The following bug report has been submitted:
Platform: Windows-10-10.0.19044
ChimeraX Version: 1.6.dev202211030048 (2022-11-03 00:48:06 UTC)
Description
Building a toolshed bundle and getting an attribute error when calling usage on one of my functions (usage measure composite). All other usage commands work as expected (i.e., usage measure intensity), and importantly the functions all work properly. Here is the full repo, if helpful: https://github.com/bscott711/ChimeraX-measure-intensity
Log:
UCSF ChimeraX version: 1.6.dev202211030048 (2022-11-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> cd C:\Users\bscott\Documents\GitHub\ChimeraX-measure-intensity
Current working directory is: C:\Users\bscott\Documents\GitHub\ChimeraX-
measure-intensity
> devel build .
running build
running build_py
running bdist_wheel
installing to build\bdist.win-amd64\wheel
running install
running install_lib
creating build\bdist.win-amd64\wheel
creating build\bdist.win-amd64\wheel\chimerax
creating build\bdist.win-amd64\wheel\chimerax\measure-intensity
copying build\lib\chimerax\measure-intensity\measure_commands.py ->
build\bdist.win-amd64\wheel\\.\chimerax\measure-intensity
copying build\lib\chimerax\measure-intensity\\__init__.py -> build\bdist.win-
amd64\wheel\\.\chimerax\measure-intensity
running install_egg_info
running egg_info
writing ChimeraX_Measure_Intensity.egg-info\PKG-INFO
writing dependency_links to ChimeraX_Measure_Intensity.egg-
info\dependency_links.txt
writing requirements to ChimeraX_Measure_Intensity.egg-info\requires.txt
writing top-level names to ChimeraX_Measure_Intensity.egg-info\top_level.txt
reading manifest file 'ChimeraX_Measure_Intensity.egg-info\SOURCES.txt'
writing manifest file 'ChimeraX_Measure_Intensity.egg-info\SOURCES.txt'
Copying ChimeraX_Measure_Intensity.egg-info to build\bdist.win-
amd64\wheel\\.\ChimeraX_Measure_Intensity-0.4.0-py3.9.egg-info
running install_scripts
creating build\bdist.win-amd64\wheel\ChimeraX_Measure_Intensity-0.4.0.dist-
info\WHEEL
creating 'dist\ChimeraX_Measure_Intensity-0.4.0-py3-none-any.whl' and adding
'build\bdist.win-amd64\wheel' to it
adding 'chimerax/measure-intensity/__init__.py'
adding 'chimerax/measure-intensity/measure_commands.py'
adding 'ChimeraX_Measure_Intensity-0.4.0.dist-info/METADATA'
adding 'ChimeraX_Measure_Intensity-0.4.0.dist-info/WHEEL'
adding 'ChimeraX_Measure_Intensity-0.4.0.dist-info/top_level.txt'
adding 'ChimeraX_Measure_Intensity-0.4.0.dist-info/RECORD'
removing build\bdist.win-amd64\wheel
Distribution is in .\dist\ChimeraX_Measure_Intensity-0.4.0-py3-none-any.whl
> devel install .
