Attempt to install Clipper 1.9 into 1.9 release candidate

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.9rc202410310525 (2024-10-31 05:25:41 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-Clipper' custom initialization failed  
warning | Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 501, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX
1.9rc202410310525\bin\Lib\importlib\\__init__.py", line 126, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 940, in exec_module  
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed  
File "C:\Users\kaibo\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\clipper\\__init__.py", line 32, in <module>  
__version__ = _version()  
^^^^^^^^^^  
File "C:\Users\kaibo\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\clipper\\__init__.py", line 30, in _version  
return pkg_resources.require('ChimeraX-Clipper')[0].version  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 1069, in require  
needed = self.resolve(parse_requirements(requirements))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 896, in resolve  
dist = self._resolve_dist(  
^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 942, in _resolve_dist  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-Core 1.9rc202410310525
(c:\program files\chimerax 1.9rc202410310525\bin\lib\site-packages),
Requirement.parse('ChimeraX-Core~=1.9.0'), {'ChimeraX-Clipper'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 375, in initialize  
api = self._get_api(session.logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 520, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\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-
Clipper's module: (ChimeraX-Core 1.9rc202410310525 (c:\program files\chimerax
1.9rc202410310525\bin\lib\site-packages), Requirement.parse('ChimeraX-
Core~=1.9.0'), {'ChimeraX-Clipper'})  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202410310525 (2024-10-31)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open D:/TisAFP7_Xtal/XDS_1_01/phenix/Refine_13/TisAFP7_X-
> ray_XDS1_refine_13.pdb

Summary of feedback from opening
D:/TisAFP7_Xtal/XDS_1_01/phenix/Refine_13/TisAFP7_X-ray_XDS1_refine_13.pdb  
---  
warning | Duplicate atom serial number found: 12200  
notes | Combining 2 symmetry atoms into HOH /S:740 H2  
Combining 2 symmetry atoms into HOH /S:648 H2  
Combining 2 symmetry atoms into HOH /S:614 H1  
Combining 2 symmetry atoms into HOH /S:233 H2  
  
Chain information for TisAFP7_X-ray_XDS1_refine_13.pdb #1  
---  
Chain | Description  
A B | No description available  
  
4441 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> open D:/TisAFP7_Xtal/XDS_1_01/phenix/Refine_13/TisAFP7_X-
> ray_XDS1_refine_13.mtz

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 501, in get_module  
m = importlib.import_module(self.package_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX
1.9rc202410310525\bin\Lib\importlib\\__init__.py", line 126, in import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "<frozen importlib._bootstrap>", line 1204, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1176, in _find_and_load  
File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 940, in exec_module  
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed  
File "C:\Users\kaibo\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\clipper\\__init__.py", line 32, in <module>  
__version__ = _version()  
^^^^^^^^^^  
File "C:\Users\kaibo\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\clipper\\__init__.py", line 30, in _version  
return pkg_resources.require('ChimeraX-Clipper')[0].version  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 1069, in require  
needed = self.resolve(parse_requirements(requirements))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 896, in resolve  
dist = self._resolve_dist(  
^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\pkg_resources\\__init__.py", line 942, in _resolve_dist  
raise VersionConflict(dist, req).with_context(dependent_req)  
pkg_resources.ContextualVersionConflict: (ChimeraX-Core 1.9rc202410310525
(c:\program files\chimerax 1.9rc202410310525\bin\lib\site-packages),
Requirement.parse('ChimeraX-Core~=1.9.0'), {'ChimeraX-Clipper'})  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\chimerax\ui\graphics.py", line 54, in event  
if self.handle_drag_and_drop(event):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\chimerax\ui\graphics.py", line 124, in handle_drag_and_drop  
mw.dropEvent(event)  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\chimerax\ui\gui.py", line 731, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\chimerax\ui\gui.py", line 2117, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 93, in cmd_open  
provider_args = mgr.open_args(data_format)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\chimerax\open_command\manager.py", line 241, in open_args  
opener_info = self.opener_info(data_format)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\chimerax\open_command\manager.py", line 250, in opener_info  
return provider_info.bundle_info.run_provider(self.session,
provider_info.name, self)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 396, in run_provider  
api = self._get_api(session.logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 520, in _get_api  
m = self.get_module()  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\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-
Clipper's module: (ChimeraX-Core 1.9rc202410310525 (c:\program files\chimerax
1.9rc202410310525\bin\lib\site-packages), Requirement.parse('ChimeraX-
Core~=1.9.0'), {'ChimeraX-Clipper'})  
  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-
Clipper's module: (ChimeraX-Core 1.9rc202410310525 (c:\program files\chimerax
1.9rc202410310525\bin\lib\site-packages), Requirement.parse('ChimeraX-
Core~=1.9.0'), {'ChimeraX-Clipper'})  
  
File "C:\Program Files\ChimeraX 1.9rc202410310525\bin\Lib\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)))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 566.07
OpenGL renderer: NVIDIA GeForce RTX 3050 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: ja_JP.cp932
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: Vivobook_ASUSLaptop K6500ZC_K6500ZC
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 16,855,437,312
MaxProcessMemory: 137,438,953,344
CPU: 16 12th Gen Intel(R) Core(TM) i7-12650H
OSLanguage: ja-JP

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 2.4.1
    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: 2.7.1
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.17
    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: 1.58.7
    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: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13
    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: 1.9rc202410310525
    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: 1.2.5
    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: 1.2
    ChimeraX-Label: 1.1.11
    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: 2.7.1
    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: 1.5.17
    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-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: 1.6.1
    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
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    ChimeraX-SchemeMgr: 1.0
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    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.2.3
    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
    comtypes: 1.4.5
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    cxservices: 1.2.3
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    Cython: 3.0.10
    debugpy: 1.8.7
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.54.1
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
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    h5py: 3.12.1
    html2text: 2024.2.26
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    imagecodecs: 2024.6.1
    imagesize: 1.4.1
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    nptyping: 2.5.0
    numexpr: 2.10.1
    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
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    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
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    pyelftools: 0.31
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    pynmrstar: 3.3.4
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    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
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.1
    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
    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
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