Bundles not installing

[Eric Pettersen]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.7.dev202306222329 (2023-06-22 23:29:13 UTC)
Description
Bundles continue to fail to install

Log:
UCSF ChimeraX version: 1.7.dev202306222329 (2023-06-22)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle ChimeraX_ArtiaX-0.3-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip is available: 23.0 -> 23.1.2  
[notice] To update, run:
/Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing /Users/pett/Downloads/ChimeraX_ArtiaX-0.3-py3-none-any.whl  
Requirement already satisfied: ChimeraX-Atomic>=1.1 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-ArtiaX==0.3) (1.46)  
Requirement already satisfied: ChimeraX-BILD~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-ArtiaX==0.3) (1.0)  
Requirement already satisfied: ChimeraX-Core>=1.3 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-ArtiaX==0.3) (1.7.dev202306222329)  
Requirement already satisfied: ChimeraX-Geometry>=1.1 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-ArtiaX==0.3) (1.3)  
Requirement already satisfied: ChimeraX-Graphics~=1.1 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-ArtiaX==0.3) (1.1.1)  
Requirement already satisfied: ChimeraX-IMOD~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-ArtiaX==0.3) (1.0)  
Requirement already satisfied: ChimeraX-Log>=1.1.4 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-ArtiaX==0.3) (1.1.5)  
Requirement already satisfied: ChimeraX-Map~=1.1 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-ArtiaX==0.3) (1.1.4)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-ArtiaX==0.3) (2.0)  
Requirement already satisfied: ChimeraX-Markers~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-ArtiaX==0.3) (1.0.1)  
Requirement already satisfied: ChimeraX-ModelPanel>=1.2.1 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-ArtiaX==0.3) (1.3.7)  
Requirement already satisfied: ChimeraX-MouseModes~=1.1 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-ArtiaX==0.3) (1.2)  
Requirement already satisfied: ChimeraX-OpenCommand>=1.7 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-ArtiaX==0.3) (1.10.2)  
Requirement already satisfied: ChimeraX-SaveCommand>=1.5 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-ArtiaX==0.3) (1.5.1)  
Requirement already satisfied: ChimeraX-UI>=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-ArtiaX==0.3) (1.30)  
Collecting superqt  
Using cached superqt-0.4.1-py3-none-any.whl (63 kB)  
Collecting starfile  
Using cached starfile-0.4.12-py3-none-any.whl (28 kB)  
Collecting geomdl  
Using cached geomdl-5.3.1-py2.py3-none-any.whl (147 kB)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=10.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic>=1.1->ChimeraX-ArtiaX==0.3) (10.0.7)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic>=1.1->ChimeraX-ArtiaX==0.3) (2.0.1)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic>=1.1->ChimeraX-ArtiaX==0.3) (2.12)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic>=1.1->ChimeraX-ArtiaX==0.3) (2.0.3)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic>=1.1->ChimeraX-ArtiaX==0.3) (2.7.2)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic>=1.1->ChimeraX-ArtiaX==0.3) (1.0.2)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Atomic>=1.1->ChimeraX-ArtiaX==0.3) (1.1)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-BILD~=1.0->ChimeraX-ArtiaX==0.3) (1.0.1)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-BILD~=1.0->ChimeraX-ArtiaX==0.3) (1.2.3)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Map~=1.1->ChimeraX-ArtiaX==0.3) (2.0.1)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-Map~=1.1->ChimeraX-ArtiaX==0.3) (2.1.1)  
Requirement already satisfied: ChimeraX-StdCommands>=1.3.1,~=1.3 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-ModelPanel>=1.2.1->ChimeraX-ArtiaX==0.3) (1.12.1)  
Requirement already satisfied: ChimeraX-IO~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-OpenCommand>=1.7->ChimeraX-ArtiaX==0.3) (1.0.1)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-UI>=1.0->ChimeraX-ArtiaX==0.3) (1.0)  
Collecting pandas  
Using cached pandas-2.0.2-cp311-cp311-macosx_10_9_x86_64.whl (11.6 MB)  
Requirement already satisfied: packaging in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from superqt->ChimeraX-ArtiaX==0.3) (21.3)  
Requirement already satisfied: pygments>=2.4.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from superqt->ChimeraX-ArtiaX==0.3) (2.14.0)  
Requirement already satisfied: qtpy>=1.1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from superqt->ChimeraX-ArtiaX==0.3) (2.3.1)  
Requirement already satisfied: typing-extensions in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from superqt->ChimeraX-ArtiaX==0.3) (4.6.3)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-MapSeries~=2.0->ChimeraX-Map~=1.1->ChimeraX-
ArtiaX==0.3) (2.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI>=1.0->ChimeraX-
ArtiaX==0.3) (1.0.1)  
Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-StdCommands>=1.3.1,~=1.3->ChimeraX-
ModelPanel>=1.2.1->ChimeraX-ArtiaX==0.3) (1.4)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ChimeraX-StdCommands>=1.3.1,~=1.3->ChimeraX-
ModelPanel>=1.2.1->ChimeraX-ArtiaX==0.3) (2.0)  
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from packaging->superqt->ChimeraX-ArtiaX==0.3) (3.1.0)  
Requirement already satisfied: python-dateutil>=2.8.2 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from pandas->starfile->ChimeraX-ArtiaX==0.3) (2.8.2)  
Requirement already satisfied: pytz>=2020.1 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from pandas->starfile->ChimeraX-ArtiaX==0.3) (2023.3)  
Requirement already satisfied: tzdata>=2022.1 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from pandas->starfile->ChimeraX-ArtiaX==0.3) (2023.3)  
Requirement already satisfied: numpy>=1.21.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from pandas->starfile->ChimeraX-ArtiaX==0.3) (1.23.5)  
Requirement already satisfied: six>=1.5 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from python-dateutil>=2.8.2->pandas->starfile->ChimeraX-ArtiaX==0.3)
(1.16.0)  
Installing collected packages: geomdl, pandas, superqt, starfile, ChimeraX-
ArtiaX  
Successfully installed ChimeraX-ArtiaX-0.3 geomdl-5.3.1 pandas-2.0.2
starfile-0.4.12 superqt-0.4.1  
\---  

