Opened 23 months ago
Closed 23 months ago
#10258 closed defect (fixed)
SyntaxError in volume.py
Reported by: | Owned by: | Tom Goddard | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Volume Data | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.22000 ChimeraX Version: 1.7rc202311300124 (2023-11-30 01:24:31 UTC) Description (Describe the actions that caused this problem to occur here) Log: Startup Errors --- errors | Bundle 'ChimeraX-Map' custom initialization failed Bundle 'ChimeraX-Dicom' custom initialization failed warnings | Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py", line 501, in get_module m = importlib.import_module(self.package_name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\importlib\\__init__.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "<frozen importlib._bootstrap>", line 1206, in _gcd_import File "<frozen importlib._bootstrap>", line 1178, in _find_and_load File "<frozen importlib._bootstrap>", line 1149, in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 690, in _load_unlocked File "<frozen importlib._bootstrap_external>", line 940, in exec_module File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\map\\__init__.py", line 29, in <module> from .volume import open_map, volume_from_grid_data File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\map\volume.py", line 3441 if allow_reseting_color_sequence and ynot any_volume_open(session): ^^^^^^^^^^^^^^^ SyntaxError: invalid syntax During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py", line 375, in initialize api = self._get_api(session.logger) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py", line 520, in _get_api m = self.get_module() ^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py", line 503, in get_module raise ToolshedError("Error importing bundle %s's module: %s" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-Map's module: invalid syntax (volume.py, line 3441) Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py", line 501, in get_module m = importlib.import_module(self.package_name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\importlib\\__init__.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "<frozen importlib._bootstrap>", line 1206, in _gcd_import File "<frozen importlib._bootstrap>", line 1178, in _find_and_load File "<frozen importlib._bootstrap>", line 1149, in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 690, in _load_unlocked File "<frozen importlib._bootstrap_external>", line 940, in exec_module File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\dicom\\__init__.py", line 15, in <module> from chimerax.map import add_map_format File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\map\\__init__.py", line 29, in <module> from .volume import open_map, volume_from_grid_data File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\map\volume.py", line 3441 if allow_reseting_color_sequence and ynot any_volume_open(session): ^^^^^^^^^^^^^^^ SyntaxError: invalid syntax During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py", line 375, in initialize api = self._get_api(session.logger) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py", line 520, in _get_api m = self.get_module() ^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py", line 503, in get_module raise ToolshedError("Error importing bundle %s's module: %s" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-Dicom's module: invalid syntax (volume.py, line 3441) UCSF ChimeraX version: 1.7rc202311300124 (2023-11-30) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:\Users\eeast\Downloads\5xh3.pdb format pdb 5xh3.pdb title: Crystal structure of A novel pet hydrolase R103G/S131A mutant In complex with hemt from ideonella sakaiensis 201-F6 [more info...] Chain information for 5xh3.pdb #1 --- Chain | Description A | petase Non-standard residues in 5xh3.pdb #1 --- 856 — O 4-(2-hydroxyethyl) O 1-methyl benzene-1,4-dicarboxylate GOL — glycerol (glycerin; propane-1,2,3-triol) SO4 — sulfate ion Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\toolbar\tool.py", line 165, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py", line 397, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider return cls._get_func(api, "run_provider")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\\__init__.py", line 66, in run_provider shortcuts.run_provider(session, name) File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py", line 1376, in run_provider keyboard_shortcuts(session).try_shortcut(name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py", line 1341, in keyboard_shortcuts register_shortcuts(ks) File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py", line 29, in register_shortcuts scuts, catcols = standard_shortcuts(ks.session) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py", line 124, in standard_shortcuts ('sM', run_on_maps('volume %s show', visible_only=False), 'Show map', mapcat, sesarg, mmenu), ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\shortcuts\shortcuts.py", line 532, in run_on_maps from chimerax.map import Volume File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\map\\__init__.py", line 29, in <module> from .volume import open_map, volume_from_grid_data File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\map\volume.py", line 3441 if allow_reseting_color_sequence and ynot any_volume_open(session): ^^^^^^^^^^^^^^^ SyntaxError: invalid syntax File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\map\volume.py", line 3441 if allow_reseting_color_sequence and ynot any_volume_open(session): ^^^^^^^^^^^^^^^ SyntaxError: invalid syntax File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\map\\__init__.py", line 29, in from .volume import open_map, volume_from_grid_data See log for complete Python traceback. OpenGL version: 3.3.0 - Build 31.0.101.4575 OpenGL renderer: Intel(R) Iris(R) Xe Graphics OpenGL vendor: Intel Python: 3.11.2 Locale: en_US.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: Dell Inc. Model: Inspiron 15 3511 OS: Microsoft Windows 11 Home (Build 22000) Memory: 16,901,771,264 MaxProcessMemory: 137,438,953,344 CPU: 8 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.13.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.2 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: 2.10.5 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: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7rc202311300124 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 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: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.1.2 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: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 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: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.3 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 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: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.3 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: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 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: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 comtypes: 1.1.14 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.45.1 funcparserlib: 2.0.0a0 glfw: 2.6.3 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.0 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.7 numpy: 1.25.1 openvr: 1.23.701 packaging: 23.2 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.0.0 prompt-toolkit: 3.0.41 psutil: 5.9.5 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pywin32: 305 pyzmq: 25.1.1 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.8.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 WMI: 1.5.1
Change History (2)
comment:1 by , 23 months ago
Component: | Unassigned → Volume Data |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → SyntaxError in volume.py |
comment:2 by , 23 months ago
Resolution: | → fixed |
---|---|
Status: | assigned → closed |
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Fixed and release candidate build restarted to minimize the reporting of this.
Accidentally added a "y" in copying a volume coloring code change yesterday from develop branch to the 1.7 release candidate branch. This error appears on startup of last night's release candidate because the volume code custom init tries to import the file with the syntax error.