id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7965 Usage: arg_type is str brandon.scott@… Greg Couch "{{{ 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('%s: %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 }}} " defect closed normal Command Line limitation all ChimeraX