![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#7410 closed defect (fixed)
Crash creating SEQCROW QMenuBar in ARM tech preview
| Reported by: | Owned by: | Tony Schaefer | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | chimerax-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.5-arm64-arm-64bit
ChimeraX Version: 1.5.dev202208030611 (2022-08-03 06:11:58 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000102634580 (most recent call first):
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2415 in shown
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2194 in _mw_set_shown
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1888 in _tool_window_request_shown
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2097 in shown
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 785 in set_tool_shown
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 342 in set_tool_shown
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 175 in
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 360 in thread_safe
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 174 in display
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 561 in start_tool
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/cmd.py", line 219 in ui_tool_show
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1655 in
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 279 in event_loop
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__init__.py", line 1023 in init
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 5 in
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
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"procLaunch" : "2022-08-05 18:29:44.2561 -0700",
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"version" : 2,
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"sleepWakeUUID" : "F76B3FCF-D519-418A-85B6-4C80BC1BECAB",
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"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
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"uuid" : "32f1ab48-7fc1-33fa-b918-ea0528425a8f",
"path" : "\/Volumes\/VOLUME\/*\/ChimeraX_techpreview.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
"name" : "libqcocoa.dylib"
},
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"arch" : "arm64e",
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"size" : 5533696,
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"size" : 3358720,
"uuid" : "7112f6f2-a77e-39db-83c8-f627b8a49df8",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
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"source" : "P",
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"size" : 15437824,
"uuid" : "07bc3607-552a-3eb9-a941-4911c589dbc5",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2113.60.148"
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"path" : "\/Volumes\/VOLUME\/*\/ChimeraX_techpreview.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.5.0.0"
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"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
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"path" : "\/Volumes\/VOLUME\/*\/ChimeraX_techpreview.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
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"uuid" : "5431bff3-be1a-3fe5-a552-bcdbb3e0536e",
"path" : "\/Volumes\/VOLUME\/*\/ChimeraX_techpreview.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/scipy\/.dylibs\/libopenblas.0.dylib",
"name" : "libopenblas.0.dylib"
}
],
"sharedCache" : {
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},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=2.8G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.8G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1152K 9 \nActivity Tracing 256K 1 \nCG backing stores 4480K 8 \nCG image 3168K 57 \nCG raster data 256K 1 \nColorSync 624K 27 \nCoreAnimation 6592K 66 \nCoreGraphics 48K 3 \nCoreUI image data 4768K 40 \nFoundation 32K 2 \nKernel Alloc Once 48K 2 \nMALLOC 443.5M 90 \nMALLOC guard page 192K 11 \nMALLOC_MEDIUM (reserved) 1.1G 10 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.5M 35 \nStack 153.3M 35 \nVM_ALLOCATE 170.0M 374 \nVM_ALLOCATE (reserved) 512.0M 4 reserved VM address space (unallocated)\n__AUTH 2624K 311 \n__AUTH_CONST 20.6M 509 \n__CTF 756 1 \n__DATA 25.3M 714 \n__DATA_CONST 28.3M 712 \n__DATA_DIRTY 1804K 216 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 612.8M 202 \n__OBJC_CONST 3665K 282 \n__OBJC_RO 83.0M 1 \n__OBJC_RW 3168K 1 \n__TEXT 756.7M 730 \n__UNICODE 592K 1 \ndyld private memory 1216K 3 \nmapped file 186.6M 55 \nshared memory 3168K 25 \n=========== ======= ======= \nTOTAL 4.5G 4548 \nTOTAL, minus reserved VM space 2.5G 4548 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
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"factorPackIds" : {
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}
}
System Profile:
Network Service: Wi-Fi, AirPort, en0
Thunderbolt Bus: MacBook Pro, Apple Inc.
Thunderbolt Bus: MacBook Pro, Apple Inc.
Thunderbolt Bus: MacBook Pro, Apple Inc.
