"toolshed uninstall" failure

[Eric Pettersen]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-05-09)
Description
Trying to uninstall Maestro bundle from release candidate.  It shouldn't have been allowed to install in the first place AFAIK

Log:
UCSF ChimeraX version: 1.0rc202005091901 (2020-05-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed list

List of installed bundles:  

AddH (1.0): Add hydrogens AlignmentAlgorithms (1.0): Sequence alignment
algorithms AlignmentHdrs (1.0): Alignment header support AlignmentMatrices
(1.0): Sequence alignment similarity matrices Alignments (1.0): Sequence
alignment support Arrays (1.0): C++ library for parsing numpy arrays
AtomSearch (1.0): 3D atom search Atomic (1.0): Atomic-structure functionality
BILD (0.2): BILD file reader BasicActions (0.1): Basic actions for user-
defined specifier names BlastProtein (0.2): Search PDB/NR using BLAST BondRot
(1.0): Bond rotation support Bug-Reporter (1.0): Report bugs when an error
occurs BuildStructure (1.0): Create/modify structures Bumps (1.0): Find
protrusions in density maps ButtonPanel (1.0): Create custom user interface
panels Cage-Builder (1.0): Build polygonal meshes for oligomeric molecular
assemblies CellPack (1.0): Fetch cellPACK models from web ChemGroup (1.0):
Detect chemically functional groups Clashes (1.0): Find clashes/contacts in
structures ColorActions (1.0): Simple interface for coloring objects
ColorGlobe (1.0): Show directional resolution colored sphere CommandLine
(1.0): Command line support Connect-Structure (1.0): Add bonds to structures
that lack them Contacts (1.0): Display chain contact maps Core
(1.0rc202005091901): ChimeraX Core Package CoreFormats (1.0): ChimeraX session
support Crosslinks (1.0): Analyze crosslinks Crystal (1.0): Crystal symmetries
DataFormats (1.0): Data format management Dicom (1.0): Read medical imaging
and segmentations in DICOM format Dist-Monitor (1.0): Interactive distance
display Dist-UI (1.0): Distance measurement user interface Dssp (1.0):
Compute/assign secondary structure ExperimentalCommands (1.0): Experimental
commands FileHistory (1.0): File History Panel FunctionKey (1.0): Assign
function keys to run commands Geometry (1.0): Vector and coordinate system
routines Graphics (1.0): OpenGL graphics rendering HKCage (1.0): Create
icosahedral mesh of hexagons and pentagons Hbonds (1.0): Identify hydrogen
bonds in and among structures Help (0.9a1): Show ChimeraX Help IHM (1.0):
Integrative Hybrid Models file reader IO (1.0): Python convenience
input/output functions ImageFormats (1.0): Support for saving images Label
(1.0): Add text labels to graphics List-Info (0.1): Report attributes for
selected atomic data Log (1.0): Log support MD-crds (1.0): Molecular dynamics
support MLP (1.0): Molecular lipophilicity calculation MMTF (1.0): MMTF format
read/write Map (1.0): Density maps MapData (1.0): Volume data file formats
MapEraser (1.0): Map eraser MapFilter (1.0): Operations on maps MapFit (1.0):
Fit molecules into maps MapSeries (1.0): Volume series Markers (1.0): Place
markers on density maps Mask (1.0): Mask a volume to a surface MatchMaker
(1.0): Superimpose structures MedicalToolbar (1.0): Toolbar for medical image
analysis Meeting (1.0): Shared interactive VR sessions. ModelPanel (1.0):
ChimeraX Model Panel ModelSeries (1.0): Display sequences of models one by one
Modeller (1.0): Interface to Modeller Mol2 (1.0): Mol2 reader/writer Morph
(1.0): Morph atomic structures MouseModes (1.0): Provide right button mouse
mode tool Movie (1.0): Commands to record movies Nucleotides (0.1): Create
nucleotide-specific displays OpenCommand (1.0): Manages 'open' command
extensibility PDB (1.0): PDB format read/write PickBlobs (1.0): Measure and
color blobs Preset-Mgr (1.0): Preset management PubChem (1.0): PubChem fetch
Read-Pbonds (1.0): Read in pseudobonds from a file Registration (0.1):
Register ChimeraX RemoteControl (1.0): Control ChimeraX from other apps
ResidueFit (1.0): Display fit of residues to density map RestServer (0.1):
Starts REST server to execute commands from network requests Rotamer-Lib-Mgr
(1.0): Manage rotamer libraries RotamerLibs-Dunbrack (1.0): Dunbrack rotamer
library RotamerLibs-Dynameomics (1.0): Dynameomics rotamer library
RotamerLibs-Richardson (1.0): Richardson rotamer libraries SDF (1.0): SDF file
reader STL (1.0): STL file read/write SaveCommand (1.0): Manages 'save'
command extensibility Scheme-Mgr (1.0): HTTP scheme management Segger (1.0):
Segment map Segment (1.0): Watershed segment calculation SeqView (1.0):
Sequence viewer Shape (1.0): Make models for geometric shapes Shell (1.0):
Interactive Python shell Shortcuts (1.0): Button and keyboard shortcuts
ShowAttr (1.0): Render/select by attribute ShowSequences (1.0): Choose/show
structure sequences SideView (1.0): Side view of scene Smiles (1.0): SMILES
fetch SmoothLines (1.0): Smooth network of lines SpaceNavigator (1.0): Space
Navigator device support StdCommands (1.0): Standard commands Storm (1.0):
STORM file reader Struts (1.0): struts for 3D printing Surface (1.0): Surface
calculations SwapAA (1.0): Swap amino acid SwapRes (1.0): Swap residue side
chains TapeMeasure (1.0): Tape measure mouse mode Test (1.0): simple
regression test Texture (1.0): Apply images to surfaces Toolbar (0.1): Toolbar
Tug (1.0): Tug on atoms with molecular dynamics UI (1.0): ChimeraX user
interface VTK (1.0): Legacy VTK file reader and writer ViewDockX (0.1):
Analyze ligand-receptor docking results Vive (1.1): Virtual reality headset
support VolumeMenu (1.0): Volume menu WavefrontOBJ (1.0): Wavefront OBJ file
read/write WebServices (1.0): Web service and HTTP request support Zone (1.0):
Mouse mode to show atom and map zones gltf (1.0): Read/write glTF 3d scene
files mmCIF (1.1): mmCIF format read/write uniprot (1.0): UniProt database
support

