Opened 3 years ago

Closed 3 years ago

#7806 closed defect (fixed)

Deprecation warnings

Reported by: goddard@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard, Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-12.6-arm64-arm-64bit
ChimeraX Version: 1.5.dev202210102058 (2022-10-10 20:58:47 UTC)
Description
Several deprecation warnings (numpy and inspect modules) appear when running ChimeraX with the --debug option.

Log:
Startup Messages  
---  
notes | Initializing core  
Initializing bundles  
/Users/goddard/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py:33: DeprecationWarning: `np.bool` is a
deprecated alias for the builtin `bool`. To silence this warning, use `bool`
by itself. Doing this will not modify any behavior and is safe. If you
specifically wanted the numpy scalar type, use `np.bool_` here.  
Deprecated in NumPy 1.20; for more details and guidance:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations  
from numpy import int8, uint8, int32, uint32, float64, float32, byte, bool as
npy_bool  
/Users/goddard/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/molarray.py:12: DeprecationWarning: `np.bool` is a
deprecated alias for the builtin `bool`. To silence this warning, use `bool`
by itself. Doing this will not modify any behavior and is safe. If you
specifically wanted the numpy scalar type, use `np.bool_` here.  
Deprecated in NumPy 1.20; for more details and guidance:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations  
from numpy import uint8, int32, uint32, float64, float32, uintp, byte, bool as
npy_bool, integer, empty, array  
Starting main interface  

Finished initialization  
UCSF ChimeraX version: 1.5.dev202210102058 (2022-10-10)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open batch.py

> open /Users/goddard/Downloads/ChimeraX/PDB/1grl.cif

1grl.cif title:  
The crystal structure of the bacterial chaperonin groel At 2.8 angstroms [more
info...]  

Chain information for 1grl.cif #1  
---  
Chain | Description | UniProt  
A B C D E F G | GROEL (HSP60 CLASS) | CH60_ECOLI  

1grl.cif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| software_defined_assembly  

Opened 1grl.cif with 29274 atoms  

> open /Users/goddard/Downloads/ChimeraX/EMDB/emd_1080.map

Summary of feedback from opening
/Users/goddard/Downloads/ChimeraX/EMDB/emd_1080.map  
---  
notes |
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py:152: DeprecationWarning:
inspect.getargspec() is deprecated since Python 3.0, use inspect.signature()
or inspect.getfullargspec()  
args = getargspec(open_func).args  
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_data/mrc/mrc_format.py:265: DeprecationWarning: The
binary mode of fromstring is deprecated, as it behaves surprisingly on unicode
inputs. Use frombuffer instead  
values = fromstring(string, etype)  
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py:393: DeprecationWarning: `np.bool` is a
deprecated alias for the builtin `bool`. To silence this warning, use `bool`
by itself. Doing this will not modify any behavior and is safe. If you
specifically wanted the numpy scalar type, use `np.bool_` here.  
Deprecated in NumPy 1.20; for more details and guidance:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations  
from numpy import ones, bool  

Opened emd_1080.map as #2, grid size 100,100,100, pixel 2.7, shown at level
1.68, step 1, values float32  
Opened emd_1080.map with grid size 100, 100, 100  

> turn y 90

> save image.png

executed batch.py  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

   Hardware Overview:

     Model Name: MacBook Pro
     Model Identifier: MacBookPro18,2
     Chip: Apple M1 Max
     Total Number of Cores: 10 (8 performance and 2 efficiency)
     Memory: 32 GB
     System Firmware Version: 7459.141.1
     OS Loader Version: 7459.141.1

Software:

   System Software Overview:

     System Version: macOS 12.6 (21G115)
     Kernel Version: Darwin 21.6.0
     Time since boot: 26 days 43 minutes

Graphics/Displays:

   Apple M1 Max:

     Chipset Model: Apple M1 Max
     Type: GPU
     Bus: Built-In
     Total Number of Cores: 32
     Vendor: Apple (0x106b)
     Metal Family: Supported, Metal GPUFamily Apple 7
     Displays:
       Color LCD:
         Display Type: Built-in Liquid Retina XDR Display
         Resolution: 3456 x 2234 Retina
         Main Display: Yes
         Mirror: Off
         Online: Yes
         Automatically Adjust Brightness: No
         Connection Type: Internal


