Opened 3 years ago

Last modified 3 years ago

#8686 assigned defect

SEQCROW: No module named 'send2trash'

Reported by: chimerax-bug-report@… Owned by: Tony Schaefer
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: chimera-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/jamisonlaw/OneDrive - The Ohio State
> University/OSBP/Bell/Data/Structure/ChimeraX/FraB conservation mapped onto
> structure (SIS domains).cxs" format session

Log from Tue Mar 21 12:59:36 2023 Startup Messages  
---  
warnings | Unable to find icon for toolbar provider 'Dump Bead Data' in bundle
'ChimeraX-GenomeTools'  
Unable to find icon for toolbar provider 'Highlight' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Bed Models' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Bead Overlap' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Genome Distance' in bundle
'ChimeraX-GenomeTools'  
1 messages similar to the above omitted  
  
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/jamisonlaw/Library/CloudStorage/OneDrive-
> TheOhioStateUniversity/OSBP/Bell/Data/Synchrotron/refmac8-KZ.pdb format pdb

refmac8-KZ.pdb title:  
Salmonella typhimurium LT2 At 2.12 A Re [more info...]  
  
Chain information for refmac8-KZ.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Non-standard residues in refmac8-KZ.pdb #1  
---  
MG — (MG)  
  

> open /Users/jamisonlaw/Downloads/W654rqQEudpM__msa_out.afa

Summary of feedback from opening
/Users/jamisonlaw/Downloads/W654rqQEudpM__msa_out.afa  
---  
notes | Alignment identifier is W654rqQEudpM__msa_out.afa  
Associated refmac8-KZ.pdb chain B to FraB_N_Terminal (1-166) with 0 mismatches  
Associated refmac8-KZ.pdb chain C to FraB_N_Terminal (1-166) with 0 mismatches  
Associated refmac8-KZ.pdb chain A to FraB_N_Terminal (1-166) with 0 mismatches  
Associated refmac8-KZ.pdb chain D to FraB_N_Terminal (1-166) with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment W654rqQEudpM__msa_out.afa  
  
Opened 701 sequences from W654rqQEudpM__msa_out.afa  

> color byattribute seq_conservation palette blue:red:yellow

10105 atoms, 1517 residues, atom seq_conservation range -1.08 to 5.48  

> color byattribute seq_conservation palette blue:red:yellow range -2,2
> noValueColor silver key true

> key blue:-2 red:0 yellow:2 showTool true

> ui mousemode right "color key"

10105 atoms, 1517 residues, atom seq_conservation range -1.08 to 5.48  

> ui mousemode right translate

> ui mousemode right "color key"

> key blue:-2 red:0 yellow:

> key blue:-2 red:0 yellow:4

> key blue:- red:0 yellow:4

> key blue:-4 red:0 yellow:4

> key blue:- red:0 yellow:4

> key blue:-1 red:0 yellow:4

> key blue:-10 red:0 yellow:4

> key blue:-10 red:0 yellow:

> key blue:-10 red:0 yellow:1

> key blue:-10 red:0 yellow:10

> ui mousemode right translate

> color byattribute seq_conservation palette blue:red:yellow range -10,10
> noValueColor silver key true

> key blue:-10 red:0 yellow:10 showTool true

> ui mousemode right "color key"

10105 atoms, 1517 residues, atom seq_conservation range -1.08 to 5.48  

> key blue:-10 red:0 yellow:1

> key blue:-10 red:0 yellow:

> key blue:-10 red:0 yellow:5

> key blue:-1 red:0 yellow:5

> key blue:- red:0 yellow:5

> key blue:-5 red:0 yellow:5

> ui mousemode right translate

> color byattribute seq_conservation palette blue:red:yellow range -5,5
> noValueColor silver key true

> key blue:-5 red:0 yellow:5 showTool true

> ui mousemode right "color key"

10105 atoms, 1517 residues, atom seq_conservation range -1.08 to 5.48  

> color byattribute seq_conservation palette blue:red:yellow range -2,3
> noValueColor silver key true

> key blue:-2.0 red:0.5 yellow:3.0 showTool true

10105 atoms, 1517 residues, atom seq_conservation range -1.08 to 5.48  

> color byattribute seq_conservation palette blue:red:yellow range -1,1
> noValueColor silver key true