  
Downloading bundle ChimeraX_Maestro-1.5-py3-none-any.whl  
Successfully installed ChimeraX-Maestro-1.5  
Installed ChimeraX-Maestro (1.5)  

> info

Unknown command: toolshed info  

> info

0 models  
  

> help info

> info path user

user versioned cache directory: /Users/pett/Library/Caches/ChimeraX/1.0  
user versioned config directory: /Users/pett/Library/Application
Support/ChimeraX/1.0  
user versioned data directory: /Users/pett/Library/Application
Support/ChimeraX/1.0  
user versioned log directory: /Users/pett/Library/Logs/ChimeraX/1.0  
user versioned state directory: /Users/pett/Library/Application
Support/ChimeraX/1.0  
user unversioned cache directory: /Users/pett/Library/Caches/ChimeraX  
user unversioned config directory: /Users/pett/Library/Application
Support/ChimeraX  
user unversioned data directory: /Users/pett/Library/Application
Support/ChimeraX  
user unversioned log directory: /Users/pett/Library/Logs/ChimeraX  
user unversioned state directory: /Users/pett/Library/Application
Support/ChimeraX  

> usage toolshed

Subcommands are:

  * toolshed cache
  * toolshed hide
  * toolshed install
  * toolshed list
  * toolshed reload
  * toolshed show
  * toolshed uninstall
  * toolshed url

  

