythonrc
$ which python3.8
/mingw64/bin/python3.8
$ python3.8 -m pip freeze
C:/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/bin/python3.8.exe: No module named pip
$ python3.8 -c "import sys; print(sys.builtin_module_names)"
('_abc', '_ast', '_codecs', '_collections', '_functools', '_imp', '_io', '_locale', '_operator', '_signal', '_sre', '_stat', '_string', '_symtable', '_thread', '_tracemalloc', '_warnings', '_weakref', '_winapi', 'atexit', 'builtins', 'errno', 'faulthandler', 'gc', 'itertools', 'marshal', 'msvcrt', 'nt', 'sys', 'time', 'winreg', 'xxsubtype')

EDIT #3: Posting as requested, plus additional info.

$ cat .pythonrc
import os
print( "Reading " + os.path.realpath(__file__) )

# enable syntax completion
try:
    import readline
    print( "readline is in " + readline.__file__ )
except ImportError:
    print("Module readline not available.")
else:
    import rlcompleter
    readline.parse_and_bind("tab: complete")

# From https://docs.python.org/2/tutorial/interactive.html

# Add auto-completion and a stored history file of commands to your Python
# interactive interpreter. Requires Python 2.0+, readline. Autocomplete is
# bound to the Esc key by default (you can change it - see readline docs).
#
# Store the file in ~/.pystartup, and set an environment variable to point
# to it:  "export PYTHONSTARTUP=~/.pystartup" in bash.

import atexit
import os
#import readline
#import rlcompleter

historyPath = os.path.expanduser("~/.pyhistory")

def save_history(historyPath=historyPath):
    import readline
    readline.write_history_file(historyPath)

if os.path.exists(historyPath):
    #import readline
    readline.read_history_file(historyPath)

atexit.register(save_history)
del os, atexit, readline, rlcompleter, save_history, historyPath

I don't see why which python3.8 and PYTHONPATH were out of sync:

$ cygpath -w $(which python3.8)
C:\Users\user1\Documents\appls_mydocs\PortableApps\MSYS2Portable\App\msys32\mingw64\bin\python3.8.exe
$ echo $PYTHONPATH
/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8:/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages
$ cygpath -w /c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8
C:\Users\user1\Documents\appls_mydocs\PortableApps\MSYS2Portable\App\msys32\mingw64\lib\python3.8
$ cygpath -w /c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages
C:\Users\user1\Documents\appls_mydocs\PortableApps\MSYS2Portable\App\msys32\mingw64\lib\python3.8\site-packages
$ which python
/usr/bin/python

I seem to have two incomplete/broken python installations (3.7, 3.8). I don't know what led to an "incomplete" upgrade. A couple of observations (see code below):

python points to 3.7
readline is available for 3.7 and not for 3.8. I don't know why.
pandas (and many others) is available for 3.8 and not for 3.7. Many of them won't import in 3.8 anyway, due to missing dependencies (which I guess are available in 3.7). I don't know why.
python3.8 reports the location of .pythonrc in Windows format, while 3.7 reports it in Cygwin format. Is that normal?
Removing PYTHONPATH does not help.

$ unset PYTHONPATH
$ python3.8
Python 3.8.2 (default, Apr  9 2020, 13:17:39)  [GCC 9.3.0 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
Reading C:/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/home/user1/.pythonrc
Module readline not available.
Traceback (most recent call last):
  File "C:/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/home/user1/.pythonrc", line 42, in <module>
    del os, atexit, readline, rlcompleter, save_history, historyPath
NameError: name 'readline' is not defined
>>> import pandas
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages/pandas/__init__.py", line 16, in <module>
    raise ImportError(
ImportError: Unable to import required dependencies:
numpy: DLL load failed while importing _ctypes: No se puede encontrar el módulo especificado.
>>> exit()
Error in atexit._run_exitfuncs:
Traceback (most recent call last):
  File "<frozen importlib._bootstrap>", line 991, in _find_and_load
  File "<frozen importlib._bootstrap>", line 973, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'readline'
$ python
Python 3.7.4 (default, Jul 11 2019, 10:29:54)
[GCC 9.1.0] on msys
Type "help", "copyright", "credits" or "license" for more information.
Reading /home/user1/.pythonrc
readline is in /usr/lib/python3.7/lib-dynload/readline.cpython-37m.dll
>>> import pandas
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'pandas'
>>> exit()

EDIT #4:

I checked for all python packages, and I found something strange. It seems the basic python installation comprises two separate packages, one mingw64 and another msys. I wouldn't know what does each one do.

