pyenv Library property empty. Unable to resolve the name (Linux:Pop OS 22.04, python 3.9, R2022a)

Hello All,

I've hit a wall trying to call python from MATLAB.

Since, MATLAB R2022a supports python 3.8 and 3.9 (ref) I've installed python3.9 via my system's package manager. (Note that python 3.10 was installed first, and is used system wide)

However, Python 3.9 is definitly working

$which python3.9
/usr/bin/python3.9

$python3.9 --version
Python 3.9.13

Trying to configure pyenv in MATLAB(following these instructions), yeilds:

>>pyenv('Version','/usr/bin/python3.9')
    ans = 
    
      PythonEnvironment with properties:
    
              Version: "3.9"
           Executable: "/usr/bin/python3.9"
              Library: ""
                 Home: "/usr"
               Status: NotLoaded
        ExecutionMode: InProcess

Note, the library propery of the pyenv object is empty.

Then trying to force python to load by calling a simple python function yields:

>> py.print("Printed from python")
Unable to resolve the name 'py.print'.  

I was able to replicate this issue on Ununtu 22.04 also with python3.9.

The closest related post I've found is on OSX, in which the user had a simmilar empty propery issue.

Can anyone advise on how to correct this, and get python calls working?

Thank you!

Answer 1

[Jorian Khan]

Wow, @Al Danial

Really thank you for your post! It inspired me!

TLDR: the library property can be set by editing matlab.mlsettings particualrily: /fsroot/settingstree/matlab/external/interfaces/python/settings.json

{
    "attributes": {
        "groupName": "python",
        "readonly": false,
        "validationFcn": {},
        "visible": false
    },
    "path": "\/settingstree\/matlab\/external\/interfaces\/python",
    "settings": [
        {
            "attributes": {
                "readonly": false,
                "runtimeDefaultFcn": {},
                "settingValueValidator": {},
                "validationFcn": {},
                "visible": false
            },
            "hasValue": true,
            "isUserDefined": false,
            "isVector": true,
            "name": "Version",
            "value": "{\"mwdata\":[\"3.9\",\"\\\/usr\\\/bin\\\/python3.9\",\"\\\/usr\\\/bin\\\/python3.9\",\"\\\/usr\\\/lib\\\/x86_64-linux-gnu\\\/libpython3.9.so.1\"],\"mwsize\":[1,4],\"mwtype\":\"cell\"}"
        }
    ]
}

Editing "value" to include /usr/lib/x86_64-linux-gnu/libpython3.9.so.1 as Library and /usr/bin/python3.9 as home fixed this issue!

Now calling pyenv yeilds:

>> pyenv

ans = 

  PythonEnvironment with properties:

          Version: "3.9"
       Executable: "/usr/bin/python3.9"
          Library: "/usr/lib/x86_64-linux-gnu/libpython3.9.so.1"
             Home: "/usr/bin/python3.9"
           Status: NotLoaded
    ExecutionMode: InProcess

>> py.print('Printed from Python 3.9!')
Printed from Python 3.9!

>> pyenv

ans = 

  PythonEnvironment with properties:

          Version: "3.9"
       Executable: "/usr/bin/python3.9"
          Library: "/usr/lib/x86_64-linux-gnu/libpython3.9.so.1"
             Home: "/usr/bin/python3.9"
           Status: Loaded
    ExecutionMode: InProcess
        ProcessID: "487263"
      ProcessName: "MATLAB"

Unfortunately, I don't think this setting can be eddited via the settings api as settings.matlab does not contain an 'external' property. i.e.:

>> s = settings

s = 

  SettingsGroup with properties:

    slhistory: [1×1 SettingsGroup]
       matlab: [1×1 SettingsGroup]
     Simulink: [1×1 SettingsGroup]

>> s.matlab

ans = 

  SettingsGroup 'matlab' with properties:

              colors: [1×1 SettingsGroup]
         appdesigner: [1×1 SettingsGroup]
        codeanalyzer: [1×1 SettingsGroup]
    toolboxpathcache: [1×1 SettingsGroup]
              editor: [1×1 SettingsGroup]
            keyboard: [1×1 SettingsGroup]
       commandwindow: [1×1 SettingsGroup]
          appearance: [1×1 SettingsGroup]
            latestgr: [1×1 SettingsGroup]
               fonts: [1×1 SettingsGroup]
             general: [1×1 SettingsGroup]

So settings.json must be editied manually, I guess.

Finally!

[Al Danial]

That's impressive and well beyond what I knew about the Python interface in MATLAB, great info here for future reference!

[Francesco De Biasio]

Hello,

I have the same problem and almost the same environment:

>> pyenv

ans =

PythonEnvironment with properties:

Version: "3.9"

Executable: "/usr/bin/python3.9"

Library: ""

Home: "/usr"

Status: NotLoaded

ExecutionMode: OutOfProcess

ubuntu 22.04

matlab 22.04

python 3.9.16

however I am not able to find the file "settings.json" in my linux box. I do not even find the path of the folder that should contain it: "/fsroot/settingstree/matlab/external/interfaces/python/"

Is there anybody that could address me to the right file?

many thanks,

Francesco

[Francesco De Biasio]

Well,

I was able to answer my question thanks to this thread:

https://it.mathworks.com/matlabcentral/answers/697115-read-matlab-settings-form-matlab-mlsettings

(thanks to Marco Pasquali)

And, the solution proposed by @Al Danial worked for me too. But I found it a little tricky the procedure, and poorly documented, not to mention that I was not able to recompact the file /home/myself/.matlab/R2022b/matlab.mlsettings to the original dimensions

Thanks

Francesco

Answer 2

[Al Danial]

On my Ubuntu 20.04 system pyenv returns

>> pyenv
ans = 
PythonEnvironment with properties:
Version: "3.9"
Executable: "/usr/local/anaconda3/2021.05/envs/matpy/bin/python"
Library: "/usr/local/anaconda3/2021.05/envs/matpy/lib/libpython3.9.so"
Home: "/usr/local/anaconda3/2021.05/envs/matpy"
Status: Loaded
ExecutionMode: InProcess
ProcessID: "1527848"
ProcessName: "MATLAB"

so try finding the libpython3.9.so shared library and explicitly setting the Library field with that path. For example on my system that would be

>> pyenv('Library','/usr/local/anaconda3/2021.05/envs/matpy/lib/libpython3.9.so')

If your Python shared libraries for both 3.9 and 3.10 exist in the same directory I can see how that will cause you grief. Ideally you'd your 3.9 installation would live in its own directory. I don't know if apt install gives you that freedom if that's what you did. My recommendation is to uninstall 3.9 then install Anaconda Python since that lets you control the location.

[Jorian Khan]

Hello,

Thanks taking the time to reply!

So, libpthon3.9.so.1 is definitly on my system. It's located at:

/usr/lib/x86_64-linux-gnu/libpython3.9.so.1

However, the Library property of PythonEnvironment cannot be set like you've described. From the documentation (here) vailid input arguments for pyenv are soley 'Version' and 'ExecutionMode'

So trying so set 'Library' yeids:

>>pyenv('Library', '/usr/lib/x86_64-linux-gnu/libpython3.9.so.1')
Error using pyenv
Invalid input Library. Key must be 'Version' or 'ExecutionMode'.

Also I'm not sure I want to go the anaconda route yet as the intended the target platform is admisitrated and only has python 3.10 and python 3.9.

Thank you for the solution sugestion!