pyKVFinder: missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.4-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
Could not find tool "StarMap"  

> set selectionWidth 4

Done loading forcefield  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  

> open /Users/pod4001/Library/CloudStorage/OneDrive-
> WeillCornellMedicine/OCA2/OCA2_Data_collection_and_screening/Janelia_K1_20250321_N160_NR_cit/J577/cryosparc_P145_J577_005_volume_map_sharp.mrc

Opened cryosparc_P145_J577_005_volume_map_sharp.mrc as #1, grid size
180,180,180, pixel 1.34, shown at level 0.0899, step 1, values float32  

> volume #1 level 0.1165

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 1 maps.  

> surface dust #1 size 13.4

> open /Users/pod4001/Library/CloudStorage/OneDrive-
> WeillCornellMedicine/OCA2/OCA2_Data_collection_and_screening/Janelia_K1_20250321_N160_NR_cit/J563/N160chA_to_J563.pdb

Chain information for N160chA_to_J563.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open /Users/pod4001/Library/CloudStorage/OneDrive-
> WeillCornellMedicine/OCA2/OCA2_Data_collection_and_screening/Janelia_K1_20250321_N160_NR_cit/J563/N160_to_J563.pdb

Chain information for N160_to_J563.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.  

> hide #!3 models

> fitmap #2 inMap #1

Fit molecule N160chA_to_J563.pdb (#2) to map
cryosparc_P145_J577_005_volume_map_sharp.mrc (#1) using 4438 atoms  
average map value = 0.3555, steps = 60  
shifted from previous position = 0.142  
rotated from previous position = 0.347 degrees  
atoms outside contour = 1255, contour level = 0.11654  
  
Position of N160chA_to_J563.pdb (#2) relative to
cryosparc_P145_J577_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998182 -0.00208909 -0.00565671 0.84940256  
0.00208644 0.99999771 -0.00047509 -0.08719335  
0.00565769 0.00046327 0.99998389 -0.76813350  
Axis 0.07757129 -0.93532608 0.34517796  
Axis point 129.01823653 0.00000000 151.35777731  
Rotation angle (degrees) 0.34654822  
Shift along axis -0.11769929  
  

> volume #1 level 0.1232

> show #!3 models

> hide #!2 models

> fitmap #3 inMap #1

Fit molecule N160_to_J563.pdb (#3) to map
cryosparc_P145_J577_005_volume_map_sharp.mrc (#1) using 6778 atoms  
average map value = 0.3174, steps = 72  
shifted from previous position = 0.283  
rotated from previous position = 0.983 degrees  
atoms outside contour = 2158, contour level = 0.1232  
  
Position of N160_to_J563.pdb (#3) relative to
cryosparc_P145_J577_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99989945 -0.00577642 -0.01295070 2.19740348  
0.00565109 0.99993705 -0.00969321 0.73663399  
0.01300588 0.00961905 0.99986915 -2.85053629  
Axis 0.56284701 -0.75649264 0.33304974  
Axis point 214.07157990 0.00000000 179.73927565  
Rotation angle (degrees) 0.98300729  
Shift along axis -0.26982658  
  

> save "/Users/pod4001/OneDrive - Weill Cornell
> Medicine/OCA2/OCA2_Data_collection_and_screening/Janelia_K1_20250321_N160_NR_cit/J577/N160_to_J577.pdb"
> models #3 relModel #1

> open /Users/pod4001/Library/CloudStorage/OneDrive-
> WeillCornellMedicine/OCA2/OCA2_Phenix/RealSpaceRefine_242/refined198_ECD_1_real_space_refined_242.pdb

Chain information for refined198_ECD_1_real_space_refined_242.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show Matchmaker

> matchmaker #!4 to #2

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker N160chA_to_J563.pdb, chain A (#2) with
refined198_ECD_1_real_space_refined_242.pdb, chain A (#4), sequence alignment
score = 2942.9  
RMSD between 571 pruned atom pairs is 0.000 angstroms; (across all 571 pairs:
0.000)  
  

> hide #!3 models

> fitmap #4 inMap #1

Fit molecule refined198_ECD_1_real_space_refined_242.pdb (#4) to map
cryosparc_P145_J577_005_volume_map_sharp.mrc (#1) using 8874 atoms  
average map value = 0.2591, steps = 64  
shifted from previous position = 0.116  
rotated from previous position = 0.232 degrees  
atoms outside contour = 3855, contour level = 0.1232  
  