$ pacman -Sl | grep "python" | grep "installed"
...
mingw64 mingw-w64-x86_64-python 3.8.2-2 [installed]
...
msys python 3.8.2-1 [installed: 3.7.4-1]
...

On one hand, there was a mismatch in installed versions mingw64 (3.8.2-2) vs msys (3.7.4-1). On the other hand, the subversions available are not exactly the same for both (3.8.2-2) vs (3.8.2-1). Anyway, I proceeded upgrading msys python, and this fixed things significantly.

$ pacman -S python
...
$ python
Python 3.8.2 (default, Apr 16 2020, 15:31:48)
[GCC 9.3.0] on msys
Type "help", "copyright", "credits" or "license" for more information.
Reading /home/user1/.pythonrc
Traceback (most recent call last):
  File "/home/user1/.pythonrc", line 9, in <module>
    import readline
  File "/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages/readline.py", line 6, in <module>
    from pyreadline.rlmain import Readline
  File "/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages/pyreadline/__init__.py", line 12, in <module>
    from . import logger, clipboard, lineeditor, modes, console
  File "/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages/pyreadline/clipboard/__init__.py", line 13, in <module>
    from .win32_clipboard import GetClipboardText, SetClipboardText
  File "/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages/pyreadline/clipboard/win32_clipboard.py", line 37, in <module>
    import ctypes.wintypes as wintypes
  File "/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/ctypes/wintypes.py", line 20, in <module>
    class VARIANT_BOOL(ctypes._SimpleCData):
ValueError: _type_ 'v' not supported
Failed calling sys.__interactivehook__
Traceback (most recent call last):
  File "/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site.py", line 412, in register_readline
    import readline
  File "/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages/readline.py", line 6, in <module>
    from pyreadline.rlmain import Readline
  File "/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages/pyreadline/__init__.py", line 12, in <module>
    from . import logger, clipboard, lineeditor, modes, console
  File "/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages/pyreadline/clipboard/__init__.py", line 13, in <module>
    from .win32_clipboard import GetClipboardText, SetClipboardText
  File "/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages/pyreadline/clipboard/win32_clipboard.py", line 37, in <module>
    import ctypes.wintypes as wintypes
  File "/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/ctypes/wintypes.py", line 20, in <module>
    class VARIANT_BOOL(ctypes._SimpleCData):
ValueError: _type_ 'v' not supported

So I have readline in 3.8 now. But there is another issue that pops up during loading of .pythonrc.

Plus, there is a problem with numpy. It does not stem from the python version (/usr/bin/python points now to 3.8).

$ python --version
Python 3.8.2
$ python
...
>>> import numpy
Traceback (most recent call last):
  File "/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages/numpy/core/__init__.py", line 24, in <module>
    from . import multiarray
  File "/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages/numpy/core/multiarray.py", line 14, in <module>
    from . import overrides
  File "/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages/numpy/core/overrides.py", line 7, in <module>
    from numpy.core._multiarray_umath import (
ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages/numpy/__init__.py", line 142, in <module>
    from . import core
  File "/c/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/site-packages/numpy/core/__init__.py", line 54, in <module>
    raise ImportError(msg)
ImportError:

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy c-extensions failed.
- Try uninstalling and reinstalling numpy.
- If you have already done that, then:
  1. Check that you expected to use Python3.8 from "/usr/bin/python.exe",
     and that you have no directories in your PATH or PYTHONPATH that can
     interfere with the Python and numpy version "1.18.3" you're trying to use.
  2. If (1) looks fine, you can open a new issue at
     https://github.com/numpy/numpy/issues.  Please include details on:
     - how you installed Python
     - how you installed numpy
     - your operating system
     - whether or not you have multiple versions of Python installed
     - if you built from source, your compiler versions and ideally a build log

- If you're working with a numpy git repository, try `git clean -xdf`
  (removes all files not under version control) and rebuild numpy.

