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
Hi Ilse, You can install pandas into ChimeraX's Python using 'pip install' as described in this mailing-list message: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-June/001216.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-June/001216.html> . The caveat is that though this will work on all platforms, the actual later "Import pandas" will fail on at least some Linux platforms because some of our Linux installers don't include the bz2 module in their Python, which pandas depends on. I will add you to the cc list for the ticket we have open for this problem, in case it matters to you. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jun 9, 2021, at 3:09 AM, Lagerwaard, I.M. (Ilse) via ChimeraX-users <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>
Hi Eric, Thank you for the reply! Unfortunately, even though I followed your instructions and do have the bz2 module (I use Windows), I still get the same error. I can ‘import pandas’ in ChimeraX’s Python, but not from within the application itself. Do you have any idea what else might be going on? Ilse Van: Eric Pettersen <pett@cgl.ucsf.edu> Verzonden: 09 June 2021 19:12 Aan: Lagerwaard, I.M. (Ilse) <i.m.lagerwaard@students.uu.nl> CC: chimerax-users@cgl.ucsf.edu Onderwerp: Re: [chimerax-users] using pandas Hi Ilse, You can install pandas into ChimeraX's Python using 'pip install' as described in this mailing-list message: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-June/001216.html . The caveat is that though this will work on all platforms, the actual later "Import pandas" will fail on at least some Linux platforms because some of our Linux installers don't include the bz2 module in their Python, which pandas depends on. I will add you to the cc list for the ticket we have open for this problem, in case it matters to you. --Eric Eric Pettersen UCSF Computer Graphics Lab 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://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
I've had this problem before. The root cause turned out to be that "/path/to/ChimeraX/python3.8 -m pip install --user" installed to the Python user directory rather than the ChimeraX user directory. Try running: "C:\Program Files\ChimeraX\bin\ChimeraX-console.exe" -m pip install --user pandas ________________________________ From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Lagerwaard, I.M. (Ilse) via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: 10 June 2021 09:27 To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] using pandas Hi Eric, Thank you for the reply! Unfortunately, even though I followed your instructions and do have the bz2 module (I use Windows), I still get the same error. I can ‘import pandas’ in ChimeraX’s Python, but not from within the application itself. Do you have any idea what else might be going on? Ilse Van: Eric Pettersen <pett@cgl.ucsf.edu> Verzonden: 09 June 2021 19:12 Aan: Lagerwaard, I.M. (Ilse) <i.m.lagerwaard@students.uu.nl> CC: chimerax-users@cgl.ucsf.edu Onderwerp: Re: [chimerax-users] using pandas Hi Ilse, You can install pandas into ChimeraX's Python using 'pip install' as described in this mailing-list message: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-June/001216.html . The caveat is that though this will work on all platforms, the actual later "Import pandas" will fail on at least some Linux platforms because some of our Linux installers don't include the bz2 module in their Python, which pandas depends on. I will add you to the cc list for the ticket we have open for this problem, in case it matters to you. --Eric Eric Pettersen UCSF Computer Graphics Lab 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://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
Actually, come to think about it: the approach specified in https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-June/001216.html probably won't work for Windows, since on that platform sys.executable is ChimeraX.exe rather than ChimeraX-console.exe - and running "-m pip install ..." only works for the latter. ________________________________ From: Tristan Croll <tic20@cam.ac.uk> Sent: 10 June 2021 15:53 To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>; Lagerwaard, I.M. (Ilse) <i.m.lagerwaard@students.uu.nl> Subject: Re: [chimerax-users] using pandas I've had this problem before. The root cause turned out to be that "/path/to/ChimeraX/python3.8 -m pip install --user" installed to the Python user directory rather than the ChimeraX user directory. Try running: "C:\Program Files\ChimeraX\bin\ChimeraX-console.exe" -m pip install --user pandas ________________________________ From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Lagerwaard, I.M. (Ilse) via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: 10 June 2021 09:27 To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] using pandas Hi Eric, Thank you for the reply! Unfortunately, even though I followed your instructions and do have the bz2 module (I use Windows), I still get the same error. I can ‘import pandas’ in ChimeraX’s Python, but not from within the application itself. Do you have any idea what else might be going on? Ilse Van: Eric Pettersen <pett@cgl.ucsf.edu> Verzonden: 09 June 2021 19:12 Aan: Lagerwaard, I.M. (Ilse) <i.m.lagerwaard@students.uu.nl> CC: chimerax-users@cgl.ucsf.edu Onderwerp: Re: [chimerax-users] using pandas Hi Ilse, You can install pandas into ChimeraX's Python using 'pip install' as described in this mailing-list message: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-June/001216.html . The caveat is that though this will work on all platforms, the actual later "Import pandas" will fail on at least some Linux platforms because some of our Linux installers don't include the bz2 module in their Python, which pandas depends on. I will add you to the cc list for the ticket we have open for this problem, in case it matters to you. --Eric Eric Pettersen UCSF Computer Graphics Lab 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://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
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> 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>
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>
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@sonic.net> Verzonden: 11 June 2021 06:47 Aan: Lagerwaard, I.M. (Ilse) <i.m.lagerwaard@students.uu.nl> CC: chimerax-users@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@sonic.net<mailto: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://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users
participants (4)
-
Eric Pettersen -
Lagerwaard, I.M. (Ilse) -
Tom Goddard -
Tristan Croll