Installed version number not updated

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.7.dev202309180647 (2023-09-18 06:47:42 UTC)
Description
Another subtle ToolShed problem: I incremented the version number of Clipper in its bundle_info.xml from 0.22.0 to 0.22.1 and rebuilt. The wheel file is correctly built with the version number 0.22.1 and it installs (I checked, and the bug I was fixing is gone) - but ChimeraX still believes the installed version is 0.22.0. Tail end of the terminal output from `make app-install` is below.

removing build\bdist.win-amd64\wheel
Distribution is in .\dist\ChimeraX_Clipper-0.22.1-cp311-cp311-win_amd64.whl
Installing bundle
Executing: toolshed install .\dist\ChimeraX_Clipper-0.22.1-cp311-cp311-win_amd64.whl
Errors may have occurred when running pip:
pip standard error:
---

[notice] A new release of pip is available: 23.0 -> 23.2.1
[notice] To update, run: C:\Program Files\ChimeraX-daily\bin\python.exe -m pip install --upgrade pip
---
pip standard output:
---
Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing c:\users\tristan croll\my_gits\chimerax-clipper\dist\chimerax_clipper-0.22.1-cp311-cp311-win_amd64.whl
Requirement already satisfied: ChimeraX-Core<1.8,>=1.7.dev202306142048 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Clipper==0.22.1) (1.7.dev202309180647)
Requirement already satisfied: ChimeraX-Atomic~=1.36 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Clipper==0.22.1) (1.47.2)
Requirement already satisfied: ChimeraX-AtomicLibrary~=10.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Clipper==0.22.1) (10.0.8)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Clipper==0.22.1) (1.1)
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (2.0.1)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.3)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.1.1)
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (2.12.1)
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (2.0.3)
Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (2.7.2)
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.0.2)
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.2.3)
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.10.2)
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.5.1)
Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.0.1)
Requirement already satisfied: ChimeraX-UI~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.31.5)
Requirement already satisfied: ChimeraX-IO~=1.0.1 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-PDB~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.0.1)
Requirement already satisfied: ChimeraX-Map~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.1.4)
Requirement already satisfied: ChimeraX-MapData~=2.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (2.0)
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.12.2)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.2)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.0)
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (2.0.1)
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (2.1.1)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.0.1)
Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (1.4)
Requirement already satisfied: ChimeraX-Dssp~=2.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (2.0)
Requirement already satisfied: ChimeraX-MapFit~=2.0 in c:\program files\chimerax-daily\bin\lib\site-packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.36->ChimeraX-Clipper==0.22.1) (2.0)
Installing collected packages: ChimeraX-Clipper
Successfully installed ChimeraX-Clipper-0.22.0
---
Successfully installed ChimeraX-Clipper-0.22.0
Installed ChimeraX-Clipper (0.22.0)

UCSF ChimeraX version: 1.7.dev202309180647 (2023-09-18)
© 2016-2023 Regents of the University of California.  All rights reserved.

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.7.dev202309180647 (2023-09-18)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed list

List of installed bundles:  

