Handle tinyarray in session save/restore

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-09-11)
Description
Using the zone mouse mode and saving session causes an error and session is not saved.  Caused by View center of rotation set to a tinyarray which is not handled by session saving.

Need session saving to handle tinyarray values.  Currently trying to save a tinyarray in a session raises an error and session saving fails, and it is difficult to figure out where the tinyarray comes from.  

Log:
UCSF ChimeraX version: 0.8 (2018-09-11)  
How to cite UCSF ChimeraX  

open 1a0m format mmCIF fromDatabase pdb ↵

1a0m title:  
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more&nbspinfo...;]  
  
Chain information for 1a0m #1  
---  
Chain | Description  
A B | α-conotoxin [TYR15]-epi  
  
  

ui mousemode rightMode zone ↵

save test.cxs ↵

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

Traceback (most recent call last):  
  File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 205, in execute  
    cmd.run(cmd_text)  
  File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/save.py", line 61, in save  
    fmt.export(session, filename, fmt.nicknames[0], **kw)  
  File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 198, in export  
    result = self.export_func(session, path, **kw)  
  File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 717, in save  
    session.save(output, version=version)  
  File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 490, in save  
    mgr.discovery(self._state_containers)  
  File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 234, in discovery  
    self.processed[key] = self.process(obj)  
  File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 265, in process  
    return copy_state(data, convert=self._add_obj)  
  File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/state.py", line 172, in copy_state  
    return _copy(data)  
  File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/state.py", line 159, in _copy  
    items = [(_copy(k), _copy(v)) for k, v in data.items()]  
  File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/state.py", line 159, in <listcomp>  
    items = [(_copy(k), _copy(v)) for k, v in data.items()]  
  File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/state.py", line 170, in _copy  
    return convert(data)  
  File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 240, in _add_obj  
    uid = _UniqueName.from_obj(self.session, obj)  
  File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 128, in from_obj  
    obj_cls.__module__, obj_cls.__name__))  
RuntimeError: No bundle information for tinyarray.ndarray_float  
  

RuntimeError: No bundle information for tinyarray.ndarray_float  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/session.py", line 128, in from_obj  
obj_cls.__module__, obj_cls.__name__))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GTX 680MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation

[Tom Goddard]

Since atom coordinates use tinyarray these values are likely to get into session saving state of lots of tools. They need to be saved and restored like numpy arrays.

[Greg Couch]

Added support for tinyarray.ndarray_float, .ndarray_int, and .ndarray_complex.