Installed Packages:
   alabaster: 0.7.12
   appdirs: 1.4.4
   appnope: 0.1.3
   asttokens: 2.0.8
   Babel: 2.10.3
   backcall: 0.2.0
   blockdiag: 3.0.0
   build: 0.8.0
   certifi: 2021.10.8
   cftime: 1.6.2
   charset-normalizer: 2.1.1
   ChimeraX-AddCharge: 1.4
   ChimeraX-AddH: 2.2
   ChimeraX-AlignmentAlgorithms: 2.0
   ChimeraX-AlignmentHdrs: 3.2.1
   ChimeraX-AlignmentMatrices: 2.0
   ChimeraX-Alignments: 2.6
   ChimeraX-AlphaFold: 1.0
   ChimeraX-AltlocExplorer: 1.0.3
   ChimeraX-AmberInfo: 1.0
   ChimeraX-Arrays: 1.0
   ChimeraX-ArtiaX: 0.1
   ChimeraX-Atomic: 1.41.4
   ChimeraX-AtomicLibrary: 8.0.2
   ChimeraX-AtomSearch: 2.0.1
   ChimeraX-AxesPlanes: 2.3
   ChimeraX-BasicActions: 1.1.2
   ChimeraX-BILD: 1.0
   ChimeraX-BlastProtein: 2.1.2
   ChimeraX-BondRot: 2.0.1
   ChimeraX-BugReporter: 1.0.1
   ChimeraX-BuildStructure: 2.7.1
   ChimeraX-Bumps: 1.0
   ChimeraX-BundleBuilder: 1.2
   ChimeraX-ButtonPanel: 1.0.1
   ChimeraX-CageBuilder: 1.0.1
   ChimeraX-CellPack: 1.0
   ChimeraX-Centroids: 1.3.1
   ChimeraX-ChangeChains: 1.0.2
   ChimeraX-CheckWaters: 1.3
   ChimeraX-ChemGroup: 2.0
   ChimeraX-Clashes: 2.2.4
   ChimeraX-Clipper: 0.19.0.dev0
   ChimeraX-ColorActions: 1.0.3
   ChimeraX-ColorGlobe: 1.0
   ChimeraX-ColorKey: 1.5.2
   ChimeraX-CommandLine: 1.2.4
   ChimeraX-ConnectStructure: 2.0.1
   ChimeraX-Contacts: 1.0.1
   ChimeraX-Core: 1.5.dev202210102058
   ChimeraX-CoreFormats: 1.1
   ChimeraX-coulombic: 1.3.2
   ChimeraX-Crosslinks: 1.0
   ChimeraX-Crystal: 1.0
   ChimeraX-CrystalContacts: 1.0.1
   ChimeraX-DataFormats: 1.2.2
   ChimeraX-Dicom: 1.1
   ChimeraX-DistMonitor: 1.3
   ChimeraX-DockPrep: 1.0
   ChimeraX-Dssp: 2.0
   ChimeraX-EMDB-SFF: 1.0
   ChimeraX-ExperimentalCommands: 1.0
   ChimeraX-FileHistory: 1.0.1
   ChimeraX-FunctionKey: 1.0.1
   ChimeraX-Geometry: 1.2
   ChimeraX-gltf: 1.0
   ChimeraX-Graphics: 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-ISOLDE: 1.5.dev0
   ChimeraX-ItemsInspection: 1.0.1
   ChimeraX-Label: 1.1.7
   ChimeraX-ListInfo: 1.1.1
   ChimeraX-Log: 1.1.5
   ChimeraX-LookingGlass: 1.1
   ChimeraX-Maestro: 1.8.2
   ChimeraX-Map: 1.1.1
   ChimeraX-MapData: 2.0
   ChimeraX-MapEraser: 1.0.1
   ChimeraX-MapFilter: 2.0
   ChimeraX-MapFit: 2.0
   ChimeraX-MapSeries: 2.1.1
   ChimeraX-Markers: 1.0.1
   ChimeraX-Mask: 1.0.1
   ChimeraX-MatchMaker: 2.0.9
   ChimeraX-MDcrds: 2.6
   ChimeraX-MedicalToolbar: 1.0.2
   ChimeraX-Meeting: 1.0.1
   ChimeraX-MLP: 1.1
   ChimeraX-mmCIF: 2.8
   ChimeraX-MMTF: 2.2
   ChimeraX-Modeller: 1.5.6
   ChimeraX-ModelPanel: 1.3.6
   ChimeraX-ModelSeries: 1.0.1
   ChimeraX-Mol2: 2.0
   ChimeraX-Mole: 1.0
   ChimeraX-Morph: 1.0.1
   ChimeraX-MouseModes: 1.1.1
   ChimeraX-Movie: 1.0
   ChimeraX-Neuron: 1.0
   ChimeraX-Nucleotides: 2.0.3
   ChimeraX-OpenCommand: 1.9.1
   ChimeraX-PDB: 2.6.8
   ChimeraX-PDBBio: 1.0
   ChimeraX-PDBLibrary: 1.0.2
   ChimeraX-PDBMatrices: 1.0
   ChimeraX-PhenixUI: 1.0.4
   ChimeraX-PickBlobs: 1.0.1
   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-RenumberResidues: 1.1
   ChimeraX-ResidueFit: 1.0.1
   ChimeraX-RestServer: 1.1
   ChimeraX-RNALayout: 1.0
   ChimeraX-RotamerLibMgr: 2.0.1
   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
   ChimeraX-Segger: 1.0
   ChimeraX-Segment: 1.0
   ChimeraX-SelInspector: 1.0
   ChimeraX-SeqView: 2.7.2
   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
   ChimeraX-SmoothLines: 1.0
