ChimeraX shell command-line: ValueError: list.remove(x): x not in list

[mbopf@…]

From: "Bopf, Mike (NIH/NIAID) [C]" <>
Subject: Running Quick Submit test on Mac
Date: May 17, 2024 at 1:55:24 PM PDT
To: Eric Pettersen , Tom Goddard

Eric or Tom,
I’m getting a strange error when running a quick submit on my Mac, and I can’t tell if it’s a configuration error or what. I’ve installed the latest Mac binary from today’s daily and the 1.1.18 NIHPresets. I’m trying to run the attached ‘run_4jnc_QS.sh’ script.

I get the following strange error:

"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 261, in open_pending_files

self._bad_drop_events.remove(bad_drop)

ValueError: list.remove(x): x not in list


BUG: ValueError: list.remove(x): x not in list

The full output is attached in ‘error.txt’.

Let me know if you have any ideas, or if you think it’s an issue specific to my setup.

Thanks,
Mike

Mike Bopf
NIAID/BCBB

[Tom Goddard]

Eric, you made a couple changes to the code that remedies the annoying macOS behavior where every shell command-line argument is passed to ChimeraX as a file drop event. Here are the two changes you made

​https://github.com/RBVI/ChimeraX/commit/3b278d93eaeecf0ee8d0de7a76d7aa5b646f0372

​https://github.com/RBVI/ChimeraX/commit/4597be6b26a332bff80710805893988eb6661c57

You replaces a set.discard(element) call which generates no error when the element is not in the set with a list.remove(element) call which is an error when the element is not in the list.

I changed your code to the following so Mike can get on with his NIH3D testing

if element in list:
  list.remove(element)

But that may not be right because according to comments your reason for changing the set to the list in the first place was to handle multiple instances of the same file on the command-line. I'll let you re-analyze the multi-file fix you were attempting.

[Tom Goddard]

Here is the temporary fix I made, only on the develop branch

​https://github.com/RBVI/ChimeraX/commit/e1e0de39d0e2f238808417f73af3ee63d4bbd43b

[Tom Goddard]

If I recall Zach recently sent an email or made ticket commenting on this same bug so he may also have a ticket open for this bug.

[mbopf@…]

Tom & Eric,
This fix is only on your dev  branch, right? Is there a nightly build that I can grab to try it out?

FYI, I noticed a reference to Mac OS in the comments. I was just upgraded to Sonoma (v 14.4.1) in case that has any bearing on this issue.

mike

From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Friday, May 17, 2024 at 19:44
To: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>, Bopf, Mike (NIH/NIAID) [C] <mbopf@mail.nih.gov>
Cc: zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>
Subject: [EXTERNAL] Re: [ChimeraX] #15242: ChimeraX shell command-line: ValueError: list.remove(x): x not in list
#15242: ChimeraX shell command-line: ValueError: list.remove(x): x not in list
-------------------------------+----------------------
          Reporter:  mbopf@…   |      Owner:  pett
              Type:  defect    |     Status:  assigned
          Priority:  moderate  |  Milestone:
         Component:  Core      |    Version:
        Resolution:            |   Keywords:
        Blocked By:            |   Blocking:
Notify when closed:            |   Platform:  all
           Project:  ChimeraX  |
-------------------------------+----------------------
Comment (by Tom Goddard):

 Eric, you made a couple changes to the code that remedies the annoying
 macOS behavior where every shell command-line argument is passed to
 ChimeraX as a file drop event.  Here are the two changes you made

 https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FRBVI%2FChimeraX%2Fcommit%2F3b278d93eaeecf0ee8d0de7a76d7aa5b646f0372&data=05%7C02%7Cmbopf%40mail.nih.gov%7Cba8e7cedf7d14b00b60c08dc76cb49a9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638515862685660783%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=Uz%2B78H9k7%2FOW4HB2Kuv66bBcwi0chpyDrKe2zW54Ilw%3D&reserved=0<https://github.com/RBVI/ChimeraX/commit/3b278d93eaeecf0ee8d0de7a76d7aa5b646f0372>

 https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FRBVI%2FChimeraX%2Fcommit%2F4597be6b26a332bff80710805893988eb6661c57&data=05%7C02%7Cmbopf%40mail.nih.gov%7Cba8e7cedf7d14b00b60c08dc76cb49a9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638515862685670209%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=uhMhGzy7lhAdkzcUS5a8Kt4Qo2lPKdFFr%2B%2Bg2PdVv7o%3D&reserved=0<https://github.com/RBVI/ChimeraX/commit/4597be6b26a332bff80710805893988eb6661c57>

 You replaces a set.discard(element) call which generates no error when the
 element is not in the set with a list.remove(element) call which is an
 error when the element is not in the list.

 I changed your code to the following so Mike can get on with his NIH3D
 testing

 {{{
 if element in list:
   list.remove(element)
 }}}

 But that may not be right because according to comments your reason for
 changing the set to the list in the first place was to handle multiple
 instances of the same file on the command-line.  I'll let you re-analyze
 the multi-file fix you were attempting.
--
Ticket URL: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F15242%23comment%3A1&data=05%7C02%7Cmbopf%40mail.nih.gov%7Cba8e7cedf7d14b00b60c08dc76cb49a9%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638515862685676454%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=a5w8VnfmOFby9eKEhXUU2U7XUSJ7HaDHa2wDXtbQYK0%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15242#comment:1>>
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[Eric Pettersen]

Yes, the "daily build" listed on the download page: ​https://www.cgl.ucsf.edu/chimerax/download.html

[Eric Pettersen]

Went with a different fix: ​https://github.com/RBVI/ChimeraX/commit/e4d0168e48e0c5a073c99d76001fd5f65c1e3d1c

Apparently the arguments to --cmd and --script now also appear as drop events, so had to account for that.