Qt6 problems

[j.r.lewandowski@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
ChimeraX Version: 1.4.dev202202240543 (2022-02-24 05:43:43 UTC)
Description
Hi, 
I am trying the technology preview daily build. Two things to report for my configuration.
1. When opening ChimeraX command line tool the bar loads docked where the File menu is (not much of a problem because after undocking I can dock it in a more reasonable place).
2. Command history does not seem to open up.

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-Registration' custom initialization failed  
warning | Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202202240543\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 360, in initialize  
api._api_caller.initialize(api, session, self)  
File "C:\Program Files\ChimeraX 1.4.dev202202240543\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1278, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
File "C:\Program Files\ChimeraX 1.4.dev202202240543\bin\lib\site-
packages\chimerax\registration\\__init__.py", line 41, in initialize  
nag(session)  
File "C:\Program Files\ChimeraX 1.4.dev202202240543\bin\lib\site-
packages\chimerax\registration\nag.py", line 37, in nag  
if not check_registration(logger=session.logger):  
File "C:\Program Files\ChimeraX 1.4.dev202202240543\bin\lib\site-
packages\chimerax\registration\nag.py", line 56, in check_registration  
param = _get_registration(logger)  
File "C:\Program Files\ChimeraX 1.4.dev202202240543\bin\lib\site-
packages\chimerax\registration\nag.py", line 131, in _get_registration  
for line in f:  
File "C:\Program Files\ChimeraX 1.4.dev202202240543\bin\lib\codecs.py", line
322, in decode  
(result, consumed) = self._buffer_decode(data, self.errors, final)  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xf3 in position 155:
invalid continuation byte  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202202240543\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 554, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "C:\Program Files\ChimeraX 1.4.dev202202240543\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1266, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "C:\Program Files\ChimeraX 1.4.dev202202240543\bin\lib\site-
packages\chimerax\cmd_line\\__init__.py", line 31, in start_tool  
return CommandLine.get_singleton(session)  
File "C:\Program Files\ChimeraX 1.4.dev202202240543\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 322, in get_singleton  
return tools.get_singleton(session, CommandLine, 'Command Line Interface',
**kw)  
File "C:\Program Files\ChimeraX 1.4.dev202202240543\bin\lib\site-
packages\chimerax\core\tools.py", line 193, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File "C:\Program Files\ChimeraX 1.4.dev202202240543\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 191, in __init__  
self.tool_window.manage(placement="bottom")  
File "C:\Program Files\ChimeraX 1.4.dev202202240543\bin\lib\site-
packages\chimerax\ui\gui.py", line 2081, in manage  
placement = self.window_placement_to_text[placement]  
KeyError: 2  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4.dev202202240543\bin\lib\site-
packages\chimerax\core\tools.py", line 394, in start_tools  
bi.start_tool(session, tool_name)  
File "C:\Program Files\ChimeraX 1.4.dev202202240543\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 559, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Command
Line Interface in bundle ChimeraX-CommandLine:  
2  
  
Tool "Command Line Interface" failed to start:  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Command
Line Interface in bundle ChimeraX-CommandLine:  
2  
  
File "C:\Program Files\ChimeraX 1.4.dev202202240543\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 559, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  
UCSF ChimeraX version: 1.4.dev202202240543 (2022-02-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 472.88
OpenGL renderer: Quadro RTX 5000 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Locale: en_GB.cp1252
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: Precision 7550
OS: Microsoft Windows 11 Enterprise (Build 22000)
Memory: 137,053,155,328
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Xeon(R) W-10885M CPU @ 2.40GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.5.2
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.36.2
    ChimeraX-AtomicLibrary: 6.0.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.1
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202202240543
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.1
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.8
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.7.7
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16.1
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.5.1
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.29.1
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.26
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.9.2
    kiwisolver: 1.3.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.0
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.4
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.0
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.28
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.7
    PyQt6-commercial: 6.2.3
    PyQt6-sip: 13.2.0
    PyQt6-WebEngine-commercial: 6.2.1
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 303
    pyzmq: 22.3.0
    qtconsole: 5.2.2
    QtPy: 2.0.1
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.8
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

[Eric Pettersen]

Reported by Jozef Lewandowski

[Eric Pettersen]

Did not occur on my home Mac or huck (Windows 10) at work.

[J.R.Lewandowski@…]

It might be Win 11 issue. Even though the log says I am on Win 10 but I am actually running Win 11 (which has some occasional weird things with graphics that I have not seen on Win 10).
Best,
Józef

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: 25 February 2022 22:20
Cc: chimera-programmers@cgl.ucsf.edu; goddard@cgl.ucsf.edu; Lewandowski, Jozef <J.R.Lewandowski@warwick.ac.uk>
Subject: Re: [ChimeraX] #6248: Qt6 problems

#6248: Qt6 problems
----------------------------------------+-------------------------
          Reporter:  j.r.lewandowski@…  |      Owner:  Tom Goddard
              Type:  defect             |     Status:  assigned
          Priority:  normal             |  Milestone:
         Component:  Window Toolkit     |    Version:
        Resolution:                     |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+-------------------------

Comment (by pett):

 Did not occur on my home Mac or huck (Windows 10) at work.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6248#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Greg Couch]

By any chance is this on a laptop with hybrid graphics? If so, we've seen the weirdness, but we don't have a way of reproducing it.

[Zach Pearson]

Downloaded today's tech preview and daily builds on Windows 11 (I have the same build as you, Windows-10-10.0.22000) but I'm unable to reproduce.

[Greg Couch]

And if you do have hybrid graphics, please run the dxdiag program, click on "Save All Information" and send us the text file. The potential workaround are (1) to configure the ChimeraX shortcut to use the better graphics -- I believe this is possible by right-clicking on the shortcut, showing the properties, and then something, or (2) set the graphics in the BIOS to always be the better graphics -- you'll get shorter battery life, but much better graphics.

[Tom Goddard]

There are two errors. The one about command line placement is a bug in the ChimeraX gui panel layout code. You placed your command line with the right panel and saved that placement at some point in the past. The ChimeraX code that restores that remembered placement is broken in Qt 6.

Reassigning to Eric to fix this. Or it could be reassigned to Zach who handles Qt 6 bugs. After that is fixed can reassign to Greg to look at checking for updates error.

The GUI placement problem is in ui/gui.py in

    window_placement_to_text = {
        Qt.DockWidgetArea.RightDockWidgetArea: "right",
        Qt.DockWidgetArea.LeftDockWidgetArea: "left",
        Qt.DockWidgetArea.TopDockWidgetArea: "top",
        Qt.DockWidgetArea.BottomDockWidgetArea: "bottom"
    }

where in Qt 6 Qt.DockWidgetArea.RightDockWidgetArea is an object not an integer and the value saved in preferences from Qt 5 is an integer that is not a key to this table.

[Eric Pettersen]

PyQt6 uses Python enums for these values now, whereas I believe PySide6 continues to use ints. I now pass the value through a wrapper function that will return an int regardless.

Reassigning to Greg to investigate the checking for updates error.