Opened 5 years ago

Closed 5 years ago

#4094 closed defect (duplicate)

Python shell autocomplete: _queue.Empty

Reported by: goddard@… Owned by: Eric Pettersen
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.dev202012242219 (2020-12-24 22:19:47 UTC)
Description
Typed mi<tab> in shell, got this error.

Log:
UCSF ChimeraX version: 1.2.dev202012242219 (2020-12-24)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Shell

ERROR:ipykernel.inprocess.ipkernel:Exception in message handler:  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\ipykernel\kernelbase.py", line 268, in dispatch_shell  
yield gen.maybe_future(handler(stream, idents, msg))  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\tornado\gen.py", line 762, in run  
value = future.result()  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\tornado\gen.py", line 234, in wrapper  
yielded = ctx_run(next, result)  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\ipykernel\kernelbase.py", line 583, in complete_request  
matches = yield gen.maybe_future(self.do_complete(code, cursor_pos))  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\ipykernel\ipkernel.py", line 360, in do_complete  
return self._experimental_do_complete(code, cursor_pos)  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\ipykernel\ipkernel.py", line 385, in _experimental_do_complete  
completions = list(_rectify_completions(code, raw_completions))  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\IPython\core\completer.py", line 484, in rectify_completions  
completions = list(completions)  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\IPython\core\completer.py", line 1818, in completions  
for c in self._completions(text, offset,
_timeout=self.jedi_compute_type_timeout/1000):  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\IPython\core\completer.py", line 1861, in _completions  
matched_text, matches, matches_origin, jedi_matches = self._complete(  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\IPython\core\completer.py", line 2029, in _complete  
completions = self._jedi_matches(  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\IPython\core\completer.py", line 1373, in _jedi_matches  
interpreter = jedi.Interpreter(  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\jedi\api\\__init__.py", line 725, in __init__  
super().__init__(code, environment=environment,  
TypeError: __init__() got an unexpected keyword argument 'column'  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\qtconsole\console_widget.py", line 427, in eventFilter  
return self._event_filter_console_keypress(event)  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\qtconsole\frontend_widget.py", line 339, in
_event_filter_console_keypress  
return super(FrontendWidget, self)._event_filter_console_keypress(event)  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\qtconsole\console_widget.py", line 1416, in
_event_filter_console_keypress  
if self._tab_pressed():  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\qtconsole\frontend_widget.py", line 283, in _tab_pressed  
self._complete()  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\qtconsole\frontend_widget.py", line 721, in _complete  
msg_id = self.kernel_client.complete(code=code, cursor_pos=cursor_pos)  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\ipykernel\inprocess\client.py", line 117, in complete  
self._dispatch_to_kernel(msg)  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\ipykernel\inprocess\client.py", line 179, in _dispatch_to_kernel  
idents, reply_msg = self.session.recv(stream, copy=False)  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\jupyter_client\session.py", line 807, in recv  
msg_list = socket.recv_multipart(mode, copy=copy)  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\site-
packages\ipykernel\inprocess\socket.py", line 57, in recv_multipart  
return self.queue.get_nowait()  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\queue.py", line 198, in
get_nowait  
return self.get(block=False)  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\queue.py", line 167, in
get  
raise Empty  
_queue.Empty  
  
_queue.Empty  
  
File "C:\Program Files\ChimeraX-Dec-28-2020\bin\lib\queue.py", line 167, in
get  
raise Empty  
  
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
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PySide2 version: 5.15.2
Qt version: 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.3.0
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.10
    ChimeraX-AtomicLibrary: 1.1
    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
    ChimeraX-BuildStructure: 2.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    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.dev202012242219
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 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: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.2
    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: 2.2
    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: 1.4
    ChimeraX-PDB: 2.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.3
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    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: 1.2.2
    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: 1.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.3.2
    ChimeraX-uniprot: 2.1
    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
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.0
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.5.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.1
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.8
    parso: 0.8.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 20.3.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.8
    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
    PySide2: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2020.5
    pywin32: 228
    pyzmq: 20.0.0
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    shiboken2: 5.15.2
    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: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → General Controls
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Python shell autocomplete: _queue.Empty

comment:2 by Eric Pettersen, 5 years ago

Resolution: → duplicate
Status: accepted → closed

Duplicate of #4091; adding Tom to recipient list for that ticket

Note: See TracTickets for help on using tickets.