Errors in Python scripts should show traceback just for the script

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202104010057 (2021-04-01 00:57:00 UTC)
Description
When I open a Python script file that contains an erro it gives a traceback that is almost entirely all the ChimeraX code leading up to opening the file (about 10 stack frames).  It would make more sense to just show the traceback startnig from the Python file that I opened.  Also the traceback lines in the file I opened don't  show the lines of code, only the line numbers.

Log:
UCSF ChimeraX version: 1.2.dev202104010057 (2021-04-01)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/chimerax/src/bundles/test.py

Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX April 1
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File "/Users/goddard/Desktop/ChimeraX April 1
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "/Users/goddard/Desktop/ChimeraX April 1
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/Users/goddard/Desktop/ChimeraX April 1
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "/Users/goddard/Desktop/ChimeraX April 1
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/Users/goddard/Desktop/ChimeraX April 1
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 404, in collated_open  
return func(*func_args, **func_kw)  
File "/Users/goddard/Desktop/ChimeraX April 1
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 48, in open  
return open_python_script(session, data, file_name)  
File "/Users/goddard/Desktop/ChimeraX April 1
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/scripting.py", line 82, in open_python_script  
_exec_python(session, code, argv)  
File "/Users/goddard/Desktop/ChimeraX April 1
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/scripting.py", line 59, in _exec_python  
exec(code, sandbox.__dict__)  
File "test.py", line 3, in <module>  
File "test.py", line 2, in myfunc  
NameError: name '__file__' is not defined  
  
NameError: name '__file__' is not defined  
  
File "test.py", line 2, in myfunc  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2)
      Kernel Version: Darwin 19.6.0
      Time since boot: 111 days 15:36

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.0
    backcall: 0.2.0
    biopython: 1.78
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.4
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13
    ChimeraX-AtomicLibrary: 3.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
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    ChimeraX-BundleBuilder: 1.1
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    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202104010057
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
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    ChimeraX-MapData: 2.0
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    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
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    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
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    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
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    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
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    ChimeraX-PDB: 2.4
    ChimeraX-PDBBio: 1.0
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    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
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    ChimeraX-WavefrontOBJ: 1.0
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[Tom Goddard]

Fixed.

The code that runs the script is using Python exec(). When it raises an error the entire stack trace including all the ChimeraX calls above opening the script are included.

I've made the code that catches the error remove the ChimeraX calls prior to opening the script.

The exec() call also was using a code object that did not have the correct path to the Python file, only the file name, so the traceback did not show the lines of code. Changed it to use the full path.

It is unclear whether a Report a Bug button should appear on these errors. If a script calls into ChimeraX code that is the cause of the error I would like users to report that bug. But that is probably a rare case compared to the case where the user written Python script has the error. So for now I have it not showing "Report a Bug" button -- it is treated as a user error.