  * AddCharge (1.5.11): Add partial charges to atoms
  * AddH (2.2.5): Add hydrogens
  * AlignmentAlgorithms (2.0.1): Sequence alignment algorithms
  * AlignmentHdrs (3.4): Alignment header support
  * AlignmentMatrices (2.1): Sequence alignment similarity matrices
  * Alignments (2.9.3): Sequence alignment support
  * AlphaFold (1.0): Predict or fetch AlphaFold structures
  * AltlocExplorer (1.1.1): Examine/change alternate atomic locations
  * AmberInfo (1.0): Provide information about AmberTools installation
  * Arrays (1.1): C++ library for parsing numpy arrays
  * Atomic (1.47.2): Atomic-structure functionality
  * AtomicLibrary (10.0.8): Atomic-structure C++ library
  * AtomSearch (2.0.1): 3D atom search
  * AxesPlanes (2.3.2): Depict axes or planes
  * BasicActions (1.1.2): Basic actions for user-defined specifier names
  * BILD (1.0): BILD file reader
  * BlastProtein (2.1.2): Search PDB/NR/AlphaFold using BLAST
  * BondRot (2.0.4): Bond rotation support
  * BugReporter (1.0.1): Report bugs when an error occurs
  * BuildStructure (2.10.5): Create/modify structures
  * Bumps (1.0): Find protrusions in density maps
  * ButtonPanel (1.0.1): Create custom user interface panels
  * CageBuilder (1.0.1): Build polygonal meshes for oligomeric molecular assemblies
  * CellPack (1.0): Fetch cellPACK models from web
  * Centroids (1.3.2): Depict centroid of atoms
  * ChangeChains (1.0.3): Change chain IDs
  * CheckWaters (1.3.1): Check water placement in maps
  * ChemGroup (2.0.1): Detect chemically functional groups
  * Clashes (2.2.4): Find clashes/contacts in structures
  * Clipper (0.22.0): Clipper: Efficient handling of volumetric data and symmetry
  * ColorActions (1.0.3): Simple interface for coloring objects
  * ColorGlobe (1.0): Show directional resolution colored sphere
  * ColorKey (1.5.4): Add color key to graphics
  * CommandLine (1.2.5): Command line support
  * ConnectStructure (2.0.1): Add bonds to structures that lack them
  * Contacts (1.0.1): Display chain contact maps
  * Core (1.7.dev202309180647): ChimeraX Core Package
  * CoreFormats (1.1): ChimeraX session support
  * coulombic (1.4.2): Compute/show electrostatic potential
  * Crosslinks (1.0): Analyze crosslinks
  * Crystal (1.0): Crystal symmetries
  * CrystalContacts (1.0.1): Show contacting asymmetric units in a crystal
  * DataFormats (1.2.3): Data format management
  * Dicom (1.2): Read medical imaging and segmentations in DICOM format
  * DistMonitor (1.4): Interactive distance display
  * DockPrep (1.1.2): Prepare structures for docking
  * Dssp (2.0): Compute/assign secondary structure
  * EMDB-SFF (1.0): EMDB SFF file reader
  * ESMFold (1.0): Predict or fetch ESMFold structures
  * FileHistory (1.0.1): File History Panel
  * FunctionKey (1.0.1): Assign function keys to run commands
  * Geometry (1.3): Vector and coordinate system routines
  * gltf (1.0): Read/write glTF 3d scene files
  * Graphics (1.1.1): OpenGL graphics rendering
  * Hbonds (2.4): Identify hydrogen bonds in and among structures
  * Help (1.2.2): Show ChimeraX Help
  * HKCage (1.3): Create icosahedral mesh of hexagons and pentagons
  * IHM (1.1): Integrative Hybrid Models file reader
  * ImageFormats (1.2): Support for saving images
  * IMOD (1.0): IMOD model file reader
  * IO (1.0.1): Python convenience input/output functions
  * ISOLDE (1.7.dev0): ISOLDE: Interactive Structure Optimisation by Local Direct Exploration
  * ItemsInspection (1.0.1): Inspection of attributes of a set of items
  * IUPAC (1.0): IUPAC fetch
  * Label (1.1.8): Add text labels to graphics
  * ListInfo (1.2.1): Report attributes for selected atomic data
  * Log (1.1.5): Log support
  * LookingGlass (1.1): LookingGlass holographic display
  * Maestro (1.9.1): Maestro reader
  * Map (1.1.4): Density maps
  * MapData (2.0): Volume data file formats
  * MapEraser (1.0.1): Map eraser
  * MapFilter (2.0.1): Operations on maps
  * MapFit (2.0): Fit molecules into maps
  * MapSeries (2.1.1): Volume series
  * Markers (1.0.1): Place markers on density maps
  * Mask (1.0.2): Mask a volume to a surface
  * MatchMaker (2.1.2): Superimpose structures
  * MCopy (1.0): Copy atomic structure attributes to another structure
  * MDcrds (2.6): Molecular dynamics support