Boot Volume File System Type: apfs
Memory Module: LPDDR5
USB Device: USB31Bus
USB Device: USB31Bus
USB Device: USB31Bus
Display: Color LCD, 3024 x 1964 Retina, Main, MirrorOff, Online
Display: P24h-10, 2560 x 1440 (QHD/WQHD - Wide Quad High Definition), MirrorOff, Online
Model: MacBookPro18,3, BootROM 7459.141.1, proc 10:8:2 processors, 16 GB, SMC
Graphics: Apple M1 Pro, Apple M1 Pro, Built-In
AirPort: Wi-Fi, wl0: Apr 6 2022 05:55:54 version 20.90.45.0.8.7.118 FWID 01-e7138ff2
Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports
===== Log before crash start =====
UCSF ChimeraX version: 1.5.dev202208030611 (2022-08-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Successfully installed 'SEQCROW==1.2.2'
Found existing installation: SEQCROW 1.2.2
Uninstalling SEQCROW-1.2.2:
Successfully uninstalled SEQCROW-1.2.2
> toolshed install /Users/tylerbenton/Downloads/SEQCROW-1.5a1-py3-none-any.whl
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing
/Users/tylerbenton/Downloads/SEQCROW-1.5a1-py3-none-any.whl Requirement
already satisfied: scipy in
/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.5a1) (1.9.0) Requirement already satisfied: psutil
in
/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.5a1) (5.9.1) Requirement already satisfied:
Send2Trash in /Users/tylerbenton/Library/Application
Support/ChimeraX/1.5/site-packages (from SEQCROW==1.5a1) (1.8.0) ERROR: Could
not find a version that satisfies the requirement ChimeraX-Core=1.2
(from seqcrow) (from versions: none) ERROR: No matching distribution found for
ChimeraX-Core=1.2 WARNING: You are using pip version 21.3.1; however,
version 22.2.2 is available. You should consider upgrading via the
'/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/MacOS/ChimeraX
-m pip install --upgrade pip' command.
> toolshed show
> toolshed install /Users/tylerbenton/SEQCROW-1.4.4-py3-none-any.whl
Errors may have occurred when running pip:
pip standard error:
\---
WARNING: Value for scheme.platlib does not match. Please report this to
distutils: /Users/tylerbenton/Library/Application Support/ChimeraX/1.5/site-
packages
sysconfig: /Users/tylerbenton/Library/Python/3.9/lib/python/site-packages
WARNING: Value for scheme.purelib does not match. Please report this to
distutils: /Users/tylerbenton/Library/Application Support/ChimeraX/1.5/site-
packages
sysconfig: /Users/tylerbenton/Library/Python/3.9/lib/python/site-packages
WARNING: Value for scheme.headers does not match. Please report this to
distutils: /Users/tylerbenton/Library/Application
Support/ChimeraX/include/python3.9/SEQCROW
sysconfig: /Users/tylerbenton/Library/Python/3.9/include/SEQCROW
WARNING: Value for scheme.scripts does not match. Please report this to
distutils: /Users/tylerbenton/Library/Application Support/ChimeraX/bin
sysconfig: /Users/tylerbenton/Library/Python/3.9/bin
WARNING: Value for scheme.data does not match. Please report this to
distutils: /Users/tylerbenton/Library/Application Support/ChimeraX
sysconfig: /Users/tylerbenton/Library/Python/3.9
WARNING: Additional context:
user = True
home = None
root = None
prefix = None
WARNING: Value for scheme.headers does not match. Please report this to
distutils: /Users/tylerbenton/Library/Application
Support/ChimeraX/include/python3.9/UNKNOWN
sysconfig: /Users/tylerbenton/Library/Python/3.9/include/UNKNOWN
WARNING: You are using pip version 21.3.1; however, version 22.2.2 is
available.
You should consider upgrading via the
'/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/MacOS/ChimeraX
-m pip install --upgrade pip' command.
