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@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@cgl.ucsf.edu <mailto:chimerax-users@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>