[chimerax-users] Bundle dependency

[Anthony James Schaefer]

Katie,

I'm not sure. I tried adding pdb-objects to one of my bundle's dependencies, and it was installed. I'm testing this on a ChimeraX 1.4 daily build.

My bundle_info.xml has this:
            <Dependencies>
                <Dependency name="ChimeraX-Core" version=">=1.2.dev"/>
                <Dependency name="pdb-objects"/>
            </Dependencies>

and my log has this after installing (along with a bunch of other stuff):
Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing c:\users\normn\documents\github\chimerax_themes\dist\chimerax_themes-0.3.1-py3-none-any.whl
Requirement already satisfied: ChimeraX-Core>=1.2.dev in e:\chimerax 1.4.dev202202010639\bin\lib\site-packages (from ChimeraX-themes==0.3.1) (1.4.dev202202010639)
Collecting pdb-objects
Using cached pdb_objects-0.1.3-py3-none-any.whl (6.6 kB)
Installing collected packages: pdb-objects, ChimeraX-themes
Successfully installed ChimeraX-themes-0.3.1 pdb-objects-0.1.3
---
Successfully installed ChimeraX-themes-0.3.1 pdb-objects-0.1.3
Installed ChimeraX-themes (0.3.1)

Towards the bottom, it says it installed pdb-objects and my bundle. I can then go into the shell and import pdb_objects without error.

Best,

Tony

________________________________
From: Zeng, Katie <jingrou.zeng18 at imperial.ac.uk>
Sent: Monday, February 21, 2022 2:59 PM
To: Anthony James Schaefer <tony.schaefer at uga.edu>
Subject: Re: Bundle dependency

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hi Tony,

Thanks for pointing that out. I've now changed the dependency to pdb-objects, but I still get the same error when I try to use the bundle in ChimeraX. Have you got any idea why it's giving this error?

Best Regards,
Katie
________________________________
From: Anthony James Schaefer <tony.schaefer at uga.edu>
Sent: 21 February 2022 17:57
To: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>; Zeng, Katie <jingrou.zeng18 at imperial.ac.uk>
Subject: Re: Bundle dependency


This email from tony.schaefer at uga.edu originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address.



Katie,

It looks like PDB objects on PyPI is called pdb-objects, not pdb_objects. For dependencies, ChimeraX looks for the package name and not the import name.

Best,

Tony
________________________________
From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of Zeng, Katie via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
Sent: Monday, February 21, 2022 11:50 AM
To: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: [chimerax-users] Bundle dependency

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hi,

I'm currently working on building a membrane builder bundle and it requires the use of a python library called 'pdb_objects'.

Following the tutorial on the website, I'm adding the following line to my bundle_info.xml file under the dependencies tag:

<Dependency name="pdb_objects"/>

It still gives me an error of <No module named 'pdb_objects'> when I load my bundle in ChimeraX. How can I allow the use of this library in my bundle?

Thanks for your help!

Best Regards,
Katie
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