\---
pip standard output:
\---
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing /Users/tylerbenton/SEQCROW-1.4.4-py3-none-any.whl
Requirement already satisfied: scipy in
/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.4.4) (1.9.0)
Requirement already satisfied: ChimeraX-Core=1.2 in
/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.4.4) (1.5.dev202208030611)
Requirement already satisfied: Send2Trash in
/Users/tylerbenton/Library/Application Support/ChimeraX/1.5/site-packages
(from SEQCROW==1.4.4) (1.8.0)
Requirement already satisfied: psutil in
/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.4.4) (5.9.1)
Requirement already satisfied: jinja2 in
/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.4.4) (3.1.2)
Requirement already satisfied: MarkupSafe>=2.0 in
/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from jinja2->SEQCROW==1.4.4) (2.1.1)
Requirement already satisfied: numpy=1.18.5 in
/private/var/folders/jr/wpxt5sn540ggqj6sl4ztfn5c0000gn/T/AppTranslocation/7E19DCF3-E38F-4389-B090-4636FA1A4DBA/d/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from scipy->SEQCROW==1.4.4) (1.23.1)
Installing collected packages: SEQCROW
Successfully installed SEQCROW-1.4.4
\---
Successfully installed SEQCROW-1.4.4
Installed SEQCROW (1.4.4)
> ui tool show "Build QM Input"
settings migrated from version 2
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5.dev202208030611 (2022-08-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 7459.141.1
OS Loader Version: 7459.141.1
Software:
System Software Overview:
System Version: macOS 12.5 (21G72)
Kernel Version: Darwin 21.6.0
Time since boot: 2 days 23:37
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
P24h-10:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.0.5
Babel: 2.10.3
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.7.0
certifi: 2021.10.8
cftime: 1.6.1
charset-normalizer: 2.1.0
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: 2.5.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.7
ChimeraX-AtomicLibrary: 7.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1.1
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChangeChains: 1.0
ChimeraX-CheckWaters: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.1
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5.dev202208030611
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.6
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.2.1
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.5
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.7
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
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: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.21.4
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.2
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 0.9.1
filelock: 3.4.2
fonttools: 4.34.4
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.33
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 4.12.0
ipykernel: 6.15.1
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 4.11.1
kiwisolver: 1.4.4
line-profiler: 3.4.0
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.3
msgpack: 1.0.4
nest-asyncio: 1.5.5
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.3
numpy: 1.23.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.12.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.30
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.1
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.1
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.2.0
qtconsole: 5.3.1
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.28.1
scipy: 1.9.0
Send2Trash: 1.8.0
SEQCROW: 1.4.4
setuptools: 62.6.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
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
stack-data: 0.3.0
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.11
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.3.0
zipp: 3.8.1
Change History (14)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash creating SEQCROW QMenuBar in ARM tech preview |
follow-up: 2 comment:2 by , 3 years ago
There's a lot in the crash log. How can we tell the issue is with the QMenuBar specifically? I'm not saying I think it's something else, I just can't tell from this.
The log does have "settings migrated from version 2", which gets printed here: https://github.com/QChASM/SEQCROW/blob/75d11ce0d983d3f162e2e16c2dfcbbf76d7ce01a/src/tools/input_generator.py#L297. It would have finished running the "_build_ui" method and the QMenuBar would be instantiated by this point, but I'm not sure if the menu would be drawn. The next things the tool does in __init__ are:
1. save that it migrated the settings
2. refresh the menu for the different preset options on the tool
* clear the presets menu
* add stored presets
3. setup triggers to see if structures have been changed
4. shrink tool unless the position has been saved
Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, August 8, 2022 2:17 PM
Cc: chimerax-bug-report@cgl.ucsf.edu <chimerax-bug-report@cgl.ucsf.edu>; chimerax-programmers@cgl.ucsf.edu <chimerax-programmers@cgl.ucsf.edu>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #7410: Crash creating SEQCROW QMenuBar in ARM tech preview (was: ChimeraX bug report submission)
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
#7410: Crash creating SEQCROW QMenuBar in ARM tech preview
--------------------------------------------+---------------------------
Reporter: chimerax-bug-report@… | Owner: Tony Schaefer
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Window Toolkit | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------------+---------------------------
Changes (by pett):
* status: new => assigned
* cc: chimerax-programmers (added)
* component: Unassigned => Window Toolkit
* project: => ChimeraX
* platform: => all
* owner: (none) => Tony Schaefer
Comment:
Perhaps it would be worth checking if SEQCROW works in the ARM tech
preview?