> toolshed uninstall ChimeraX-Maestro

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/metadata.py", line 732, in __init__  
self._data = json.loads(data)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/json/__init__.py",
line 348, in loads  
return _default_decoder.decode(s)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/json/decoder.py",
line 337, in decode  
obj, end = self.raw_decode(s, idx=_w(s, 0).end())  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/json/decoder.py",
line 355, in raw_decode  
raise JSONDecodeError("Expecting value", s, err.value) from None  
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 275, in toolshed_uninstall  
deps = bi.dependents(logger)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 661, in dependents  
for d in DistributionPath().get_distributions():  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/database.py", line 213, in get_distributions  
self._generate_cache()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/database.py", line 167, in _generate_cache  
for dist in self._yield_distributions():  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/database.py", line 148, in _yield_distributions  
metadata = Metadata(fileobj=stream, scheme='legacy')  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/metadata.py", line 742, in __init__  
scheme=scheme)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/metadata.py", line 285, in __init__  
self.read_file(fileobj)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/metadata.py", line 383, in read_file  
self.set(field, value)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/metadata.py", line 478, in set  
if not scheme.is_valid_constraint_list(value):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/version.py", line 713, in is_valid_constraint_list  
return self.is_valid_matcher('dummy_name (%s)' % s)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/version.py", line 703, in is_valid_matcher  
self.matcher(s)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/version.py", line 104, in __init__  
r = self.parse_requirement(s)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/version.py", line 98, in parse_requirement  
return parse_requirement(s)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/util.py", line 237, in parse_requirement  
versions, _ = get_versions(s)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/util.py", line 220, in get_versions  
raise SyntaxError('invalid constraint: %s' % ver_remaining)  
File "<string>", line None  
SyntaxError: invalid constraint:  
  
File "", line None  
SyntaxError: invalid constraint:  
  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/util.py", line 220, in get_versions  
raise SyntaxError('invalid constraint: %s' % ver_remaining)  
  
See log for complete Python traceback.  
  

> toolshed uninstall ChimeraX-Maestro

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/metadata.py", line 732, in __init__  
self._data = json.loads(data)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/json/__init__.py",
line 348, in loads  
return _default_decoder.decode(s)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/json/decoder.py",
line 337, in decode  
obj, end = self.raw_decode(s, idx=_w(s, 0).end())  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/json/decoder.py",
line 355, in raw_decode  
raise JSONDecodeError("Expecting value", s, err.value) from None  
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/toolshed.py", line 275, in toolshed_uninstall  
deps = bi.dependents(logger)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 661, in dependents  
for d in DistributionPath().get_distributions():  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/database.py", line 213, in get_distributions  
self._generate_cache()  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/database.py", line 167, in _generate_cache  
for dist in self._yield_distributions():  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/database.py", line 148, in _yield_distributions  
metadata = Metadata(fileobj=stream, scheme='legacy')  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/metadata.py", line 742, in __init__  
scheme=scheme)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/metadata.py", line 285, in __init__  
self.read_file(fileobj)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/metadata.py", line 383, in read_file  
self.set(field, value)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/metadata.py", line 478, in set  
if not scheme.is_valid_constraint_list(value):  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/version.py", line 713, in is_valid_constraint_list  
return self.is_valid_matcher('dummy_name (%s)' % s)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/version.py", line 703, in is_valid_matcher  
self.matcher(s)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/version.py", line 104, in __init__  
r = self.parse_requirement(s)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/version.py", line 98, in parse_requirement  
return parse_requirement(s)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/util.py", line 237, in parse_requirement  
versions, _ = get_versions(s)  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/util.py", line 220, in get_versions  
raise SyntaxError('invalid constraint: %s' % ver_remaining)  
File "<string>", line None  
SyntaxError: invalid constraint:  
  
File "", line None  
SyntaxError: invalid constraint:  
  
File
"/Applications/ChimeraX-1.0-rc-2020.05.09.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/distlib/util.py", line 220, in get_versions  
raise SyntaxError('invalid constraint: %s' % ver_remaining)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.16
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac16,2
      Processor Name: Intel Core i5
      Processor Speed: 2.8 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Memory: 16 GB
      Boot ROM Version: 232.0.0.0.0
      SMC Version (system): 2.32f20

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G3020)
      Kernel Version: Darwin 18.7.0
      Time since boot: 5:38

Graphics/Displays:

    Intel Iris Pro Graphics 6200:

      Chipset Model: Intel Iris Pro Graphics 6200
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1622
      Revision ID: 0x000a
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        iMac:
          Display Type: LCD
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DisplayPort

[Greg Couch]

This error should be no more. Much better compatibility testing before installing. Don't use distlib anymore. Newer version of setuptools. Etc.