Opened 2 years ago

Closed 14 months ago

#10036 closed enhancement (fixed)

Add programming documentation on how to include PyPi dependencies in a bundle.

Reported by: vincent.mallet96@… Owned by: Eric Pettersen
Priority: moderate Milestone:
Component: Tool Shed Version:
Keywords: Cc: chimerax-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

On Oct 20, 2023, at 4:58 AM, Vincent Mallet via ChimeraX-users <chimerax-users@…> wrote:

Hello,

Thanks for the tool and the tutorials. I have a machine learning tool based on pytorch to analyse cryo-EM data. I was hoping to package (bundle) it for Chimerax and started to follow tutorials, but I don't think you mention the right way to set up a code environment with depencies. I see a numpy import in the save_new_format tutorial, but it's not listed in the "dependencies" section of the xml file.

I guess my question is : can I add arbitrary packages in a bundle ? Is there a way to install pip packages only ? Should I copy all source code in the folder and deal with my imports like that ? In particular, I am thinking of torch that is not so easy to replace...

I am hoping you can help me, thanks in advance for the help !

Best,
Vincent

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Owner: changed from Zach Pearson to Eric Pettersen

Non-ChimeraX Python package dependencies are mentioned under "Dependencies" here: ​https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/bundle_info.html . It certainly could be mentioned in more places and in more examples.

comment:2 by Eric Pettersen, 14 months ago

Resolution: → fixed
Status: assigned → closed

Added an explicit mention of declaring dependencies on PyPi packages to the tutorial.

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