"toolshed install" not allowing upgrade from wheel file

[Eric Pettersen]

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
The bug isn't in fact the traceback (which has already been reported), but the fact that the toolshed wanted to report a "bundle already installed" error.  The installed AddH was version 2.1.1.  The wheel I was trying to install was 2.1.3.

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help toolshed

> toolshed install browse

browse does not match any bundles  

> toolshed install
> /Users/pett/src/chimerax/src/bundles/addh/dist/ChimeraX_AddH-2.1.3-py38-none-
> any.whl

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 298, in toolshed_install  
ts.install_bundle(bundles, logger, **kw)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 903, in install_bundle  
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
AttributeError: 'str' object has no attribute 'name'  
  
AttributeError: 'str' object has no attribute 'name'  
  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
  
See log for complete Python traceback.  
  

> help toolshed

> toolshed list

List of installed bundles:  

  * AddH (2.1.1): Add hydrogens
  * AlignmentAlgorithms (2.0): Sequence alignment algorithms
  * AlignmentHdrs (3.2): Alignment header support
  * AlignmentMatrices (2.0): Sequence alignment similarity matrices
  * Alignments (2.1): Sequence alignment support
  * Arrays (1.0): C++ library for parsing numpy arrays
  * AtomSearch (2.0): 3D atom search
  * Atomic (1.6.1): Atomic-structure functionality
  * AxesPlanes (2.0): Depict axes or planes
  * BILD (1.0): BILD file reader
  * BasicActions (1.1): Basic actions for user-defined specifier names
  * BlastProtein (1.0.1): Search PDB/NR using BLAST
  * BondRot (2.0): Bond rotation support
  * BugReporter (1.0): Report bugs when an error occurs
  * BuildStructure (2.0): Create/modify structures
  * Bumps (1.0): Find protrusions in density maps
  * ButtonPanel (1.0): Create custom user interface panels
  * CageBuilder (1.0): Build polygonal meshes for oligomeric molecular assemblies
  * CellPack (1.0): Fetch cellPACK models from web
  * Centroids (1.1): Depict centroid of atoms
  * ChemGroup (2.0): Detect chemically functional groups
  * Clashes (2.0): Find clashes/contacts in structures
  * ColorActions (1.0): Simple interface for coloring objects
  * ColorGlobe (1.0): Show directional resolution colored sphere
  * CommandLine (1.1.3): Command line support
  * ConnectStructure (2.0): Add bonds to structures that lack them
  * Contacts (1.0): Display chain contact maps
  * Core (1.1): ChimeraX Core Package
  * CoreFormats (1.0): ChimeraX session support
  * Crosslinks (1.0): Analyze crosslinks
  * Crystal (1.0): Crystal symmetries
  * DataFormats (1.0): Data format management
  * Dicom (1.0): Read medical imaging and segmentations in DICOM format
  * DistMonitor (1.1): Interactive distance display
  * DistUI (1.0): Distance measurement user interface
  * Dssp (2.0): Compute/assign secondary structure
  * EMDB-SFF (1.0): EMDB SFF file reader
  * ExperimentalCommands (1.0): Experimental commands
  * FileHistory (1.0): File History Panel
  * FunctionKey (1.0): Assign function keys to run commands
  * Geometry (1.1): Vector and coordinate system routines
  * Graphics (1.0): OpenGL graphics rendering
  * HKCage (1.0): Create icosahedral mesh of hexagons and pentagons
  * Hbonds (2.0): Identify hydrogen bonds in and among structures
  * Help (1.0): Show ChimeraX Help
  * IHM (1.0): Integrative Hybrid Models file reader
  * IMOD (1.0): IMOD model file reader
  * IO (1.0): Python convenience input/output functions
  * ImageFormats (1.0): Support for saving images
  * Label (1.0): Add text labels to graphics
  * ListInfo (1.0): Report attributes for selected atomic data
  * Log (1.1.1): Log support
  * LookingGlass (1.1): LookingGlass holographic display
  * MDcrds (2.0): Molecular dynamics support
  * MLP (1.0): Molecular lipophilicity calculation
  * MMTF (2.0): MMTF format read/write
  * Map (1.0.1): Density maps
  * MapData (2.0): Volume data file formats
  * MapEraser (1.0): Map eraser
  * MapFilter (2.0): Operations on maps
  * MapFit (2.0): Fit molecules into maps
  * MapSeries (2.0): Volume series
  * Markers (1.0): Place markers on density maps
  * Mask (1.0): Mask a volume to a surface
  * MatchMaker (1.1): Superimpose structures
  * MedicalToolbar (1.0.1): Toolbar for medical image analysis
  * Meeting (1.0): Shared interactive VR sessions.
  * ModelPanel (1.0): ChimeraX Model Panel
  * ModelSeries (1.0): Display sequences of models one by one
  * Modeller (1.0): Interface to Modeller
  * Mol2 (2.0): Mol2 reader/writer
  * Morph (1.0): Morph atomic structures
  * MouseModes (1.0): Provide right button mouse mode tool
  * Movie (1.0): Commands to record movies
  * Neuron (1.0): Read SWC neuron trace files
  * Nucleotides (2.0): Create nucleotide-specific displays
  * OpenCommand (1.2.1): Manages 'open' command extensibility
