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Opened 4 hours ago
#20790 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.5.2-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
NameError: name 'compare_model' is not defined NameError: name 'compare_model' is not defined File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/check_waters/tool.py", line 124, in _finalize_init self.compared_waters = compare_waters(compare_model, check_model) ^^^^^^^^^^^^^
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/maxbo/Desktop/wt/forEVL/Coot/260721_RSR01_SC01_ISOLDE_real_space_refined_005-coot-0.pdb
Summary of feedback from opening
/Users/maxbo/Desktop/wt/forEVL/Coot/260721_RSR01_SC01_ISOLDE_real_space_refined_005-coot-0.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO a 2 ILE a 6 1 5
Start residue of secondary structure not found: HELIX 2 2 PRO a 9 LYS a 29 1
21
Start residue of secondary structure not found: HELIX 3 3 ALA a 54 VAL a 61 1
8
Start residue of secondary structure not found: HELIX 4 4 THR a 62 ILE a 65 1
4
Start residue of secondary structure not found: HELIX 5 5 GLU a 66 ASN a 68 1
3
234 messages similar to the above omitted
Chain information for
260721_RSR01_SC01_ISOLDE_real_space_refined_005-coot-0.pdb #1
---
Chain | Description
Aa | No description available
Ab | No description available
Ac | No description available
Computing secondary structure
> open
> /Users/maxbo/Desktop/wt/forEVL/CryoSPARC/J315/cryosparc_P2_J315_localfilter.mrc
Opened cryosparc_P2_J315_localfilter.mrc as #2, grid size 384,384,384, pixel
0.837, shown at level 0.0142, step 2, values float32
> lighting soft
> set bgColor white
> volume #2 step 1
> volume #2 level 0.03667
> volume #2 level 0.04546
> ui tool show "Water Placement"
Populating font family aliases took 89 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
> phenix douse #2 nearModel #1 keepInputWater false verbose true resolution
> 2.4
Command:
/Users/maxbo/Applications/phenix-2.0-5936/phenix_bin/phenix.douse map.mrc model.pdb resolution=2.4
stdout:
Starting phenix.douse
on Fri Jul 24 14:09:38 2026 by maxbo
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found real_map, map.mrc
Found model, model.pdb
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
resolution=2.4
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
model {
file = "model.pdb"
}
default_model = "model.pdb"
real_map_files = "map.mrc"
default_real_map = "map.mrc"
}
resolution = 2.4
Starting job
===============================================================================
Removing water in input model
number of water in input model to remove: 0
time (s): 0.280 (total time: 0.280)
Process per chain (mode=per_chain)
Working on chain Aa:
Normalize and re-sample input map
input map (min,max,mean): -0.182 0.362 0.008
re-scaled map (min,max,mean): 0.000 13.703 0.363
input map dimenstions: 125 88 172
input map grid steps (A): 0.837 0.837 0.837
input map (min,max,mean): 0.000 13.703 0.363
time (s): 0.390 (total time: 0.670)
Get cutoff
mean density at atom centers: 2.574
density cutoff for peak search: 0.644
time (s): 0.330 (total time: 1.000)
Mask out molecule/solvent regions
time (s): 0.340 (total time: 1.340)
Find peaks
total peaks found: 5530
B factors set to : 39.469
time (s): 0.400 (total time: 1.740)
Filter peaks by distance
distance (A), min: 2.00 max: 3.20
start: 5530
final: 733
time (s): 0.440 (total time: 2.180)
Filter peaks by sphericity
peaks left: 671
time (s): 1.920 (total time: 4.100)
Filter peaks by distance
distance (A), min: 2.00 max: 3.20
start: 671
final: 650
time (s): 0.340 (total time: 4.440)
Refine ADP
B (min/max/mean) start: 39.469 39.469 39.469
B (min/max/mean) final: 0.000 24.806 16.162
time (s): 3.120 (total time: 7.560)
Filter peaks by CC_mask
start: 650
final: 496
time (s): 0.800 (total time: 8.360)
Filter peaks by distance
distance (A), min: 2.00 max: 3.20
start: 496
final: 468
time (s): 0.340 (total time: 8.700)
Filter peaks by CC_mask and number
start: 468
final: 461
time (s): 0.770 (total time: 9.470)
Filter peaks by distance
distance (A), min: 2.00 max: 3.20
start: 461
final: 460
time (s): 0.330 (total time: 9.800)
Add to model and reset internals
new water chain ID: 'Aa'
B (min/max/mean): 0.000 24.806 13.192
time (s): 0.490 (total time: 10.290)
Working on chain Ab:
Normalize and re-sample input map
input map (min,max,mean): -0.182 0.362 0.009
re-scaled map (min,max,mean): 0.000 13.441 0.370
input map dimenstions: 110 112 162
input map grid steps (A): 0.837 0.837 0.837
input map (min,max,mean): 0.000 13.441 0.370
time (s): 0.350 (total time: 0.630)
Get cutoff
mean density at atom centers: 2.263
density cutoff for peak search: 0.566
time (s): 0.340 (total time: 0.970)
Mask out molecule/solvent regions
time (s): 0.350 (total time: 1.320)
Find peaks
total peaks found: 5322
B factors set to : 44.588
time (s): 0.390 (total time: 1.710)
Filter peaks by distance
distance (A), min: 2.00 max: 3.20
start: 5322
final: 687
time (s): 0.440 (total time: 2.150)
Filter peaks by sphericity
peaks left: 627
time (s): 1.820 (total time: 3.970)
Filter peaks by distance
distance (A), min: 2.00 max: 3.20
start: 627
final: 610
time (s): 0.340 (total time: 4.310)