Note: this error has many possible causes, so please don't comment on
an existing issue about this - open a new one instead.

Original error was: No module named 'numpy.core._multiarray_umath'

EDIT #5 As per @a_guest suggestion, and pointing me to "ValueError: _type_ 'v' not supported" error after installing PyReadline, I removed pyreadline, and this problem is gone.

Now the only remaining issue seems to be that numpy cannot load, possibly (but not certainly) due to two alternative python 3.8 systems present.

So the questions now is: Msys2: Two python installations?

Peaslee answered 4/4, 2020 at 13:15 Comment(20)

That is very odd indeed. Try switching python back to python 3.7, then do python -m pip install pandas-- then see if that works. – Parakeet 17/4, 2020 at 3:21

@Xilpex - What would that prove? What would be the following steps, depending on the outcome? I am not certain this action is not risky (breaking my system even further). Notice that I never installed any msys2 package with pip, but always with pacman. I guess the reasonable target is to fix python3.8, and remove the remnants of 3.7. I don't see how the proposal contributes to that. As a second option, I would have a fully functional 3.7, but then I guess every time I perform an update, it would include 3.7->3.8. I think I cannot permanently refrain from doing that. – Peaslee 17/4, 2020 at 4:46

This may not be particularly helpful after-the-fact, but this is why you should keep your system python concerns separate from concerns of your projects. You should probably not use the system package manager for installing python packages you need for everyday use. This is more or less the same reason why you should not use pip on the system-installed versions of Python. Instead, you should use a virtual environment. Try uninstalling or reinstalling/updating your python packages with pacman. – Blague 20/4, 2020 at 17:25

@Blague - On the conceptual side, I guess this issue is different from python system-wide vs. user-level (or project-level, or environment-level) packages. This digression is in general interesting, but does not affect the present status or line-of-action. On the practical side, I will see how can I proceed with uninstalling/installing. – Peaslee 21/4, 2020 at 8:37

I don't know if it helps, but I had the same issue a while ago with the error message "cannot import name 'open_code' from 'io'". The issue was that the python 3.8 version which I have used was older than the commit "github.com/python/cpython/commit/…", where io.open_code has been added. The newest mingw-python seems to be based on python 3.8.2. Have you tried to install it? – Oreopithecus 21/4, 2020 at 9:13

@Oreopithecus - You are right, I had 3.8.1-1. I have updated to 3.8.2-2, but I get the same error. – Peaslee 21/4, 2020 at 10:49

@sancho.sReinstateMonicaCellio Apparently you are trying to start the broken installation of Python 3.7. In (1) you type python and it drops you in 3.7.4. Then in (4) you remove the link to stdlib modules and in (5) you start python again. It's the same binary executable as in (1) so what did you expect to change anyway? Did you try and start Python 3.8? Either by python3.8 or by modifying your PATH so it points to the relevant directory. – Drift 21/4, 2020 at 13:10

@Drift - You have identified part of the problem. Please see edits in the OP, at two points. – Peaslee 21/4, 2020 at 13:47

@sancho.sReinstateMonicaCellio Could you provide more information such as echo $PATH $PYTHONPATH $PYTHONSTARTUP as well as which python3.8 and python3.8 -m pip freeze and python3.8 -c "import sys; print(sys.builtin_module_names)". – Drift 21/4, 2020 at 15:10

@Drift - Please see edit at the bottom. – Peaslee 21/4, 2020 at 16:39

@sancho.sReinstateMonicaCellio What's the content of /home/user1/.pythonrc? You can see from which python3.8 and echo $PYTHONPATH that they are out of sync. They are pointing to different installations of Python. I suggest you remove the export PYTHONPATH from wherever it's stored right now. – Drift 22/4, 2020 at 8:58

@Drift - Please see EDIT #3 at the bottom. My comments: 1) I do not see how which python3.8 and echo $PYTHONPATH are out of sync. 2) I think they point to the same installation. The issue is hinted at by the fact that python points to 3.7. 3) Removing PYTHONPATH did not help. – Peaslee 22/4, 2020 at 10:0