  * PDB (2.1): PDB format read/write
  * PDBBio (1.0): PDB biological assembly fetch
  * PickBlobs (1.0): Measure and color blobs
  * Positions (1.0): Read and write model position matrices
  * PresetMgr (1.0): Preset management
  * PubChem (2.0): PubChem fetch
  * RNALayout (1.0): Make RNA models
  * Read-Pbonds (1.0): Read in pseudobonds from a file
  * Registration (1.1): Register ChimeraX
  * RemoteControl (1.0): Control ChimeraX from other apps
  * ResidueFit (1.0): Display fit of residues to density map
  * RestServer (1.0): Starts REST server to execute commands from network requests
  * RotamerLibMgr (2.0): Manage rotamer libraries
  * RotamerLibsDunbrack (2.0): Dunbrack rotamer library
  * RotamerLibsDynameomics (2.0): Dynameomics rotamer library
  * RotamerLibsRichardson (2.0): Richardson rotamer libraries
  * SDF (2.0): SDF file reader
  * STL (1.0): STL file read/write
  * SaveCommand (1.2): Manages 'save' command extensibility
  * SchemeMgr (1.0): HTTP scheme management
  * Segger (1.0): Segment map
  * Segment (1.0): Watershed segment calculation
  * SeqView (2.2): Sequence viewer
  * Shape (1.0.1): Make models for geometric shapes
  * Shell (1.0): Interactive Python shell
  * Shortcuts (1.0): Button and keyboard shortcuts
  * ShowAttr (1.0): Render/select by attribute
  * ShowSequences (1.0): Choose/show structure sequences
  * SideView (1.0): Side view of scene
  * Smiles (2.0): SMILES fetch
  * SmoothLines (1.0): Smooth network of lines
  * SpaceNavigator (1.0): Space Navigator device support
  * StdCommands (1.0.4): Standard commands
  * Storm (1.0): STORM file reader
  * Struts (1.0): struts for 3D printing
  * Surface (1.0): Surface calculations
  * SwapAA (2.0): Swap amino acid
  * SwapRes (2.0): Swap residue side chains
  * TapeMeasure (1.0): Tape measure mouse mode
  * Test (1.0): simple regression test
  * Toolbar (1.0): Toolbar
  * ToolshedUtils (1.0): Toolshed bundle utilities
  * Tug (1.0): Tug on atoms with molecular dynamics
  * UI (1.2.3): ChimeraX user interface
  * VTK (1.0): Legacy VTK file reader and writer
  * ViewDockX (1.0): Analyze ligand-receptor docking results
  * Vive (1.1): Virtual reality headset support
  * VolumeMenu (1.0): Volume menu
  * WavefrontOBJ (1.0): Wavefront OBJ file read/write
  * WebCam (1.0): Combine camera video with graphics
  * WebServices (1.0): Web service and HTTP request support
  * Zone (1.0): Mouse mode to show atom and map zones
  * coulombic (1.0.1): Compute/show electrostatic potential
  * gltf (1.0): Read/write glTF 3d scene files
  * mmCIF (2.2): mmCIF format read/write
  * uniprot (2.0): UniProt database support
  * SEQCROW (0.17): Structure Editing and Quantum Chemical Representation and Organization for Workflows

  

> help toolshed

> toolshed install
> /Users/pett/src/chimerax/src/bundles/addh/dist/ChimeraX_AddH-2.1.3-py38-none-
> any.whl

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 298, in toolshed_install  
ts.install_bundle(bundles, logger, **kw)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 903, in install_bundle  
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
AttributeError: 'str' object has no attribute 'name'  
  
AttributeError: 'str' object has no attribute 'name'  
  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolshed_utils/__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2.8 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Memory: 16 GB
      Boot ROM Version: 236.0.0.0.0
      SMC Version (system): 2.32f21

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H15)
      Kernel Version: Darwin 19.6.0
      Time since boot: 3:32

Graphics/Displays:

    Intel Iris Pro Graphics 6200:

      Chipset Model: Intel Iris Pro Graphics 6200
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1622
      Revision ID: 0x000a
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        iMac:
          Display Type: LCD
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    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: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    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: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    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: 2.0
    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: 2.0
    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
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    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
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    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: 1.2.3
    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: 0.29.20
    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: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    Send2Trash: 1.5.0
    SEQCROW: 0.17
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    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: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2