   ChimeraX-SpaceNavigator: 1.0
   ChimeraX-StdCommands: 1.10
   ChimeraX-STL: 1.0
   ChimeraX-Storm: 1.0
   ChimeraX-StructMeasure: 1.1
   ChimeraX-Struts: 1.0.1
   ChimeraX-Surface: 1.0
   ChimeraX-SwapAA: 2.0.1
   ChimeraX-SwapRes: 2.1.3
   ChimeraX-TapeMeasure: 1.0
   ChimeraX-Test: 1.0
   ChimeraX-Toolbar: 1.1.2
   ChimeraX-ToolshedUtils: 1.2.1
   ChimeraX-Tug: 1.0.1
   ChimeraX-UI: 1.24.2
   ChimeraX-uniprot: 2.2.1
   ChimeraX-UnitCell: 1.0.1
   ChimeraX-ViewDockX: 1.1.3
   ChimeraX-VIPERdb: 1.0
   ChimeraX-Vive: 1.1
   ChimeraX-VolumeMenu: 1.0.1
   ChimeraX-VTK: 1.0
   ChimeraX-WavefrontOBJ: 1.0
   ChimeraX-WebCam: 1.0.1
   ChimeraX-WebServices: 1.1.0
   ChimeraX-Zone: 1.0.1
   colorama: 0.4.5
   cxservices: 1.2
   cycler: 0.11.0
   Cython: 0.29.32
   debugpy: 1.6.3
   decorator: 5.1.1
   Deprecated: 1.2.13
   docutils: 0.19
   entrypoints: 0.4
   executing: 1.1.0
   filelock: 3.7.1
   fonttools: 4.37.4
   funcparserlib: 1.0.0
   future: 0.18.2
   grako: 3.16.5
   graphtools: 1.5.2
   h5py: 3.7.0
   html2text: 2020.1.16
   idna: 3.4
   ihm: 0.33
   imagecodecs: 2022.2.22
   imageio: 2.22.1
   imagesize: 1.4.1
   importlib-metadata: 5.0.0
   ipykernel: 6.15.3
   ipython: 8.4.0
   ipython-genutils: 0.2.0
   jedi: 0.18.1
   Jinja2: 3.1.2
   joblib: 1.2.0
   jupyter-client: 7.3.4
   jupyter-core: 4.11.1
   kiwisolver: 1.4.4
   line-profiler: 3.5.1
   llvmlite: 0.39.1
   lxml: 4.9.1
   lz4: 4.0.2
   MarkupSafe: 2.1.1
   matplotlib: 3.5.2
   matplotlib-inline: 0.1.6
   mrcfile: 1.4.3
   msgpack: 1.0.4
   nest-asyncio: 1.5.6
   netCDF4: 1.6.0
   networkx: 2.8.5
   numba: 0.56.2
   numexpr: 2.8.3
   numpy: 1.23.1
   openvr: 1.23.701
   packaging: 21.3
   pandas: 1.4.3
   ParmEd: 3.4.3
   parso: 0.8.3
   pep517: 0.13.0
   pexpect: 4.8.0
   phate: 1.0.8
   pickleshare: 0.7.5
   Pillow: 9.2.0
   pip: 22.2.2
   pkginfo: 1.8.3
   prompt-toolkit: 3.0.31
   psutil: 5.9.1
   ptyprocess: 0.7.0
   pure-eval: 0.2.2
   pycollada: 0.7.2
   pydicom: 2.3.0
   Pygments: 2.12.0
   PyGSP: 0.5.1
   pynndescent: 0.5.7
   PyOpenGL: 3.1.5
   PyOpenGL-accelerate: 3.1.5
   pyparsing: 3.0.9
   PyQt6: 6.3.1
   PyQt6-Qt6: 6.3.2
   PyQt6-sip: 13.4.0
   PyQt6-WebEngine: 6.3.1
   PyQt6-WebEngine-Qt6: 6.3.2
   pyqtgraph: 0.13.1
   python-dateutil: 2.8.2
   pytz: 2022.4
   PyWavelets: 1.4.1
   PyYAML: 6.0
   pyzmq: 24.0.1
   qtconsole: 5.3.1
   QtPy: 2.2.1
   RandomWords: 0.4.0
   requests: 2.28.1
   s-gd2: 1.8
   scikit-image: 0.19.3
   scikit-learn: 1.1.2
   scipy: 1.9.0
   scprep: 1.2.1
   Send2Trash: 1.8.0
   setuptools: 59.8.0
   setuptools-scm: 7.0.5
   sfftk-rw: 0.7.2
   six: 1.16.0
   sklearn: 0.0
   snowballstemmer: 2.2.0
   sortedcontainers: 2.4.0
   Sphinx: 5.1.1
   sphinx-autodoc-typehints: 1.19.1
   sphinxcontrib-applehelp: 1.0.2
   sphinxcontrib-blockdiag: 3.0.0
   sphinxcontrib-devhelp: 1.0.2
   sphinxcontrib-htmlhelp: 2.0.0
   sphinxcontrib-jsmath: 1.0.1
   sphinxcontrib-qthelp: 1.0.3
   sphinxcontrib-serializinghtml: 1.1.5
   stack-data: 0.5.1
   starfile: 0.4.11
   superqt: 0.3.3
   tables: 3.7.0
   tasklogger: 1.2.0
   threadpoolctl: 3.1.0
   tifffile: 2022.7.31
   tinyarray: 1.2.4
   tomli: 2.0.1
   torch: 1.12.1
   tornado: 6.2
   tqdm: 4.64.1
   traitlets: 5.3.0
   typing-extensions: 4.3.0
   urllib3: 1.26.12
   wcwidth: 0.2.5
   webcolors: 1.12
   wheel: 0.37.1
   wheel-filename: 1.4.1
   wiggle: 0.2.2
   wrapt: 1.14.1
   zipp: 3.8.1

