Opened 14 months ago
Closed 14 months ago
#15780 closed defect (can't reproduce)
MatchMaker: circular import of _sw
Reported by: | Owned by: | Eric Pettersen | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Sequence | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.19045 ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "E:/sui lab/pink/final-pdb/pk-51-90-final.pdb" Chain information for pk-51-90-final.pdb #1 --- Chain | Description A B | No description available C | No description available D | No description available > open "E:/sui lab/pink/202405new > map/pk-90-fkbp51/cryosparc_P6_J3235_002_volume_map_sharp.mrc" Opened cryosparc_P6_J3235_002_volume_map_sharp.mrc as #2, grid size 280,280,280, pixel 0.87, shown at level 0.141, step 2, values float32 > set bgColor white > lighting soft > volume #2 step 1 > hide #!2 models > color #1 cyan transparency 0 > graphics silhouettes true > select /B 5196 atoms, 5280 bonds, 1 pseudobond, 637 residues, 2 models selected > ui tool show "Color Actions" > color sel dodger blue > select /C 2639 atoms, 2694 bonds, 2 pseudobonds, 343 residues, 2 models selected > ui tool show "Color Actions" > color sel gold > select /D 3229 atoms, 3287 bonds, 409 residues, 1 model selected > ui tool show "Color Actions" > color sel hot pink > color sel magenta > color sel violet > select clear > hide atoms > select ::name="ADP" 54 atoms, 58 bonds, 2 residues, 1 model selected > show sel atoms > color sel red > color sel byhetero > select clear > select ::name="MG" 2 atoms, 2 residues, 1 model selected > show sel atoms > color sel lime > select clear > show #!2 models > color #2 #dfdfdf models transparency 0 > transparency 50 > volume #2 level 0.1627 > ui tool show "Hide Dust" > surface dust #2 size 5.22 > volume #2 level 0.09858 > volume #2 level 0.1199 > volume #2 level 0.1093 > surface dust #2 size 6.75 > volume #2 level 0.1413 > open "E:/sui lab/pink/final-pdb/pk-90A-37-final-coot-1.pdb" Chain information for pk-90A-37-final-coot-1.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available E | No description available > hide #!2 models > hide #!1 models > select #3/C:441 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 78 atoms, 80 bonds, 11 residues, 1 model selected > select up 1822 atoms, 1859 bonds, 234 residues, 1 model selected > select ~sel 28733 atoms, 29217 bonds, 7 pseudobonds, 3548 residues, 6 models selected > hide sel & #!3 cartoons > hide sel & #!3 atoms > select clear > show #!2 models > show #!1 models > hide #!2 models > hide #!3 models > show #!3 models > select #3 14295 atoms, 14535 bonds, 4 pseudobonds, 1756 residues, 2 models selected > show sel cartoons > select clear > select #3/B:171 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 49 atoms, 49 bonds, 6 residues, 1 model selected > select up 5178 atoms, 5262 bonds, 635 residues, 1 model selected > select clear > ui tool show Matchmaker Traceback (most recent call last): File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 484, in get_module m = importlib.import_module(self.package_name) File "D:\ChimeraX 1.3\bin\lib\importlib\\__init__.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "<frozen importlib._bootstrap>", line 1030, in _gcd_import File "<frozen importlib._bootstrap>", line 1007, in _find_and_load File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 680, in _load_unlocked File "<frozen importlib._bootstrap_external>", line 850, in exec_module File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed File "D:\ChimeraX 1.3\bin\lib\site- packages\chimerax\match_maker\\__init__.py", line 15, in <module> from .match import CP_SPECIFIC_SPECIFIC, CP_SPECIFIC_BEST, CP_BEST_BEST File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\match_maker\match.py", line 18, in <module> from chimerax.alignment_algs import NEEDLEMAN_WUNSCH as AA_NEEDLEMAN_WUNSCH, \ File "D:\ChimeraX 1.3\bin\lib\site- packages\chimerax\alignment_algs\\__init__.py", line 14, in <module> from . import _sw as SmithWaterman ImportError: cannot import name '_sw' from partially initialized module 'chimerax.alignment_algs' (most likely due to a circular import) (D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\alignment_algs\\__init__.py) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 553, in start_tool api = self._get_api(session.logger) File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 503, in _get_api m = self.get_module() File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 486, in get_module raise ToolshedError("Error importing bundle %s's module: %s" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX- MatchMaker's module: cannot import name '_sw' from partially initialized module 'chimerax.alignment_algs' (most likely due to a circular import) (D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\alignment_algs\\__init__.py) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1659, in <lambda> run(ses, "ui tool show %s" % StringArg.unparse(tool_name))) File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2856, in run result = ci.function(session, **kw_args) File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\cmd.py", line 219, in ui_tool_show bi.start_tool(session, name) File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 559, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Matchmaker in bundle ChimeraX-MatchMaker: Error importing bundle ChimeraX-MatchMaker's module: cannot import name '_sw' from partially initialized module 'chimerax.alignment_algs' (most likely due to a circular import) (D:\ChimeraX 1.3\bin\lib\site- packages\chimerax\alignment_algs\\__init__.py) chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Matchmaker in bundle ChimeraX-MatchMaker: Error importing bundle ChimeraX-MatchMaker's module: cannot import name '_sw' from partially initialized module 'chimerax.alignment_algs' (most likely due to a circular import) (D:\ChimeraX 1.3\bin\lib\site- packages\chimerax\alignment_algs\\__init__.py) File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 559, in start_tool raise ToolshedError( See log for complete Python traceback. > ui tool show Matchmaker Traceback (most recent call last): File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 484, in get_module m = importlib.import_module(self.package_name) File "D:\ChimeraX 1.3\bin\lib\importlib\\__init__.