@sancho.sReinstateMonicaCellio Okay seems good. I don't have any experience with MSYS2, so I can only try to answer this from the Python side. Looking at your edits, it seems that nothing is wrong with your Python 3.8 installation. Python 3.7 got uninstalled (perhaps incompletely), but otherwise doesn't seem to interfere with it. The readline module doesn't seem to be available for your system (again, I have no experience with MSYS2), so I suppose you need to install it. Your .pythonrc file contains a bug, namely it tries to del readline, rlcompleter even if they are not available. ... – Drift 22/4, 2020 at 12:14

... Regarding pandas why do you expect to be able to import this? This is a third party package and you just installed Python 3.8 completely new, so it's not a part of that installation. If you want to use pandas you need to install first. The only strange thing is that it doesn't file with ImportError: No module named 'pandas' but rather complains about missing dependencies. Maybe the upgrade from Python 3.7 to Python 3.8 just copied your site packages from one place to the other, but that generally won't work for pandas which is compiled specific to the Python version. – Drift 22/4, 2020 at 12:16

@sancho.sReinstateMonicaCellio So you could try clearing your site-packages directory, i.e. something like

cd C:/Users/user1/Documents/appls_mydocs/PortableApps/MSYS2Portable/App/msys32/mingw64/lib/python3.8/ && rm -r site-packages && mkdir site-packages

. Then try to install all the packages that you want to use. Just copying those files from one distribution to the other will only work for simple packages that are fully self-contained in Python. However numpy and pandas rely on C and Fotran extensions as compiled libraries, so these are missing then. – Drift 22/4, 2020 at 12:20

@sancho.sReinstateMonicaCellio Also take a look at this issue: bugs.python.org/issue31652 It might be that you're missing some dependencies. This question might be helpful as well. It might be that you need to reinstall your Python 3.8. In general I think the easiest is to just install Miniconda and create environments with it. – Drift 22/4, 2020 at 12:27

Let us continue this discussion in chat. – Peaslee 22/4, 2020 at 12:49

Did you try upgrading all python packages with pip, usually that solves my issues when i upgrade my python. more: #2720514 – Praiseworthy 23/4, 2020 at 11:17

@NiminUnnikrishnan - I did not. I may try doing that, by previously backing up my portable Msys2. – Peaslee 23/4, 2020 at 11:19

@Drift - Please post an answer as in chat... – Peaslee 24/4, 2020 at 2:7

The ImportError: cannot import name 'open_code' from 'io' (unknown location) comes from the fact that there are two different versions of Python conflicting with each other. python still points to the old version 3.7 but PYTHONPATH got updated to point to the new 3.8 version. As the documentation of PYTHONPATH states, it becomes prepended to the module search path and hence shadows any builtin modules:

The default search path is installation dependent, but generally begins with prefix/lib/pythonversion (see PYTHONHOME above). It is always appended to PYTHONPATH.

You can reproduce that behavior by creating two different virtual environments and then start one while having PYTHONPATH point to the other. In the following I used Miniconda to create two different environments, py37 and py38, containing a 3.7 and 3.8 installation respectively.

(py37) user@pc:~$ python --version
Python 3.7.6
(py37) user@pc:~$ PYTHONPATH=~/miniconda3/envs/py38/lib/python3.8/ python
Fatal Python error: init_sys_streams: can't initialize sys standard streams
Traceback (most recent call last):
  File "/home/user/miniconda3/envs/py38/lib/python3.8/io.py", line 54, in <module>
ImportError: cannot import name 'open_code' from 'io' (unknown location)
Aborted (core dumped)

Drift answered 24/4, 2020 at 10:40 Comment(4)

This was the first step in a chain of actions, which incrementally solved issues. I still have problems, and I posted additional questions. #61379354 #61391215 – Peaslee 24/4, 2020 at 11:55

It is not clear to me how to fix the issue that you are mentioning. Do you have any solution to propose? – Arse 9/8, 2021 at 16:59

@Arse Please post a new question, if this answer doesn't solve your problem. You can then link it here. – Drift 12/8, 2021 at 8:51

+1 I have been trying to use Automator to create an Application to start my python web server. It fires off a simple bash script to setup the environment and proceeds to start python. Been getting exceptions on startup until reading this nugget. Even though this is a clean install of python, apparently there are 2 versions of python available. When I used the full path to python3 in my startup script, the server ran perfectly. Kudos – Oxy 12/1, 2023 at 8:3

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