[chimerax-users] using pandas

[Lagerwaard, I.M. (Ilse)]

Hi Tom,

Thanks a lot for the reply, my issue is solved now.

A pip install command would indeed be great! But for now the Command Prompt also works fine for me 😊.

Ilse

Van: Tom Goddard <goddard at sonic.net>
Verzonden: 11 June 2021 06:47
Aan: Lagerwaard, I.M. (Ilse) <i.m.lagerwaard at students.uu.nl>
CC: chimerax-users at cgl.ucsf.edu
Onderwerp: Re: [chimerax-users] using pandas

Hi Ilse,

On Windows I run a Command Prompt as administrator to have permission to modify  the installed ChimeraX and use

> cd C:\Program Files\ChimeraX-1.2.5\bin
> .\python.exe -m pip install pandas

And then I can use "import pandas" in the ChimeraX shell (menu Tools / General / Shell)  without errors.

Or in a Command Prompt that is not run as administrator I run

> cd C:\Program Files\ChimeraX-1.2.5\bin
> .\ChimeraX-console.exe -m pip install pandas --user

and again pandas installs fine and imports in ChimeraX.

Definitely we should add an easy way to do this in ChimeraX without the Command Prompt rigamarole, like a ChimeraX command "pip install pandas".  But we don't have that right now.  Sadly the Python pip package does not have an API to do installs using a function call -- really poor design.  But probably we can work around that.

   Tom



On Jun 9, 2021, at 10:27 AM, Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>> wrote:

Hi Ilse,

  ChimeraX distributions include Python so you just want to install pandas into the ChimeraX Python.   This involves running the ChimeraX Python and using pip install. Here is how I do that on Mac.

$ ~/Desktop/ChimeraX.app/Contents/bin/python3.8 -m pip install pandas

On Windows or Linux it would be similar.  We should have a ChimeraX command to install PyPi packages but don't have that yet.

                Tom


On Jun 9, 2021, at 3:09 AM, Lagerwaard, I.M. (Ilse) via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

Hello everyone,

Is it possible to use the pandas package in ChimeraX? I tried opening a Python script containing the line ‘import pandas’, but I get the error: ‘ModuleNotFoundError: No module named 'pandas'’.

Kind regards,
Ilse
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