> key blue:-1 red:0 yellow:1 showTool true

10105 atoms, 1517 residues, atom seq_conservation range -1.08 to 5.48  

> key pos 0.473544,0.552729 size 0.16637,0.0208279

> key pos 0.785516,0.0713326

> ui mousemode right translate

> color byattribute seq_conservation palette blue:red:yellow range -2,2
> noValueColor silver key true

> key blue:-2 red:0 yellow:2 showTool true

> ui mousemode right "color key"

10105 atoms, 1517 residues, atom seq_conservation range -1.08 to 5.48  

> ui mousemode right translate

> color byattribute seq_conservation palette blue:red:yellow range -3,3
> noValueColor silver key true

> key blue:-3 red:0 yellow:3 showTool true

> ui mousemode right "color key"

10105 atoms, 1517 residues, atom seq_conservation range -1.08 to 5.48  

> ui mousemode right translate

> color byattribute seq_conservation palette blue:red:yellow range -2,3
> noValueColor silver key true

> key blue:-2.0 red:0.5 yellow:3.0 showTool true

> ui mousemode right "color key"

10105 atoms, 1517 residues, atom seq_conservation range -1.08 to 5.48  

> ui mousemode right translate

> color byattribute seq_conservation palette blue:red:yellow range -1,3
> noValueColor silver key true

> key blue:-1 red:1 yellow:3 showTool true

> ui mousemode right "color key"

10105 atoms, 1517 residues, atom seq_conservation range -1.08 to 5.48  

> key blue:-1 red:1 yellow:

> key blue:-1 red:1 yellow:1

> key blue:-1 red: yellow:1

> key blue:-1 red:0 yellow:1

> ui mousemode right translate

> color byattribute seq_conservation palette blue:red:yellow range -1,1
> noValueColor silver key true

> key blue:-1 red:0 yellow:1 showTool true

> ui mousemode right "color key"

10105 atoms, 1517 residues, atom seq_conservation range -1.08 to 5.48  

> ui mousemode right translate

> open /Users/jamisonlaw/Downloads/ZnIHMKRPz31R__msa_out.afa

Summary of feedback from opening
/Users/jamisonlaw/Downloads/ZnIHMKRPz31R__msa_out.afa  
---  
notes | Alignment identifier is ZnIHMKRPz31R__msa_out.afa  
Associated refmac8-KZ.pdb chain B to FraB_C_Terminus (1-159) with 3 mismatches  
Associated refmac8-KZ.pdb chain C to FraB_C_Terminus (1-159) with 4 mismatches  
Associated refmac8-KZ.pdb chain A to FraB_C_Terminus (1-159) with 3 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment ZnIHMKRPz31R__msa_out.afa  
  
Opened 701 sequences from ZnIHMKRPz31R__msa_out.afa  

> color byattribute seq_conservation palette blue:red:yellow range -1,1
> noValueColor silver key true

> key blue:-1 red:0 yellow:1 showTool true

> ui mousemode right "color key"

10105 atoms, 1517 residues, atom seq_conservation range -1.19 to 6.32  

> key pos 0.320033,0.395702 size 0.148318,0.0206847

> key pos 0.423847,0.352377 size 0.034487,0.0474787

> key pos 0.541355,0.0869434 size 0.151973,0.0186495

> ui mousemode right translate

> save "/Users/jamisonlaw/OneDrive - The Ohio State
> University/OSBP/Bell/Data/Structure/ChimeraX/FraB conservation mapped onto
> structure (SIS domains).cxs"

——— End of log from Tue Mar 21 12:59:36 2023 ———

opened ChimeraX session  

> open /Users/jamisonlaw/Downloads/HsWXeGLiO9It__msa_out.afa

Summary of feedback from opening
/Users/jamisonlaw/Downloads/HsWXeGLiO9It__msa_out.afa  
---  
notes | Alignment identifier is HsWXeGLiO9It__msa_out.afa  
Associated refmac8-KZ.pdb chain B to FraB_1-528 (1-176) with 0 mismatches  
Associated refmac8-KZ.pdb chain C to FraB_1-528 (1-176) with 0 mismatches  
Associated refmac8-KZ.pdb chain A to FraB_1-528 (1-176) with 0 mismatches  
Associated refmac8-KZ.pdb chain D to FraB_1-528 (1-176) with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment HsWXeGLiO9It__msa_out.afa  
  
Opened 701 sequences from HsWXeGLiO9It__msa_out.afa  

> color byattribute seq_conservation palette blue:red:yellow range -1,1
> noValueColor silver key true