Successfully installed ChimeraX-ArtiaX-0.3 geomdl-5.3.1 pandas-2.0.2
starfile-0.4.12 superqt-0.4.1  
No change in list of installed bundles  




OpenGL version: 4.1 INTEL-18.8.6
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
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
      System Firmware Version: 481.0.0.0.0
      OS Loader Version: 540.120.3~22
      SMC Version (system): 2.32f21

Software:

    System Software Overview:

      System Version: macOS 12.6.6 (21G646)
      Kernel Version: Darwin 21.6.0
      Time since boot: 1:29

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 Family: Supported, Metal GPUFamily macOS 1
      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: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    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: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.46
    ChimeraX-AtomicLibrary: 10.0.7
    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: 2.10.3
    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: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202306222329
    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: 1.2.1
    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-IUPAC: 1.0
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.2
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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
    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
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    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: 1.1.1
    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: 3.0
    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: 2.8.3
    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: 1.12.1
    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: 2.2.1
    ChimeraX-TapeMeasure: 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: 1.30
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.1
    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: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.1.0
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.40.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2023.3.16
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.3.1
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.8.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.6
    PyOpenGL-accelerate: 3.1.6
    pyparsing: 3.1.0
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.1.0
    qtconsole: 5.4.3
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.8.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.2
    traitlets: 5.9.0
    typing-extensions: 4.6.3
    tzdata: 2023.3
    urllib3: 2.0.3
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7

[Eric Pettersen]

Related to #9192

Now the bundle doesn't even show up in ~/Library/Python/3.11/lib/python/site-packages/

[Zach Pearson]

I forgot to write in the ticket but as I said yesterday this worked on my Mac.

~/Library/Application Support/ChimeraX/1.7/site-packages should point to ~/Library/Application Support/ChimeraX/1.7/lib/python/site-packages and the bundle should be _there_, never in the user directory the system Python sets up for users. So perhaps this ticket is a manifestation of the one you opened about the toolbar not updating to reflect new bundles.

[Eric Pettersen]

At home today, rebuilding from scratch did not fix the problem where installing NIHPresets failed with the "No change in list of installed bundles" thing. The problem was that ~/Library/Application Support/ChimeraX/1.7/site-packages already existed as an actual directory (not a link). Nuking ~/Library/Application Support/ChimeraX/1.7 entirely fixed that problem.

[Eric Pettersen]

However, then installing ArtiaX does still nuke the Tools menu.

[Zach Pearson]

Should be working tomorrow, closing because the other ticket was opened.