Position of refined198_ECD_1_real_space_refined_242.pdb (#4) relative to
cryosparc_P145_J577_005_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.56648582 -0.82401315 -0.00980588 149.51247264  
0.82404569 0.56652214 -0.00117217 -27.83528821  
0.00652114 -0.00741648 0.99995123 16.78852190  
Axis -0.00378867 -0.00990626 0.99994375  
Axis point 101.09014429 128.33649928 0.00000000  
Rotation angle (degrees) 55.49489985  
Shift along axis 16.49686763  
  

> volume #1 level 0.1632

> save "/Users/pod4001/OneDrive - Weill Cornell
> Medicine/OCA2/OCA2_Data_collection_and_screening/Janelia_K1_20250321_N160_NR_cit/J577/N160_to_J577.pdb"
> models #4 relModel #1

> show #!3 models

> hide #!3 models

> save "/Users/pod4001/OneDrive - Weill Cornell
> Medicine/OCA2/OCA2_Data_collection_and_screening/Janelia_K1_20250321_N160_NR_cit/J577/N160_to_J5771.pdb"
> models #4 relModel #1

> hide #!1 models

> hbonds /C saltOnly

Missing "saltOnly" keyword's argument  

> ui tool show H-Bonds

> hbonds interModel false intraModel false twoColors true slopColor #5cf35b
> saltOnly true intraMol false intraRes false reveal true

0 hydrogen bonds found  
0 strict hydrogen bonds found  

> ui tool show H-Bonds

> select add #4

8874 atoms, 9059 bonds, 6 pseudobonds, 1152 residues, 2 models selected  

> ui tool show H-Bonds

> hbonds showDist true interModel false intraModel false twoColors true
> slopColor #5cf35b saltOnly true intraMol false intraRes false reveal true

0 hydrogen bonds found  
0 strict hydrogen bonds found  

> ui tool show H-Bonds

> hbonds showDist true twoColors true slopColor #5cf35b saltOnly true reveal
> true

44 hydrogen bonds found  
3 strict hydrogen bonds found  

> set bgColor white

> set bgColor #ffffff00

> select subtract #4

Nothing selected  

> ui tool show "Find Cavities"

pyKVFinder module not installed; fetching from PyPi repository...  

Errors may have occurred when running pip:  

pip standard error:  
\---  
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.  
chimerax-emalign 0.1.3 requires numpy~=1.16, but you have numpy 2.2.4 which is
incompatible.  
chimerax-bundlebuilder 1.4.0 requires numpy==1.26.4, but you have numpy 2.2.4
which is incompatible.  
nptyping 2.5.0 requires numpy<2.0.0,>=1.20.0; python_version >= "3.8", but you
have numpy 2.2.4 which is incompatible.  
\---  

pip standard output:  
\---  
\---  

> kvfinder #4

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 67, in find_cavities  
run(self.session, "kvfinder %s" % concise_model_spec(self.session, structures,  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 52, in cmd_kvfinder  
num_cavities, cavity_matrix = pyKVFinder.detect(struct_input, vertices,
grid_spacing,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/pod4001/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/pyKVFinder/grid.py", line 820, in detect  
from _pyKVFinder import _detect, _detect_ladj  
ImportError: dlopen(/Users/pod4001/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/pod4001/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/pod4001/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/pod4001/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))  
  
ImportError: dlopen(/Users/pod4001/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/pod4001/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/pod4001/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/pod4001/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))  
  
File "/Users/pod4001/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/pyKVFinder/grid.py", line 820, in detect  
from _pyKVFinder import _detect, _detect_ladj  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.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: Mac Studio
      Model Identifier: Mac13,1
      Model Number: Z14J0008GLL/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 11881.101.1
      OS Loader Version: 11881.101.1

Software:

    System Software Overview:

      System Version: macOS 15.4 (24E248)
      Kernel Version: Darwin 24.4.0
      Time since boot: 5 hours, 26 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 24
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Studio Display:
          Display Type: Retina LCD
          Resolution: 5120 x 2880 Retina
          Display Serial Number: YCXY5CX3D4
          Display Firmware Version: Version 17.0 (Build 21A329)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes


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
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    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: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    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: 1.0.1
    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-Clipper: 0.24.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    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: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMalign: 0.1.3
    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-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    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: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-PICKLUSTER: 2.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    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: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    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: 1.18.1
    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
    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: 1.41
    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
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    finufft: 2.3.1
    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: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    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: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    narwhals: 1.35.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 2.2.4
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    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
    platformdirs: 4.2.2
    plotly: 6.0.1
    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: 0.7.3
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    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
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    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
    toml: 0.10.2
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    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: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2

[Eric Pettersen]

Duplicate of #17304