Refine ADP
B (min/max/mean) start: 44.588 44.588 44.588
B (min/max/mean) final: 0.000 21.159 14.096
time (s): 4.800 (total time: 9.110)
Filter peaks by CC_mask
start: 610
final: 434
time (s): 0.780 (total time: 9.890)
Filter peaks by distance
distance (A), min: 2.00 max: 3.20
start: 434
final: 392
time (s): 0.340 (total time: 10.230)
Filter peaks by CC_mask and number
start: 392
final: 383
time (s): 0.740 (total time: 10.970)
Filter peaks by distance
distance (A), min: 2.00 max: 3.20
start: 383
final: 380
time (s): 0.330 (total time: 11.300)
Add to model and reset internals
new water chain ID: 'Ab'
B (min/max/mean): 0.000 21.159 11.103
time (s): 0.460 (total time: 11.760)
Working on chain Ac:
Normalize and re-sample input map
input map (min,max,mean): -0.182 0.343 0.008
re-scaled map (min,max,mean): 0.000 13.918 0.350
input map dimenstions: 81 125 170
input map grid steps (A): 0.837 0.837 0.837
input map (min,max,mean): 0.000 13.918 0.350
time (s): 0.340 (total time: 0.620)
Get cutoff
mean density at atom centers: 2.514
density cutoff for peak search: 0.629
time (s): 0.340 (total time: 0.960)
Mask out molecule/solvent regions
time (s): 0.350 (total time: 1.310)
Find peaks
total peaks found: 5527
B factors set to : 47.112
time (s): 0.380 (total time: 1.690)
Filter peaks by distance
distance (A), min: 2.00 max: 3.20
start: 5527
final: 739
time (s): 0.450 (total time: 2.140)
Filter peaks by sphericity
peaks left: 676
time (s): 1.940 (total time: 4.080)
Filter peaks by distance
distance (A), min: 2.00 max: 3.20
start: 676
final: 657
time (s): 0.350 (total time: 4.430)
Refine ADP
B (min/max/mean) start: 47.112 47.112 47.112
B (min/max/mean) final: 0.000 25.002 17.007
time (s): 2.540 (total time: 6.970)
Filter peaks by CC_mask
start: 657
final: 458
time (s): 0.790 (total time: 7.760)
Filter peaks by distance
distance (A), min: 2.00 max: 3.20
start: 458
final: 414
time (s): 0.330 (total time: 8.090)
Filter peaks by CC_mask and number
start: 414
final: 409
time (s): 0.740 (total time: 8.830)
Filter peaks by distance
distance (A), min: 2.00 max: 3.20
start: 409
final: 407
time (s): 0.340 (total time: 9.170)
Add to model and reset internals
new water chain ID: 'Ac'
B (min/max/mean): 0.000 25.002 12.854
time (s): 0.470 (total time: 9.640)
time (s): 47.280 (total time: 47.560)
Attribute water to chains
time (s): 11.910 (total time: 59.470)
Summary
Number of water added: 1118
time (s): 0.070 (total time: 59.540)
===============================================================================
Job complete
usr+sys time: 62.81 seconds
wall clock time: 62.91 seconds
Placed 1116 waters in map "cryosparc_P2_J315_localfilter.mrc" near model
"260721_RSR01_SC01_ISOLDE_real_space_refined_005-coot-0.pdb"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 873, in customEvent
func(*args, **kw)
File "/Users/maxbo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/phenix_ui/douse.py", line 194, in <lambda>
map_range=map_range, d_ref=d: _process_results(session, douse_model, shift,
near_model,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/maxbo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/phenix_ui/douse.py", line 219, in _process_results
DouseResultsViewer(session, "Water Placement Results", near_model, model,
compared_waters, map)
File "/Users/maxbo/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/phenix_ui/tool.py", line 275, in __init__
super().__init__(session, tool_name, douse_model, compare_info=(orig_model,
compared_waters),
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/check_waters/tool.py", line 105, in __init__
self._finalize_init(check_model, compare_info, model_labels, compare_map,
category_tips)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/check_waters/tool.py", line 124, in _finalize_init
self.compared_waters = compare_waters(compare_model, check_model)
^^^^^^^^^^^^^
NameError: name 'compare_model' is not defined
NameError: name 'compare_model' is not defined
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/check_waters/tool.py", line 124, in _finalize_init
self.compared_waters = compare_waters(compare_model, check_model)
^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: Z15W0045PD/A
Chip: Apple M2
Total Number of Cores: 8 (4 Performance and 4 Efficiency)
Memory: 16 GB
System Firmware Version: 18000.121.3
OS Loader Version: 18000.121.3
Software:
System Software Overview:
System Version: macOS 26.5.2 (25F84)
Kernel Version: Darwin 25.5.0
Time since boot: 8 days, 3 hours, 50 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.25.2
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.1
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: 1.10.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-LigandRecognizer: 0.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.6.4
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 2.5.2
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: 1.45.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
finufft: 2.5.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
MolecularDynamicsViewer: 1.6
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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