Startup errors from the 12/21 daily build

[pett]

The following bug report has been submitted:
Platform:        macOS-14.6.1-arm64-arm-64bit-Mach-O
ChimeraX Version: 1.10.dev202412210559 (2024-12-21 05:59:26 UTC)
Description
Startup errors from the 12/21 daily build

Log:
Startup Errors  
---  
errors | Bundle 'ChimeraX-Segmentations' custom initialization failed  
Bundle 'ChimeraX-Dicom' custom initialization failed  
warnings | Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/core/toolshed/info.py", line 376, in initialize  
api._api_caller.initialize(api, session, self)  
~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/core/toolshed/__init__.py", line 1411, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/segmentations/bundle.py", line 11, in initialize  
from .segmentation_tracker import register_model_trigger_handlers  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/segmentations/segmentation_tracker.py", line 28, in <module>  
from chimerax.dicom import Study  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/dicom/__init__.py", line 21, in <module>  
from chimerax.dicom.dicom_fetcher import fetchers  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/dicom/dicom_fetcher.py", line 2, in <module>  
from .databases import TCIADatabase  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/dicom/databases/__init__.py", line 1, in <module>  
from .tcia import TCIADatabase  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/dicom/databases/tcia.py", line 24, in <module>  
from tcia_utils import nbia  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/tcia_utils/__init__.py", line 1, in <module>  
from . import nbia  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/tcia_utils/nbia.py", line 12, in <module>  
import matplotlib.pyplot as plt  
File "/Users/pett/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/matplotlib/__init__.py", line 159, in <module>  
from . import _api, _version, cbook, _docstring, rcsetup  
File "/Users/pett/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/matplotlib/cbook.py", line 32, in <module>  
from matplotlib import _api, _c_internal_utils  
ImportError: cannot import name '_c_internal_utils' from partially initialized
module 'matplotlib' (most likely due to a circular import)
(/Users/pett/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/matplotlib/__init__.py)  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/core/toolshed/info.py", line 501, in get_module  
m = importlib.import_module(self.package_name)  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/importlib/__init__.py",
line 88, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1387, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1360, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 935, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 1026, in exec_module  
File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/dicom/__init__.py", line 21, in <module>  
from chimerax.dicom.dicom_fetcher import fetchers  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/dicom/dicom_fetcher.py", line 2, in <module>  
from .databases import TCIADatabase  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/dicom/databases/__init__.py", line 1, in <module>  
from .tcia import TCIADatabase  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/dicom/databases/tcia.py", line 24, in <module>  
from tcia_utils import nbia  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/tcia_utils/__init__.py", line 1, in <module>  
from . import nbia  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/tcia_utils/nbia.py", line 12, in <module>  
import matplotlib.pyplot as plt  
File "/Users/pett/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/matplotlib/__init__.py", line 159, in <module>  
from . import _api, _version, cbook, _docstring, rcsetup  
File "/Users/pett/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/matplotlib/cbook.py", line 32, in <module>  
from matplotlib import _api, _c_internal_utils  
ImportError: cannot import name '_c_internal_utils' from partially initialized
module 'matplotlib' (most likely due to a circular import)
(/Users/pett/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/matplotlib/__init__.py)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/core/toolshed/info.py", line 375, in initialize  
api = self._get_api(session.logger)  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/core/toolshed/info.py", line 520, in _get_api  
m = self.get_module()  
File
"/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/core/toolshed/info.py", line 503, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-Dicom's
module: cannot import name '_c_internal_utils' from partially initialized
module 'matplotlib' (most likely due to a circular import)
(/Users/pett/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/matplotlib/__init__.py)  
notes | available bundle cache has not been initialized yet  
/Applications/ChimeraX_Daily-12-21.app/Contents/Library/Frameworks/Python.framework/Versions/3.13/lib/python3.13/site-
packages/chimerax/map/volume.py:3894: SyntaxWarning: invalid escape sequence
'\\*'  
'''  
  
UCSF ChimeraX version: 1.10.dev202412210559 (2024-12-21)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.13.1
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: Mac15,5
      Model Number: Z19K0011DLL/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 2 hours, 17 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 4.5K (4480 x 2520)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.12.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.59
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202412210559
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.5.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.7
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-ProfileGrids: 1.0
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.15
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.42.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    coverage: 7.6.9
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.11
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.9.22
    imagesize: 1.4.1
    iniconfig: 2.0.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.3.0
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.7.2
    networkx: 3.3
    nibabel: 5.2.0
    numexpr: 2.10.2
    numpy: 2.1.3
    numpy: 2.2.0
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    plotly: 5.24.1
    pluggy: 1.5.0
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pyKVFinder: 0.7.1
    pynmrstar: 3.3.4
    pynrrd: 1.1.1
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    pytest: 8.3.4
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.1
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

[Zach Pearson]

OK, this ticket is a significant improvement actually because while the original circular import is there the rest of the errors, which had to do with OpenGL, are gone.

[Zach Pearson]

I notice that ChimeraX says you have two versions of matplotlib. One is in /Users/pett/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/ and is undoubtedly built for Python 3.11. The other is in the ChimeraX distribution. Delete the Python 3.11 packages in ~/Library/Application Support/ChimeraX/1.10

[pett]

Yep, that cleared the startup errors, though it's unfortunate that this will plague any users where installing bundles caused these packages to go into their user-specific installation area.

[Greg Couch]

All toolshed bundle installation is supposed to go into the user-specific installation area. And the bundles should be for a particular ChimeraX version.

Isn't the real problem that a user has installed a bundle and/or associated Python packages, and we changed the version of Python without changing the version of ChimeraX? This should only be an issue with daily builds early in the release cycle.