  * MedicalToolbar (1.0.2): Toolbar for medical image analysis
  * Meeting (1.0.1): Shared interactive VR sessions.
  * MLP (1.1.1): Molecular lipophilicity calculation
  * mmCIF (2.12.1): mmCIF format read/write
  * MMTF (2.2): MMTF format read/write
  * Modeller (1.5.12): Interface to Modeller
  * ModelPanel (1.4): ChimeraX Model Panel
  * ModelSeries (1.0.1): Display sequences of models one by one
  * Mol2 (2.0.3): Mol2 reader/writer
  * Mole (1.0): Open JSON tunnel files from Mole
  * Morph (1.0.2): Morph atomic structures
  * MouseModes (1.2): Provide right button mouse mode tool
  * Movie (1.0): Commands to record movies
  * Neuron (1.0): Read SWC neuron trace files
  * Nifti (1.1): Read medical images in NIfTI format
  * NRRD (1.1): Read medical images in NRRD format
  * Nucleotides (2.0.3): Create nucleotide-specific displays
  * OpenCommand (1.10.2): Manages 'open' command extensibility
  * PDB (2.7.2): PDB format read/write
  * PDBBio (1.0.1): PDB biological assembly fetch
  * PDBLibrary (1.0.2): C++ PDB support
  * PDBMatrices (1.0): Crystal and biological unit matrices
  * PickBlobs (1.0.1): Measure and color blobs
  * Positions (1.0): Read and write model position matrices
  * PresetMgr (1.1): Preset management
  * PubChem (2.1): PubChem fetch
  * ReadPbonds (1.0.1): Read in pseudobonds from a file
  * Registration (1.1.2): Register ChimeraX
  * RemoteControl (1.0): Control ChimeraX from other apps
  * RenderByAttr (1.1): Depict attribute values on structures
  * RenumberResidues (1.1): Renumber residues
  * ResidueFit (1.0.1): Display fit of residues to density map
  * RestServer (1.2): Starts REST server to execute commands from network requests
  * RNALayout (1.0): Make RNA models
  * RotamerLibMgr (4.0): Manage rotamer libraries
  * RotamerLibsDunbrack (2.0): Dunbrack rotamer library
  * RotamerLibsDynameomics (2.0): Dynameomics rotamer library
  * RotamerLibsRichardson (2.0): Richardson rotamer libraries
  * SaveCommand (1.5.1): Manages 'save' command extensibility
  * SchemeMgr (1.0): HTTP scheme management
  * SDF (2.0.1): SDF file reader
  * Segger (1.0): Segment map
  * Segment (1.0.1): Watershed segment calculation
  * SelInspector (1.0): Inspect contents of selection
  * SEQCROW (1.7.3): Structure Editing and Quantum Chemical Representation and Organization for Workflows
  * SeqView (2.9.1): Sequence viewer
  * Shape (1.0.1): Make models for geometric shapes
  * Shell (1.0.1): Interactive Python shell
  * Shortcuts (1.1.1): Button and keyboard shortcuts
  * ShowSequences (1.0.1): Choose/show structure sequences
  * SideView (1.0.1): Side view of scene
  * Smiles (2.1.2): SMILES fetch
  * SmoothLines (1.0): Smooth network of lines
  * SpaceNavigator (1.0): Space Navigator device support
  * StdCommands (1.12.2): Standard commands
  * STL (1.0.1): STL file read/write
  * Storm (1.0): STORM file reader
  * StructMeasure (1.1.2): Structure measurement user interface
  * Struts (1.0.1): struts for 3D printing
  * Surface (1.0.1): Surface calculations
  * SwapAA (2.0.1): Swap amino acid
  * SwapRes (2.2.2): Swap residue side chains
  * TapeMeasure (1.0): Tape measure mouse mode
  * TaskManager (1.0): Manage background tasks in ChimeraX
  * Test (1.0): simple regression test
  * Toolbar (1.1.2): Toolbar
  * ToolshedUtils (1.2.4): Toolshed bundle utilities
  * Topography (1.0): Show a topographic surface for a 2D image
  * ToQuest (1.0): Copy scenes to VR Quest headset
  * Tug (1.0.1): Tug on atoms with molecular dynamics
  * UI (1.31.5): ChimeraX user interface
  * uniprot (2.3): UniProt database support
  * UnitCell (1.0.1): Show crystal unit cell
  * ViewDockX (1.3): Analyze ligand-receptor docking results
  * VIPERdb (1.0): Read Virus Particle Explorer .vdb files
  * Vive (1.1): Virtual reality headset support
  * VolumeMenu (1.0.1): Volume menu
  * VTK (1.0): Legacy VTK file reader and writer
  * WavefrontOBJ (1.0): Wavefront OBJ file read/write
  * WebCam (1.0.2): Combine camera video with graphics
  * WebServices (1.1.2): Web service and HTTP request support
  * XMAS (1.1.2): Analyze and visualize crosslinking mass spectrometry data in a structural context
  * Zone (1.0.1): Mouse mode to show atom and map zones

