Opened 23 months ago

Closed 23 months ago

#10342 closed defect (limitation)

ArtiaX/pandas vs. numpy

Reported by: chimerax-bug-report@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc: chimera-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.2.0-34-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database.json  
  
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show ArtiaX

Traceback (most recent call last):  
File "/home/rob/.local/share/ChimeraX/1.4/site-packages/pandas/__init__.py",
line 23, in <module>  
from pandas.compat import (  
File "/home/rob/.local/share/ChimeraX/1.4/site-
packages/pandas/compat/__init__.py", line 26, in <module>  
from pandas.compat.numpy import is_numpy_dev  
File "/home/rob/.local/share/ChimeraX/1.4/site-
packages/pandas/compat/numpy/__init__.py", line 20, in <module>  
raise ImportError(  
ImportError: this version of pandas is incompatible with numpy < 1.22.4  
your numpy version is 1.22.1.  
Please upgrade numpy to >= 1.22.4 to use this pandas version  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.4/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line
559, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "/programs/x86_64-linux/chimerax/1.4/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line
1325, in start_tool  
return cls._get_func(api, "start_tool")(session, bi, ti)  
File "/home/rob/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 27, in start_tool  
from . import tool  
File "/home/rob/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/tool.py", line 28, in <module>  
from .ArtiaX import (  
File "/home/rob/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/ArtiaX.py", line 13, in <module>  
from .io import open_particle_list, save_particle_list, get_fmt_aliases  
File "/home/rob/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/io/__init__.py", line 8, in <module>  
from .RELION import RELION_FORMAT  
File "/home/rob/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/io/RELION/__init__.py", line 3, in <module>  
from .RELIONParticleData import RELION_FORMAT  
File "/home/rob/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 5, in <module>  
import starfile  
File "/home/rob/.local/share/ChimeraX/1.4/site-packages/starfile/__init__.py",
line 1, in <module>  
from .functions import read, write  
File "/home/rob/.local/share/ChimeraX/1.4/site-
packages/starfile/functions.py", line 9, in <module>  
from .parser import StarParser  
File "/home/rob/.local/share/ChimeraX/1.4/site-packages/starfile/parser.py",
line 9, in <module>  
import pandas as pd  
File "/home/rob/.local/share/ChimeraX/1.4/site-packages/pandas/__init__.py",
line 28, in <module>  
raise ImportError(  
ImportError: C extension: None not built. If you want to import pandas from
the source directory, you may need to run 'python setup.py build_ext' to build
the C extensions first.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.4/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1685, in
<lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "/programs/x86_64-linux/chimerax/1.4/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38,
in run  
results = command.run(text, log=log, return_json=return_json)  
File "/programs/x86_64-linux/chimerax/1.4/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "/programs/x86_64-linux/chimerax/1.4/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/ui/cmd.py", line 219, in
ui_tool_show  
bi.start_tool(session, name)  
File "/programs/x86_64-linux/chimerax/1.4/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line
564, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ArtiaX in
bundle ChimeraX-ArtiaX:  
C extension: None not built. If you want to import pandas from the source
directory, you may need to run 'python setup.py build_ext' to build the C
extensions first.  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ArtiaX in
bundle ChimeraX-ArtiaX:  
C extension: None not built. If you want to import pandas from the source
directory, you may need to run 'python setup.py build_ext' to build the C
extensions first.  
  
File "/programs/x86_64-linux/chimerax/1.4/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line
564, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> ui tool show ArtiaX