running build
running build_py
running bdist_wheel
installing to build\bdist.win-amd64\wheel
running install
running install_lib
creating build\bdist.win-amd64\wheel
creating build\bdist.win-amd64\wheel\chimerax
creating build\bdist.win-amd64\wheel\chimerax\measure-intensity
copying build\lib\chimerax\measure-intensity\measure_commands.py ->
build\bdist.win-amd64\wheel\\.\chimerax\measure-intensity
copying build\lib\chimerax\measure-intensity\\__init__.py -> build\bdist.win-
amd64\wheel\\.\chimerax\measure-intensity
running install_egg_info
running egg_info
writing ChimeraX_Measure_Intensity.egg-info\PKG-INFO
writing dependency_links to ChimeraX_Measure_Intensity.egg-
info\dependency_links.txt
writing requirements to ChimeraX_Measure_Intensity.egg-info\requires.txt
writing top-level names to ChimeraX_Measure_Intensity.egg-info\top_level.txt
reading manifest file 'ChimeraX_Measure_Intensity.egg-info\SOURCES.txt'
writing manifest file 'ChimeraX_Measure_Intensity.egg-info\SOURCES.txt'
Copying ChimeraX_Measure_Intensity.egg-info to build\bdist.win-
amd64\wheel\\.\ChimeraX_Measure_Intensity-0.4.0-py3.9.egg-info
running install_scripts
creating build\bdist.win-amd64\wheel\ChimeraX_Measure_Intensity-0.4.0.dist-
info\WHEEL
creating 'dist\ChimeraX_Measure_Intensity-0.4.0-py3-none-any.whl' and adding
'build\bdist.win-amd64\wheel' to it
adding 'chimerax/measure-intensity/__init__.py'
adding 'chimerax/measure-intensity/measure_commands.py'
adding 'ChimeraX_Measure_Intensity-0.4.0.dist-info/METADATA'
adding 'ChimeraX_Measure_Intensity-0.4.0.dist-info/WHEEL'
adding 'ChimeraX_Measure_Intensity-0.4.0.dist-info/top_level.txt'
adding 'ChimeraX_Measure_Intensity-0.4.0.dist-info/RECORD'
removing build\bdist.win-amd64\wheel
Distribution is in .\dist\ChimeraX_Measure_Intensity-0.4.0-py3-none-any.whl
[toolshed install](help:user/commands/toolshed.html#install)
.\dist\ChimeraX_Measure_Intensity-0.4.0-py3-none-any.whl
[toolshed install .\dist\ChimeraX_Measure_Intensity-0.4.0-py3-none-
any.whl](cxcmd:toolshed install
.\\\dist\\\ChimeraX_Measure_Intensity-0.4.0-py3-none-any.whl)
Successfully installed ChimeraX-Measure-Intensity-0.4.0
Installed ChimeraX-Measure-Intensity (0.4.0)
> devel clean .
> usage measure intensity
measure intensity surface toMap a surfaces specifier [radius radius] [palette
a colormap] [range range] [key true or false]
— Measure local intensity relative to surface
radius: an integer ≥ 1 and ≤ 30
range: some numbers or full
> usage measure composite
Traceback (most recent call last):
File "C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
319, in execute
cmd.run(cmd_text)
File "C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\std_commands\usage.py",
line 68, in usage
usage = cli.html_usage(session, command_name, show_hidden=show_hidden)
File "C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 3162, in html_usage
text = _html_usage(name, no_aliases, show_subcommands, expand_alias,
show_hidden, registry=registry)
File "C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 3248, in _html_usage
arg_syntax.append('<i>%s</i>: %s' % (uarg_name, arg_type.html_name()))
AttributeError: 'str' object has no attribute 'html_name'
AttributeError: 'str' object has no attribute 'html_name'
File "C:\Apps\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 3248, in _html_usage
arg_syntax.append('%s: %s' % (uarg_name, arg_type.html_name()))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 496.49
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: Supermicro
Model: SYS-5039A-I
OS: Microsoft Windows 10 Education (Build 19044)
Memory: 137,115,049,984
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Xeon(R) W-2133 CPU @ 3.60GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4.1
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.8
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.43.4
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
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: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.dev202211030048
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: 1.3
ChimeraX-DockPrep: 1.0
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: 2.4
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: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
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: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-Measure-Intensity: 0.4.0
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.2
ChimeraX-PDB: 2.6.8
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-RenderByAttr: 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: 2.8
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: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.25.1
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
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
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.3
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.0.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 4.11.2
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.3
pkginfo: 1.8.3
prompt-toolkit: 3.0.31
psutil: 5.9.1
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: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pywin32: 303
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.2.1
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
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: 0.6.0
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.12
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
WMI: 1.5.1
zipp: 3.10.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Reported by Brandon Scott