> key blue:-1 red:0 yellow:1 showTool true

> ui mousemode right "color key"

10105 atoms, 1517 residues, atom seq_conservation range -1.19 to 6.32  

> ui mousemode right translate

> select clear

[Repeated 1 time(s)]

> ui mousemode right select

Drag select of 67 atoms, 1273 residues, 2 pseudobonds, 59 bonds  

> select clear

[Repeated 2 time(s)]

> ui tool show "Buried Volume"

Traceback (most recent call last):  
File
"/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/F33BC099-33B8-4EA8-BE12-D7967A707BD7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 560, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/F33BC099-33B8-4EA8-BE12-D7967A707BD7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1328, in start_tool  
return cls._get_func(api, "start_tool")(session, bi, ti)  
File "/Users/jamisonlaw/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/__init__.py", line 333, in start_tool  
from .tools import PercentVolumeBuried  
File "/Users/jamisonlaw/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/tools/__init__.py", line 9, in <module>  
from .job_manager_tool import JobQueue  
File "/Users/jamisonlaw/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/tools/job_manager_tool.py", line 23, in <module>  
from send2trash import send2trash  
ModuleNotFoundError: No module named 'send2trash'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/F33BC099-33B8-4EA8-BE12-D7967A707BD7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1660, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File
"/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/F33BC099-33B8-4EA8-BE12-D7967A707BD7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/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
"/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/F33BC099-33B8-4EA8-BE12-D7967A707BD7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/F33BC099-33B8-4EA8-BE12-D7967A707BD7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show  
bi.start_tool(session, name)  
File
"/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/F33BC099-33B8-4EA8-BE12-D7967A707BD7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 567, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Buried
Volume in bundle SEQCROW:  
No module named 'send2trash'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Buried
Volume in bundle SEQCROW:  
No module named 'send2trash'  
  
File
"/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/F33BC099-33B8-4EA8-BE12-D7967A707BD7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 567, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.9.51
OpenGL renderer: AMD Radeon Pro 555 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: 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: MacBookPro14,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.8 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 499.40.2.0.0
      OS Loader Version: 564.40.4~66
      SMC Version (system): 2.45f5

Software:

    System Software Overview:

      System Version: macOS 13.2.1 (22D68)
      Kernel Version: Darwin 22.3.0
      Time since boot: 2 days, 22 hours, 9 minutes

Graphics/Displays:

    Intel HD Graphics 630:

      Chipset Model: Intel HD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x591b
      Revision ID: 0x0004
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal Support: Metal 3

    Radeon Pro 555:

      Chipset Model: Radeon Pro 555
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 2 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c7
      ROM Revision: 113-C980AJ-927
      VBIOS Version: 113-C9801AP-A02
      EFI Driver Version: 01.A0.927
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    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: 2.1.3
    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: 0.3
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    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
    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
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-Cytoscape: 0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-DevelExtras: 0.4.2
    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-GenomeTools: 0.9
    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
    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: 1.1.2
    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-NIHPresets: 1.1.9
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-OpenCommands: 1.0
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBImages: 1.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.1.7
    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-RIBFIND: 0.2
    ChimeraX-RMF: 0.13
    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-StarMap: 1.1.70
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-StrudelScore: 0.2
    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-TestManager: 0.3
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    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-XMAS: 1.1.2
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    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
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    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: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    SEQCROW: 1.6.1
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    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: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (3)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Third Party
Owner: set to Tony Schaefer
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → SEQCROW: No module named 'send2trash'

in reply to:  2 ; comment:2 by Tony Schaefer, 3 years ago 

I'm not sure how they wouldn't have send2trash. It's listed as a SEQCROW
dependency in the bundle_info.xml. Maybe they ran `toolshed install SEQCROW
noDeps true`? I'm not sure what else is included with ChimeraX, but they
have all the other dependencies (scipy, psutil, and jinja2).

I can probably move imports around to allow other tools to work if they
don't actually require a certain dependency. send2trash is currently only
used for cleaning up any QM jobs users run through SEQCROW; it is not used
for the buried volume tool.

Tony

On Tue, Mar 21, 2023 at 12:58 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:3 by Eric Pettersen, 3 years ago

Cc: chimera-programmers added

Actually, scipy, jinja2, and psutils are shipped with ChimeraX, so perhaps they did manage to install SEQCROW with noDeps true -- which would be weird.

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