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7410#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:3 by , 3 years ago
It's this part of the messy "stack trace":
{"imageOffset":17572,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":3},{"imageOffset":1749116,"symbol":"QMenuBar::minimumSizeHint() const","symbolLocation":284,"imageIndex":4},{"imageOffset":641188,"symbol":"sipQMenuBar::minimumSizeHint() const","symbolLocation":204,"imageIndex":5},{"imageOffset":239764,"symbol":"qSmartMinSize(QWidget const*)","symbolLocation":60,"imageIndex":4},{"imageOffset":228444,"imageIndex":4},{"imageOffset":230668,"symbol":"QLayout::totalSizeHint() const","symbolLocation":184,"imageIndex":4}
There was recently a similar ticket, but even more cryptic, with a similar stack: #7409
ChimeraX doesn't use a QMenuBar anywhere in its standard distribution, so although this is probably happening in the SEQCROW code it is not necessarily SEQCROW's fault -- it could be something with Qt and native Mac M1 code. That's why I'm hoping someone with access to an M1 Mac can see if SEQCROW at least starts when run from the technology preview. That would be the first step!
--Eric
follow-up: 4 comment:4 by , 3 years ago
For #7409, the user could have tried to open an ORCA output file for a geometry optimization right before the crash. For optimization jobs, SEQCROW will automatically open a tool with a plot of energy vs optimization iteration. There's a QMenuBar on the tool so users can save the energies to a CSV file.
QMenuBars seem to have had issues for a while on Mac and a few Linux operating systems. If you use the native menu bar, I read somewhere that breaks things. If you don't use the native menu bar, the menu is invisible unless you use menubar.setVisible(True) (at least with Qt5). I'm not sure why a GUI element like a menu would default to being invisible on Mac. If I knew menus would be so problematic, I wouldn't have used them. It would not surprise me if this were some Qt oddity, but I still want to get these tools working.
I don't think anyone I personally know has an M1 Mac. It looks like the user here grabbed a SEQCROW .whl from GitHub (version 1.5a1, even though they went back to 1.4.4 before this crash). Could I put any debugging stuff in the SEQCROW 1.5 alpha that could be useful for the next bug report? Print statements throughout the tool startup methods?
Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, August 8, 2022 4:45 PM
Cc: chimerax-bug-report@cgl.ucsf.edu <chimerax-bug-report@cgl.ucsf.edu>; chimerax-programmers@cgl.ucsf.edu <chimerax-programmers@cgl.ucsf.edu>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #7410: Crash creating SEQCROW QMenuBar in ARM tech preview
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
#7410: Crash creating SEQCROW QMenuBar in ARM tech preview
--------------------------------------------+---------------------------
Reporter: chimerax-bug-report@… | Owner: Tony Schaefer
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):
It's this part of the messy "stack trace":
{"imageOffset":17572,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":3},{"imageOffset":1749116,"symbol":"QMenuBar::minimumSizeHint()
const","symbolLocation":284,"imageIndex":4},{"imageOffset":641188,"symbol":"sipQMenuBar::minimumSizeHint()
const","symbolLocation":204,"imageIndex":5},{"imageOffset":239764,"symbol":"qSmartMinSize(QWidget
const*)","symbolLocation":60,"imageIndex":4},{"imageOffset":228444,"imageIndex":4},{"imageOffset":230668,"symbol":"QLayout::totalSizeHint()
const","symbolLocation":184,"imageIndex":4}
There was recently a similar ticket, but even more cryptic, with a
similar stack: #7409
ChimeraX doesn't use a QMenuBar anywhere in its standard distribution, so
although this is probably happening in the SEQCROW code it is not
necessarily SEQCROW's fault -- it could be something with Qt and native
Mac M1 code. That's why I'm hoping someone with access to an M1 Mac can
see if SEQCROW at least starts when run from the technology preview. That
would be the first step!
--Eric
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7410#comment:3>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:5 by , 3 years ago
I tried reproducing this crash on Mac M1 with SEQCROW 1.2.2 in ChimeraX daily build (July 31, 2022) using menu Tools / AaronTools / Build QM Input, getting a traceback instead, ticket #7415.
This crash is with SEQCROW 1.4.4 but Toolshed does not offer to install that in ChimeraX 1.5 daily build because it requires ChimeraX core <= 1.4. When I download and try to install it gives an error
Error installing 'SEQCROW-1.4.4-py3-none-any.whl' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /Users/goddard/Library/Caches/ChimeraX/1.5/installers/SEQCROW-1.4.4-py3-none-any.whl Requirement already satisfied: psutil in /Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from SEQCROW==1.4.4) (5.9.1) Requirement already satisfied: scipy in /Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from SEQCROW==1.4.4) (1.9.0) Requirement already satisfied: jinja2 in /Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages (from SEQCROW==1.4.4) (3.1.2) Requirement already satisfied: Send2Trash in /Users/goddard/Library/Application Support/ChimeraX/1.5/site-packages (from SEQCROW==1.4.4) (1.8.0) ERROR: Could not find a version that satisfies the requirement ChimeraX-Core<=1.4,>=1.2 (from seqcrow) (from versions: none) ERROR: No matching distribution found for ChimeraX-Core<=1.4,>=1.2 WARNING: You are using pip version 21.3.1; however, version 22.2.1 is available. You should consider upgrading via the '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip' command.
So I am puzzled how installing SEQCROW 1.4.4 into ChimeraX 1.5 daily did not give an error in the log of this bug report.
comment:6 by , 3 years ago
I tried SEQCROW 1.4.4 in ChimeraX 1.4 Intel Mac build running under Rosetta emulation on an M1 Mac CPU, and used menu Tools / Quantum Chemistry / Build QM Input and it crashed, ticket #7416.
comment:7 by , 3 years ago
Previous comment about crash #7416 was on Intel Mac, not M1 Mac ChimeraX.
comment:8 by , 3 years ago
Clarifying the previous comment. Crash #7416 was on an Intel Mac ChimeraX 1.4 build running on an M1 Mac (using Rosetta emulation).
follow-up: 9 comment:9 by , 3 years ago
Thanks for trying that out. I'll see if I can find a workaround for menus. Maybe the native menu bar is fine to use? I think I read that a program's normal menu (File, Edit, Select, etc. for ChimeraX) doesn't come back after something else uses the native menu bar, but I'm not sure if that's true.
Thanks,
Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, August 8, 2022 6:38 PM
Cc: chimerax-bug-report@cgl.ucsf.edu <chimerax-bug-report@cgl.ucsf.edu>; chimerax-programmers@cgl.ucsf.edu <chimerax-programmers@cgl.ucsf.edu>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #7410: Crash creating SEQCROW QMenuBar in ARM tech preview
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
#7410: Crash creating SEQCROW QMenuBar in ARM tech preview
--------------------------------------------+---------------------------
Reporter: chimerax-bug-report@… | Owner: Tony Schaefer
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 Tom Goddard):
I tried reproducing this crash on Mac M1 with SEQCROW 1.2.2 in ChimeraX
daily build (July 31, 2022) using menu Tools / AaronTools / Build QM
Input, getting a traceback instead, ticket #7415.
This crash is with SEQCROW 1.4.4 but Toolshed does not offer to install
that in ChimeraX 1.5 daily build because it requires ChimeraX core <= 1.4.