Traceback (most recent call last):  
File "/home/rob/.local/share/ChimeraX/1.4/site-packages/pandas/__init__.py",
line 23, in <module>  
from pandas.compat import (  
File "/home/rob/.local/share/ChimeraX/1.4/site-
packages/pandas/compat/__init__.py", line 26, in <module>  
from pandas.compat.numpy import is_numpy_dev  
File "/home/rob/.local/share/ChimeraX/1.4/site-
packages/pandas/compat/numpy/__init__.py", line 20, in <module>  
raise ImportError(  
ImportError: this version of pandas is incompatible with numpy < 1.22.4  
your numpy version is 1.22.1.  
Please upgrade numpy to >= 1.22.4 to use this pandas version  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.4/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line
559, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "/programs/x86_64-linux/chimerax/1.4/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line
1325, in start_tool  
return cls._get_func(api, "start_tool")(session, bi, ti)  
File "/home/rob/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 27, in start_tool  
from . import tool  
File "/home/rob/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/tool.py", line 28, in <module>  
from .ArtiaX import (  
File "/home/rob/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/ArtiaX.py", line 13, in <module>  
from .io import open_particle_list, save_particle_list, get_fmt_aliases  
File "/home/rob/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/io/__init__.py", line 8, in <module>  
from .RELION import RELION_FORMAT  
File "/home/rob/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/io/RELION/__init__.py", line 3, in <module>  
from .RELIONParticleData import RELION_FORMAT  
File "/home/rob/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 5, in <module>  
import starfile  
File "/home/rob/.local/share/ChimeraX/1.4/site-packages/starfile/__init__.py",
line 1, in <module>  
from .functions import read, write  
File "/home/rob/.local/share/ChimeraX/1.4/site-
packages/starfile/functions.py", line 9, in <module>  
from .parser import StarParser  
File "/home/rob/.local/share/ChimeraX/1.4/site-packages/starfile/parser.py",
line 9, in <module>  
import pandas as pd  
File "/home/rob/.local/share/ChimeraX/1.4/site-packages/pandas/__init__.py",
line 28, in <module>  
raise ImportError(  
ImportError: C extension: None not built. If you want to import pandas from
the source directory, you may need to run 'python setup.py build_ext' to build
the C extensions first.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.4/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1685, in
<lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "/programs/x86_64-linux/chimerax/1.4/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38,
in run  
results = command.run(text, log=log, return_json=return_json)  
File "/programs/x86_64-linux/chimerax/1.4/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "/programs/x86_64-linux/chimerax/1.4/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/ui/cmd.py", line 219, in
ui_tool_show  
bi.start_tool(session, name)  
File "/programs/x86_64-linux/chimerax/1.4/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line
564, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ArtiaX in
bundle ChimeraX-ArtiaX:  
C extension: None not built. If you want to import pandas from the source
directory, you may need to run 'python setup.py build_ext' to build the C
extensions first.  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ArtiaX in
bundle ChimeraX-ArtiaX:  
C extension: None not built. If you want to import pandas from the source
directory, you may need to run 'python setup.py build_ext' to build the C
extensions first.  
  
File "/programs/x86_64-linux/chimerax/1.4/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line
564, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 535.54.03
OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: ASUSTeK COMPUTER INC.
Model: ESC8000 G4
OS: Ubuntu 22.04 jammy
Architecture: 64bit ELF
Virtual Machine: none
CPU: 96 Intel(R) Xeon(R) Gold 5220R CPU @ 2.20GHz
Cache Size: 36608 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           440Gi       9.5Gi        67Gi        46Mi       363Gi       427Gi
	Swap:           15Gi       380Mi        14Gi

Graphics:
	1b:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102 [GeForce RTX 3090] [10de:2204] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. GA102 [GeForce RTX 3090] [1043:87d5]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-ArtiaX: 0.3
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-NIHPresets: 1.1.16
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    geomdl: 5.3.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.26.2
    openvr: 1.16.802
    packaging: 21.3
    pandas: 2.1.4
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    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
    starfile: 0.5.2
    suds-community: 1.0.0
    superqt: 0.6.1
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 23 months ago

Cc: chimera-programmers added
Component: Unassigned → Tool Shed
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ArtiaX/pandas vs. numpy

Pretty weird -- pandas complains about not being compatible with numpy 1.22.1 (which is the version shipped with ChimeraX 1.4) and needing 1.22.4, despite ArtiaX supposedly being compatible with Chimera 1.3+. Then in the bug report module list, numpy is version 1.26.2(!) which is the absolute newest version -- newer than any currently shipped with ChimeraX.

comment:2 by Greg Couch, 23 months ago

Resolution: → limitation
Status: assigned → closed

User must have installed incompatible numpy. Unfortunately, pip will install packages that incompatible with what's already installed.

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