Change History (7)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tristan Croll Tom Goddard added
Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Deprecation warnings

Really should be assigned to me, T.G. and Tristan, since the warnings cover all our code, but assigning to myself for now until I fix the part I'm responsible for, then may reassign.

comment:2 by Tom Goddard, 3 years ago

Fixed numpy.bool deprecation warning in Drawing.get_display_positions().

comment:3 by Tom Goddard, 3 years ago

Use numpy frombuffer instead of deprecated fromstring in MRC file reader.

comment:4 by Tom Goddard, 3 years ago

Replace deprecated inspect.getargspec() with inspect.getfullargspec() in map file reading code.

comment:5 by Tom Goddard, 3 years ago

Cc: Eric Pettersen added; Tristan Croll removed
Owner: changed from Eric Pettersen to Tristan Croll
Status: accepted → assigned

Looks like the remaining deprecation warnings are for isolde/molarray.py. Reassigning to Tristan.

comment:6 by Eric Pettersen, 3 years ago

Looks like I misread the log and the deprecations are only in T.G and Tristan code. Since T.G. dealt with his, reassigning to Tristan.

comment:7 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed

I *think* I've gotten all of mine now (numpy.bool, numpy.int and numpy.object are all deprecated). As an added bonus, I think it picked up why ISOLDE was occasionally crashing ChimeraX when unpickling the OpenMM force field in a separate thread. Rookie mistake: I wasn't using a context manager when opening the pickle file for reading, and forgot to close it.

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