When I download and try to install it gives an error
{{{
Error installing 'SEQCROW-1.4.4-py3-none-any.whl'
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing
/Users/goddard/Library/Caches/ChimeraX/1.5/installers/SEQCROW-1.4.4-py3
-none-any.whl
Requirement already satisfied: psutil in
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9
/site-packages (from SEQCROW==1.4.4) (5.9.1)
Requirement already satisfied: scipy in
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9
/site-packages (from SEQCROW==1.4.4) (1.9.0)
Requirement already satisfied: jinja2 in
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9
/site-packages (from SEQCROW==1.4.4) (3.1.2)
Requirement already satisfied: Send2Trash in
/Users/goddard/Library/Application Support/ChimeraX/1.5/site-packages
(from SEQCROW==1.4.4) (1.8.0)
ERROR: Could not find a version that satisfies the requirement ChimeraX-
Core<=1.4,>=1.2 (from seqcrow) (from versions: none)
ERROR: No matching distribution found for ChimeraX-Core<=1.4,>=1.2
WARNING: You are using pip version 21.3.1; however, version 22.2.1 is
available.
You should consider upgrading via the
'/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/MacOS/ChimeraX -m pip
install --upgrade pip' command.
}}}
So I am puzzled how installing SEQCROW 1.4.4 into ChimeraX 1.5 daily did
not give an error in the log of this bug report.
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7410#comment:5>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
follow-up: 10 comment:10 by , 3 years ago
We considered using in-window QMenuBars initially in ChimeraX for complex tools, but ultimately decided they used too much precious screen real estate, and went with context menus instead. The downside is that context menus are less obvious. Tool windows offer a fill_context_menu() method to make it easy to use a context menu (particularly if you already have similar code for a QMenuBar). That method is described here: https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/tutorial_tool_qt.html#context-menu <https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/tutorial_tool_qt.html#context-menu>
follow-up: 11 comment:11 by , 3 years ago
I tested SEQCROW menu Quantum Chemistry / Build QM Input with the two lines commented out so it uses native menu bar. You are right it will never go back to showing the main ChimeraX menu bar. Even closing the tool panel does not bring back the ChimeraX menus at top of screen -- it just switches to having no menus except for the system UCSF ChimeraX menu. Qt is disappointing in many ways.
follow-up: 12 comment:12 by , 3 years ago
Thanks for the suggestion, Eric. I don't think context menus would be appropriate for some of SEQCROW's tools, especially the QM Input Builder. The Input Builder's menu is how you save your input file, store all the options to be recalled later, and run the computation (corresponding software must be installed). This tool is useless without these, and I think the context menu is too hidden in this case.
I'll probably look into using pushbuttons with a menu for the Input Builder. I think those are used quite a bit in ChimeraX tools, and they'd be more visible. If I make the pushbuttons flat, users might not notice that it isn't a QMenuBar.
Several of SEQCROW's tools just use the menu to export data on a visible table to a CSV file. I think that's probably ok to put in a context menu, as the user doesn't need to know that context menus exist to, e.g., get their ligand cone angles.
Thanks for testing the native menu, Tom. It's unfortunate that I can't just drop a line of code and have everything work.
Thanks,
Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, August 8, 2022 7:22 PM
To: chimerax-bug-report@cgl.ucsf.edu <chimerax-bug-report@cgl.ucsf.edu>; Anthony James Schaefer <tony.schaefer@uga.edu>
Cc: chimerax-programmers@cgl.ucsf.edu <chimerax-programmers@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #7410: Crash creating SEQCROW QMenuBar in ARM tech preview
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
#7410: Crash creating SEQCROW QMenuBar in ARM tech preview
--------------------------------------------+---------------------------
Reporter: chimerax-bug-report@… | Owner: Tony Schaefer
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):
{{{
We considered using in-window QMenuBars initially in ChimeraX for complex
tools, but ultimately decided they used too much precious screen real
estate, and went with context menus instead. The downside is that context
menus are less obvious. Tool windows offer a fill_context_menu() method to
make it easy to use a context menu (particularly if you already have
similar code for a QMenuBar). That method is described here:
https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/tutorial_tool_qt.html
#context-menu
<https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/tutorial_tool_qt.html
#context-menu>
}}}
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7410#comment:10>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
follow-up: 13 comment:13 by , 3 years ago
I ended up making my own "FakeMenu" widget. It didn't take much code:
```py
from Qt.QtCore import Qt
from Qt.QtWidgets import QPushButton, QHBoxLayout, QWidget, QMenu
class FakeMenu(QWidget):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.layout = QHBoxLayout(self)
self.layout.setContentsMargins(0, 0, 0, 0)
def addMenu(self, text):
"""adds a menu titled 'text' and returns the corresponding QMenu"""
pushbutton = QPushButton(text)
pushbutton.setFlat(True)
menu = QMenu(pushbutton)
pushbutton.setMenu(menu)
self.layout.addWidget(pushbutton, stretch=0, alignment=Qt.AlignLeft)
n_widgets = self.layout.count()
self.layout.setStretch(n_widgets - 1, 1)
if n_widgets > 1:
self.layout.setStretch(n_widgets - 2, 0)
return menu
```
I was able to swap this with QMenuBar with minimal changes. The only downside is you can't navigate the menu with alt keys like you can with QMenuBar. However, users can still use hot keys, like ctrl + C to copy an input file to their clipboard.