  

> ui tool show Shell

0.00s - Debugger warning: It seems that frozen modules are being used, which
may  
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off  
0.00s - to python to disable frozen modules.  
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to
disable this validation.  




OpenGL version: 3.3.0 NVIDIA 529.08
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: HP
Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 34,007,068,672
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-GB

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.0
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.7.22
    cftime: 1.6.2
    charset-normalizer: 3.2.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.47.2
    ChimeraX-AtomicLibrary: 10.0.8
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.3
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.4
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202309180647
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.7.dev0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.12
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.2
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    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: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.9.1
    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: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.2
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.31.5
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.2
    ChimeraX-XMAS: 1.1.2
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.4
    comtypes: 1.1.14
    contourpy: 1.1.1
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    et-xmlfile: 1.1.0
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.42.1
    funcparserlib: 1.0.1
    glfw: 2.6.2
    grako: 3.16.5
    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.38
    imagecodecs: 2023.7.10
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.3.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.6
    numpy: 1.25.1
    openpyxl: 3.1.2
    openvr: 1.23.701
    packaging: 23.1
    pandas: 2.0.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 10.0.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.10.0
    prompt-toolkit: 3.0.39
    psutil: 5.9.5
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    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: 2023.3.post1
    pywin32: 305
    pyzmq: 25.1.1
    qtconsole: 5.4.3
    QtPy: 2.4.0
    QtRangeSlider: 0.1.5
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    seaborn: 0.12.2
    Send2Trash: 1.8.2
    SEQCROW: 1.7.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.2
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.3
    traitlets: 5.9.0
    typing-extensions: 4.8.0
    tzdata: 2023.3
    urllib3: 2.0.4
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1

[Tristan Croll]

The
directory %localappdata%\UCSF\ChimeraX\1.7\site-packages\ChimeraX_Clipper-0.22.0.dist-info
wasn't deleted. I deleted that manually then did "toolshed reload" and it
now lists the correct version.

On Thu, Sep 28, 2023 at 3:32 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>

[Tristan Croll]

I see the same problem in Linux when rebuilding both Clipper and
ChimeraX-QScore (which uses pyproject.toml rather than bundle_info.xml). As
for Windows, the old dist-info directory is not being deleted after
incrementing the version number. It *is* well-behaved on my Mac, though
(but I'm guessing that might be due to my hack of
`chimerax_python_executable()` in #9861.

On Thu, Sep 28, 2023 at 3:39 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>
>

[Tom Goddard]

Increased priority, since we need to keep Tristan's work humming.

[Tristan Croll]

Turns out this will have more than just cosmetic consequences once I update the dependency version requirements (which I need to do because ChimeraX_AtomicLibrary has been bumped to version 11.0). To avoid accidentally getting Clipper's version numbering out of sync, I currently specify the version number only in the bundle_info.xml and query it on Clipper initialization:

​https://github.com/tristanic/chimerax-clipper/blob/10abef42a26cea8d60396e58f4cb44e8bb147694/src/__init__.py#L28C1-L28C1

def _version():
    import pkg_resources
    return pkg_resources.require('ChimeraX-Clipper')[0].version

__version__ = _version()

When there are multiple ...dist-info directories still present, this seems to choose the oldest, and throws an exception when that older version has unsatisfied dependencies. From the user's perspective, Clipper will appear to install correctly, but will throw an ugly traceback when they attempt to actually use it.

[Greg Couch]

I think this is a duplicate of #9877. Since uninstalls were not working, the metadata for the previous version was still present on the filesystem. So when the scan for ChimeraX metadata was done, it found the wrong version.

Regardless, an alternative technique would be:

def _version():
    try:
        from chimerax.clipper import version
        return version
    except ImportError:
        raise RuntimeError("clipper is not installed")

__version__ = _version()