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "<frozen importlib._bootstrap>", line 1030, in _gcd_import File "<frozen importlib._bootstrap>", line 1007, in _find_and_load File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 680, in _load_unlocked File "<frozen importlib._bootstrap_external>", line 850, in exec_module File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed File "D:\ChimeraX 1.3\bin\lib\site- packages\chimerax\match_maker\\__init__.py", line 15, in <module> from .match import CP_SPECIFIC_SPECIFIC, CP_SPECIFIC_BEST, CP_BEST_BEST File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\match_maker\match.py", line 18, in <module> from chimerax.alignment_algs import NEEDLEMAN_WUNSCH as AA_NEEDLEMAN_WUNSCH, \ File "D:\ChimeraX 1.3\bin\lib\site- packages\chimerax\alignment_algs\\__init__.py", line 14, in <module> from . import _sw as SmithWaterman ImportError: cannot import name '_sw' from partially initialized module 'chimerax.alignment_algs' (most likely due to a circular import) (D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\alignment_algs\\__init__.py) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 553, in start_tool api = self._get_api(session.logger) File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 503, in _get_api m = self.get_module() File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 486, in get_module raise ToolshedError("Error importing bundle %s's module: %s" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX- MatchMaker's module: cannot import name '_sw' from partially initialized module 'chimerax.alignment_algs' (most likely due to a circular import) (D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\alignment_algs\\__init__.py) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1659, in <lambda> run(ses, "ui tool show %s" % StringArg.unparse(tool_name))) File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2856, in run result = ci.function(session, **kw_args) File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\cmd.py", line 219, in ui_tool_show bi.start_tool(session, name) File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 559, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Matchmaker in bundle ChimeraX-MatchMaker: Error importing bundle ChimeraX-MatchMaker's module: cannot import name '_sw' from partially initialized module 'chimerax.alignment_algs' (most likely due to a circular import) (D:\ChimeraX 1.3\bin\lib\site- packages\chimerax\alignment_algs\\__init__.py) chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Matchmaker in bundle ChimeraX-MatchMaker: Error importing bundle ChimeraX-MatchMaker's module: cannot import name '_sw' from partially initialized module 'chimerax.alignment_algs' (most likely due to a circular import) (D:\ChimeraX 1.3\bin\lib\site- packages\chimerax\alignment_algs\\__init__.py) File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py", line 559, in start_tool raise ToolshedError( See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 517.00 OpenGL renderer: NVIDIA GeForce RTX 2060/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: LENOVO Model: 82AX OS: Microsoft Windows 10 家庭中文版 (Build 19045) Memory: 17,040,195,584 MaxProcessMemory: 137,438,953,344 CPU: 16 Intel(R) Core(TM) i7-10875H CPU @ 2.30GHz OSLanguage: zh-CN Locale: ('zh_CN', 'cp936') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.10.8 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 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: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 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: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 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 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 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: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 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: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 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 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 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: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 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: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 comtypes: 1.1.10 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.3 ParmEd: 3.2.0 parso: 0.8.3 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pywin32: 228 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 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 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 WMI: 1.5.1
Change History (2)
comment:1 by , 14 months ago
Component: | Unassigned → Sequence |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → MatchMaker: circular import of _sw |
comment:2 by , 14 months ago
Resolution: | → can't reproduce |
---|---|
Status: | accepted → closed |
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