Thanks again for the help and suggestions
Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, August 8, 2022 8:05 PM
To: chimerax-bug-report@cgl.ucsf.edu <chimerax-bug-report@cgl.ucsf.edu>; Anthony James Schaefer <tony.schaefer@uga.edu>
Cc: chimerax-programmers@cgl.ucsf.edu <chimerax-programmers@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #7410: Crash creating SEQCROW QMenuBar in ARM tech preview
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
#7410: Crash creating SEQCROW QMenuBar in ARM tech preview
--------------------------------------------+---------------------------
Reporter: chimerax-bug-report@… | Owner: Tony Schaefer
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 Tony Schaefer):
{{{
Thanks for the suggestion, Eric. I don't think context menus would be
appropriate for some of SEQCROW's tools, especially the QM Input Builder.
The Input Builder's menu is how you save your input file, store all the
options to be recalled later, and run the computation (corresponding
software must be installed). This tool is useless without these, and I
think the context menu is too hidden in this case.
I'll probably look into using pushbuttons with a menu for the Input
Builder. I think those are used quite a bit in ChimeraX tools, and they'd
be more visible. If I make the pushbuttons flat, users might not notice
that it isn't a QMenuBar.
Several of SEQCROW's tools just use the menu to export data on a visible
table to a CSV file. I think that's probably ok to put in a context menu,
as the user doesn't need to know that context menus exist to, e.g., get
their ligand cone angles.
Thanks for testing the native menu, Tom. It's unfortunate that I can't
just drop a line of code and have everything work.
Thanks,
Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, August 8, 2022 7:22 PM
To: chimerax-bug-report@cgl.ucsf.edu <chimerax-bug-report@cgl.ucsf.edu>;
Anthony James Schaefer <tony.schaefer@uga.edu>
Cc: chimerax-programmers@cgl.ucsf.edu <chimerax-programmers@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #7410: Crash creating SEQCROW QMenuBar in ARM tech
preview
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
#7410: Crash creating SEQCROW QMenuBar in ARM tech preview
--------------------------------------------+---------------------------
Reporter: chimerax-bug-report@… | Owner: Tony Schaefer
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):
{{{
We considered using in-window QMenuBars initially in ChimeraX for complex
tools, but ultimately decided they used too much precious screen real
estate, and went with context menus instead. The downside is that
context
menus are less obvious. Tool windows offer a fill_context_menu() method
to
make it easy to use a context menu (particularly if you already have
similar code for a QMenuBar). That method is described here:
https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/tutorial_tool_qt.html
#context-menu
<https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/tutorial_tool_qt.html
#context-menu>
}}}
--
Ticket URL:
<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7410#comment:10>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
}}}
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7410#comment:12>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:14 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Sounds like your fake menus are a reasonable work-around.
It might be worth commenting on existing Qt tickets about the broken non-native QMenuBar on Mac. I don't know if there are Qt project tickets for that, but letting them know people care about this may help the Qt project.
Note:
See TracTickets
for help on using tickets.
Perhaps it would be worth checking if SEQCROW works in the ARM tech preview?