Opened 5 years ago

Closed 5 years ago

#3821 closed defect (duplicate)

Shell broken on Windows in Python 3.8

Reported by: goddard@… Owned by: pett
Priority: normal Milestone:
Component: General Controls Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.dev202010122139 (2020-10-12 21:39:29 UTC)
Description
Tried Eric's new tool.py to fix shell.  Did not work.

Log:
UCSF ChimeraX version: 1.2.dev202010122139 (2020-10-12)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Shell

Traceback (most recent call last):  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\traitlets\traitlets.py", line 535, in get  
value = obj._trait_values[self.name]  
KeyError: 'iopub_socket'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\traitlets\traitlets.py", line 535, in get  
value = obj._trait_values[self.name]  
KeyError: 'iopub_thread'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 524, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1251, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\shell\\__init__.py", line 21, in start_tool  
return ShellUI(session, tool_name)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\shell\tool.py", line 37, in __init__  
kernel_manager.start_kernel()  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\ipykernel\inprocess\manager.py", line 46, in start_kernel  
self.kernel = InProcessKernel(parent=self, session=self.session)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\ipykernel\inprocess\ipkernel.py", line 72, in __init__  
super(InProcessKernel, self).__init__(**traits)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\ipykernel\ipkernel.py", line 71, in __init__  
self.shell.displayhook.pub_socket = self.iopub_socket  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\traitlets\traitlets.py", line 575, in __get__  
return self.get(obj, cls)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\traitlets\traitlets.py", line 538, in get  
default = obj.trait_defaults(self.name)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\traitlets\traitlets.py", line 1577, in trait_defaults  
return self._get_trait_default_generator(names[0])(self)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\traitlets\traitlets.py", line 975, in __call__  
return self.func(*args, **kwargs)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\ipykernel\inprocess\ipkernel.py", line 67, in _default_iopub_socket  
return self.iopub_thread.background_socket  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\traitlets\traitlets.py", line 575, in __get__  
return self.get(obj, cls)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\traitlets\traitlets.py", line 538, in get  
default = obj.trait_defaults(self.name)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\traitlets\traitlets.py", line 1577, in trait_defaults  
return self._get_trait_default_generator(names[0])(self)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\traitlets\traitlets.py", line 975, in __call__  
return self.func(*args, **kwargs)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\ipykernel\inprocess\ipkernel.py", line 59, in _default_iopub_thread  
thread = IOPubThread(self._underlying_iopub_socket)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\ipykernel\iostream.py", line 71, in __init__  
self._setup_event_pipe()  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\ipykernel\iostream.py", line 90, in _setup_event_pipe  
self._event_puller = ZMQStream(pipe_in, self.io_loop)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\zmq\eventloop\zmqstream.py", line 127, in __init__  
self._init_io_state()  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\zmq\eventloop\zmqstream.py", line 552, in _init_io_state  
self.io_loop.add_handler(self.socket, self._handle_events, self.io_loop.READ)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\tornado\platform\asyncio.py", line 100, in add_handler  
self.asyncio_loop.add_reader(fd, self._handle_events, fd, IOLoop.READ)  
File
"C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\asyncio\events.py",
line 501, in add_reader  
raise NotImplementedError  
NotImplementedError  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\ui\gui.py", line 1451, in <lambda>  
run(ses, "ui tool show %s" % (StringArg.unparse(fave))))  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\ui\cmd.py", line 187, in ui_tool_show  
bi.start_tool(session, name)  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 529, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Shell in
bundle ChimeraX-Shell:  
  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Shell in
bundle ChimeraX-Shell:  
  
  
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 529, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 398.35
OpenGL renderer: GeForce GTX 1070 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: GS65 Stealth Thin 8RF
OS: Microsoft Windows 10 Pro (Build 19041)
Memory: 34,195,668,992
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz"
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    cftime: 1.2.1
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.8.2
    ChimeraX-AtomicLibrary: 1.0
    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
    ChimeraX-BuildStructure: 2.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202010122139
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    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: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.1
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0.1
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.3.1
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.2
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    netifaces: 0.10.9
    networkx: 2.5
    numexpr: 2.7.1
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 20.2.3
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.1
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 5 years ago

Component: Unassigned → General Controls
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Shell broken on Windows in Python 3.8

comment:2 by pett, 5 years ago

Resolution: → duplicate
Status: accepted → closed
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