numpy.bool defunct

[harinivachu@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.7.dev202307180036 (2023-07-18 00:36:28 UTC)
Description
(Describe the actions that caused this problem to occur here) File "C:\Program Files\ChimeraX1\bin\Lib\site-packages\chimerax\atomic\structure.py", line 1880, in _update_graphics_if_needed     s[i].update_graphics_if_needed()   File "C:\Program Files\ChimeraX1\bin\Lib\site-packages\chimerax\atomic\structure.py", line 358, in update_graphics_if_needed     self._update_graphics(gc)   File "C:\Program Files\ChimeraX1\bin\Lib\site-packages\chimerax\atomic\structure.py", line 377, in _update_graphics     self._update_ribbon_graphics(changes)   File "C:\Program Files\ChimeraX1\bin\Lib\site-packages\chimerax\atomic\structure.py", line 669, in _update_ribbon_graphics     rd.update_ribbon_highlight()   File "C:\Program Files\ChimeraX1\bin\Lib\site-packages\chimerax\atomic\ribbon.py", line 635, in update_ribbon_highlight     from numpy import bool ImportError: cannot import name 'bool' from 'numpy' (C:\Program Files\ChimeraX1\bin\Lib\site-packages\numpy\__init__.py) Error processing trigger "graphics update": ImportError: cannot import name 'bool' from 'numpy' (C:\Program Files\ChimeraX1\bin\Lib\site-packages\numpy\__init__.py) File "C:\Program Files\ChimeraX1\bin\Lib\site-packages\chimerax\atomic\ribbon.py", line 635, in update_ribbon_highlight from numpy import bool See log for complete Python traceback.

Log:
UCSF ChimeraX version: 1.7.dev202307180036 (2023-07-18)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold predict
> MDQVMQFVEPSRQFVKDSIRLVKRCTKPDRKEFQKIAMATAIGFAIMGFIGFFVKLIHIPINNIIVGG,MPAPRAPRALAAAAPASGKAKLTHPGKAILAGGLAGGIEICITFPTEYVKTQLQLDERSHPPRYRGIGDCVRQTVRSHGVLGLYRGLSSLLYGSIPKAAVRFGMFEFLSNHMRDAQGRLDSTRGLLCGLGAGVAEAVVVVCPMETIKVKFIHDQTSPNPKYRGFFHGVREIVREQGLKGTYQGLTATVLKQGSNQAIRFFVMTSLRNWYRGDNPNKPMNPLITGVFGAIAGAASVFGNTPLDVIKTRMQGLEAHKYRNTWDCGLQILKKEGLKAFYKGTVPRLGRVCLDVAIVFVIYDEVVKLLNKVWKTD

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  
Compositor returned null texture  
[Repeated 1 time(s)]

> alphafold predict
> MDQVMQFVEPSRQFVKDSIRLVKRCTKPDRKEFQKIAMATAIGFAIMGFIGFFVKLIHIPINNIIVGG,MPAPRAPRALAAAAPASGKAKLTHPGKAILAGGLAGGIEICITFPTEYVKTQLQLDERSHPPRYRGIGDCVRQTVRSHGVLGLYRGLSSLLYGSIPKAAVRFGMFEFLSNHMRDAQGRLDSTRGLLCGLGAGVAEAVVVVCPMETIKVKFIHDQTSPNPKYRGFFHGVREIVREQGLKGTYQGLTATVLKQGSNQAIRFFVMTSLRNWYRGDNPNKPMNPLITGVFGAIAGAASVFGNTPLDVIKTRMQGLEAHKYRNTWDCGLQILKKEGLKAFYKGTVPRLGRVCLDVAIVFVIYDEVVKLLNKVWKTD

Running AlphaFold prediction  
Compositor returned null texture  
Running AlphaFold prediction  
Compositor returned null texture  
Running AlphaFold prediction  

queryDarkBorder: Unable to retrieve dark window border setting.  

[Repeated 1 time(s)]AlphaFold prediction finished  
Results in C:\Users\Harini/Downloads/ChimeraX/AlphaFold/prediction_9  

> open
> C:\Users\Harini/Downloads/ChimeraX/AlphaFold/prediction_9\best_model.pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> color bychain

> interfaces select /A & ::polymer_type>0 contacting /B & ::polymer_type>0
> areaCutoff 0

26 contacting residues  
C:\Program Files\ChimeraX1\bin\Lib\site-
packages\chimerax\atomic\ribbon.py:635: FutureWarning: In the future `np.bool`
will be defined as the corresponding NumPy scalar.  
from numpy import bool  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1880, in
_update_graphics_if_needed  
s[i].update_graphics_if_needed()  
File "C:\Program Files\ChimeraX1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 358, in update_graphics_if_needed  
self._update_graphics(gc)  
File "C:\Program Files\ChimeraX1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 377, in _update_graphics  
self._update_ribbon_graphics(changes)  
File "C:\Program Files\ChimeraX1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 669, in _update_ribbon_graphics  
rd.update_ribbon_highlight()  
File "C:\Program Files\ChimeraX1\bin\Lib\site-
packages\chimerax\atomic\ribbon.py", line 635, in update_ribbon_highlight  
from numpy import bool  
ImportError: cannot import name 'bool' from 'numpy' (C:\Program
Files\ChimeraX1\bin\Lib\site-packages\numpy\\__init__.py)  
  
Error processing trigger "graphics update":  
ImportError: cannot import name 'bool' from 'numpy' (C:\Program
Files\ChimeraX1\bin\Lib\site-packages\numpy\\__init__.py)  
  
File "C:\Program Files\ChimeraX1\bin\Lib\site-
packages\chimerax\atomic\ribbon.py", line 635, in update_ribbon_highlight  
from numpy import bool  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 528.79
OpenGL renderer: NVIDIA GeForce RTX 3060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_IN.cp1252
Qt version: PyQt6 6.5.1, Qt 6.5.1
Qt runtime version: 6.5.1
Qt platform: windows

Manufacturer: Dell Inc.
Model: Dell G15 5520
OS: Microsoft Windows 11 Home Single Language (Build 22621)
Memory: 16,849,293,312
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700H
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    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: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.2.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.46.1
    ChimeraX-AtomicLibrary: 10.0.8
    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: 2.10.4
    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.dev202307180036
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-Cytoscape: 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: 1.4
    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: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.2
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBImages: 1.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-PICKLUSTER: 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: 2.9
    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-StarMap: 1.2.15
    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: 1.30.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.2
    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
    comtypes: 1.1.14
    contourpy: 1.1.0
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
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    executing: 1.2.0
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    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.38
    imagecodecs: 2023.7.10
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
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    jedi: 0.18.2
    Jinja2: 3.1.2
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    jupyter-core: 5.3.1
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    numpy: 1.25.1
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    pure-eval: 0.2.2
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    PyQt6-WebEngine-commercial: 6.5.0
    PyQt6-WebEngine-Qt6: 6.5.1
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    python-dateutil: 2.8.2
    pytz: 2023.3
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    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
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    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: 1.5.1
    tifffile: 2023.7.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.2
    traitlets: 5.9.0
    typing-extensions: 4.7.1
    tzdata: 2023.3
    urllib3: 2.0.3
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.8
    WMI: 1.5.1

[pett]

Hi,

Thanks for reporting this problem. It was actually fixed in the build after the one you have, so if you get a current daily build then you won't run into it anymore.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab