Command line parsing error when Python shell open

[Eric Pettersen]

open 3fx2
-- start Python shell --
color blue

produces:

Traceback (most recent call last):
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/cmd_line/gui.py", line 120, in on_enter
cmd.run(cmd_text)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 2086, in run
prev_annos = self._process_positional_arguments()
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 1948, in _process_positional_arguments
value, text = self._parse_arg(anno, text, session, False)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 1795, in _parse_arg
value, replacement, rest = annotation.parse(text, session)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 1040, in parse
return anno.parse(text, session)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 901, in parse
aspec, text, rest = AtomSpecArg.parse(text, session)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/atomspec.py", line 84, in parse
return AtomSpecArg._parse_unquoted(text, session)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/atomspec.py", line 132, in _parse_unquoted
from ._atomspec import _atomspecParser
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/_atomspec.py", line 16, in <module>
from grako.parsing import graken, Parser
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/grako/init.py", line 6, in <module>
from grako import tool
File "grako/tool.py", line 16, in init grako.tool (grako/tool.c:4415)
from grako.parser import GrakoGrammarGenerator
File "grako/parser.py", line 17, in init grako.parser (grako/parser.c:1456)
from grako.bootstrap import GrakoBootstrapParser
File "grako/bootstrap.py", line 15, in init grako.bootstrap (grako/bootstrap.c:36008)
from grako.parsing import graken, Parser
File "grako/parsing.py", line 20, in init grako.parsing (grako/parsing.c:1647)
from grako.contexts import ParseContext, graken
File "grako/contexts.py", line 13, in init grako.contexts (grako/contexts.c:22548)
from grako.color import Fore, Style
File "grako/color.py", line 8, in init grako.color (grako/color.c:924)
_colorama.init(autoreset=True)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/colorama/initialise.py", line 37, in init
wrap_stream(orig_stdout, convert, strip, autoreset, wrap)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/colorama/initialise.py", line 76, in wrap_stream
convert=convert, strip=strip, autoreset=autoreset)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/colorama/ansitowin32.py", line 67, in init
strip = conversion_supported or (not wrapped.closed and not is_a_tty(wrapped))
AttributeError: 'PseudoFileOut' object has no attribute 'closed'

[Greg Couch]

Worked around by extending wx's PseudoFile class (the base class of PseudoFileOut) to have a 'closed' attribute, which is part of the Python file API. Unfortunately, closed is always false because the PseudoFile{In,Out,Err} API is missing a way to detect if the encapsulated object is gone. So, in this case, colorama initializes, but generates a traceback, when ChimeraX exits, trying to write to a dead object. But that is better than having 'color blue' fail.

[Greg Couch]

The next version of grako will require explicit colorization and thus the backtrace on exit should go away.