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Opened 17 months ago
Closed 17 months ago
#15629 closed defect (limitation)
ArtiaX/pandas vs. numpy
| Reported by: | Owned by: | Utz Ermel | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-4.18.0-513.9.1.el8_9.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Traceback (most recent call last):
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/pandas/__init__.py", line 26, in <module>
from pandas.compat import (
File "/home/eberle/.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/eberle/.local/share/ChimeraX/1.4/site-
packages/pandas/compat/numpy/__init__.py", line 21, 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
"/g/easybuild/x86_64/Rocky/8/haswell/software/ChimeraX/1.4/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/g/easybuild/x86_64/Rocky/8/haswell/software/ChimeraX/1.4/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/g/easybuild/x86_64/Rocky/8/haswell/software/ChimeraX/1.4/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 63, in run_provider
from .toolbar import run_provider
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/toolbar/__init__.py", line 3, in <module>
from .toolbar import *
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/toolbar/toolbar.py", line 4, in <module>
from ..particle.ParticleList import delete_selected_particles,
invert_selection
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/particle/__init__.py", line 2, in <module>
from .ParticleList import ParticleList
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/particle/ParticleList.py", line 18, in <module>
from ..io.ParticleData import ParticleData
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/io/__init__.py", line 8, in <module>
from .RELION import RELION_FORMAT
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/io/RELION/__init__.py", line 3, in <module>
from .RELIONParticleData import RELION_FORMAT
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 5, in <module>
import starfile
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/starfile/__init__.py", line 1, in <module>
from .functions import read, write
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/starfile/functions.py", line 9, in <module>
from .parser import StarParser
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/starfile/parser.py", line 10, in <module>
import pandas as pd
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/pandas/__init__.py", line 31, 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.
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.
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/pandas/__init__.py", line 31, in
raise ImportError(
See log for complete Python traceback.
> artiax start
Traceback (most recent call last):
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/pandas/__init__.py", line 26, in <module>
from pandas.compat import (
File "/home/eberle/.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/eberle/.local/share/ChimeraX/1.4/site-
packages/pandas/compat/numpy/__init__.py", line 21, 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
"/g/easybuild/x86_64/Rocky/8/haswell/software/ChimeraX/1.4/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/g/easybuild/x86_64/Rocky/8/haswell/software/ChimeraX/1.4/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/g/easybuild/x86_64/Rocky/8/haswell/software/ChimeraX/1.4/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/__init__.py", line 64, in run_provider
run_provider(session, name)
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/toolbar/toolbar.py", line 67, in run_provider
run(session, what)
File
"/g/easybuild/x86_64/Rocky/8/haswell/software/ChimeraX/1.4/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
"/g/easybuild/x86_64/Rocky/8/haswell/software/ChimeraX/1.4/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/cmd/cmd.py", line 29, in artiax_start
get_singleton(session)
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/cmd/cmd.py", line 20, in get_singleton
from ..tool import ArtiaXUI
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/tool.py", line 27, in <module>
from .ArtiaX import (
File "/home/eberle/.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/eberle/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/io/__init__.py", line 8, in <module>
from .RELION import RELION_FORMAT
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/io/RELION/__init__.py", line 3, in <module>
from .RELIONParticleData import RELION_FORMAT
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 5, in <module>
import starfile
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/starfile/__init__.py", line 1, in <module>
from .functions import read, write
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/starfile/functions.py", line 9, in <module>
from .parser import StarParser
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/starfile/parser.py", line 10, in <module>
import pandas as pd
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/pandas/__init__.py", line 31, 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.
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.
File "/home/eberle/.local/share/ChimeraX/1.4/site-
packages/pandas/__init__.py", line 31, in
raise ImportError(
See log for complete Python traceback.
OpenGL version: 4.5 (Core Profile) Mesa 23.1.4
OpenGL renderer: llvmpipe (LLVM 16.0.6, 256 bits)
OpenGL vendor: Mesa
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=
DESKTOP_SESSION=
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=
DISPLAY=localhost:67.0
Manufacturer: Dell Inc.
Model: PowerEdge R730
OS: Rocky Linux 8.9 Green Obsidian
Architecture: 64bit ELF
Virtual Machine: none
CPU: 64 Intel(R) Xeon(R) CPU E5-2698 v3 @ 2.30GHz
Cache Size: 20480 KB
Memory:
total used free shared buff/cache available
Mem: 251Gi 89Gi 48Gi 6.5Gi 113Gi 153Gi
Swap: 2.9Ti 478Gi 2.4Ti
Graphics:
05:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM204GL [Tesla M60] [10de:13f2] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:115e]
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: 0.2
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-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-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-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: 2.0.0
openvr: 1.16.802
packaging: 21.3
pandas: 2.2.2
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
pyarrow: 17.0.0
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: 0.5.8
suds-community: 1.0.0
superqt: 0.6.7
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
typing-extensions: 4.12.2
tzdata: 2024.1
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 , 17 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Third Party |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ArtiaX/pandas vs. numpy |
comment:2 by , 17 months ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
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Hi Robin,
--Eric