from chimerax.core.toolshed import NewerVersionQuery
NewerVersionQuery.SESSION_SAVE=False

from chimerax.core.commands import run
run(session, "save /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison_linux.cxs")
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py:262, in _SaveManager.discovery(self, containers)
    261 try:
--> 262     self.processed[key] = self.process(obj, parents)
    263 except UserError:

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py:299, in _SaveManager.process(self, obj, parents)
    298     return add_obj(obj, parents)
--> 299 return copy_state(data, convert=convert)

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/state.py:219, in copy_state(data, convert)
    217         return convert(data)
--> 219 return _copy(data)

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/state.py:204, in copy_state.<locals>._copy(data)
    203 if isinstance(data, Mapping):
--> 204     items = [(_copy(k), _copy(v)) for k, v in data.items()]
    205 elif isinstance(data, numpy.ndarray):

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/state.py:204, in <listcomp>(.0)
    203 if isinstance(data, Mapping):
--> 204     items = [(_copy(k), _copy(v)) for k, v in data.items()]
    205 elif isinstance(data, numpy.ndarray):

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/state.py:204, in copy_state.<locals>._copy(data)
    203 if isinstance(data, Mapping):
--> 204     items = [(_copy(k), _copy(v)) for k, v in data.items()]
    205 elif isinstance(data, numpy.ndarray):

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/state.py:204, in <listcomp>(.0)
    203 if isinstance(data, Mapping):
--> 204     items = [(_copy(k), _copy(v)) for k, v in data.items()]
    205 elif isinstance(data, numpy.ndarray):

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/state.py:217, in copy_state.<locals>._copy(data)
    215 else:
    216     # Use state methods to convert object to primitives
--> 217     return convert(data)

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py:298, in _SaveManager.process.<locals>.convert(obj, parents, add_obj)
    297 def convert(obj, parents=parents + (obj,), add_obj=self._add_obj):
--> 298     return add_obj(obj, parents)

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py:270, in _SaveManager._add_obj(self, obj, parents)
    269 def _add_obj(self, obj, parents=()):
--> 270     uid = _UniqueName.from_obj(self.session, obj)
    271     self._found_objs.append(uid)

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py:143, in _UniqueName.from_obj(cls, session, obj)
    142     if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
--> 143         raise RuntimeError(
    144             'Unable to restore objects of %s class in %s bundle'
    145             ' because the class name is not listed in the name to class table'
    146             ' for session restore' %
    147             (obj_cls.__name__, bundle_info.name))
    149 if not known_class and bundle_info != 'builtin':

RuntimeError: Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore

During handling of the above exception, another exception occurred:

ValueError                                Traceback (most recent call last)
Cell In[2], line 2
      1 from chimerax.core.commands import run
----> 2 run(session, "save /home/dzyla/OneDrive/Code/work/FectoFab_paper/figure_notebooks/F_mabs_session_comparison_linux.cxs")

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/run.py:38, in run(session, text, log, downgrade_errors, return_json, return_list)
     36 command = Command(session)
     37 try:
---> 38     results = command.run(text, log=log, return_json=return_json)
     39 except UserError as err:
     40     if downgrade_errors:

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py:2897, in Command.run(self, text, log, log_only, return_json, _used_aliases)
   2895     kw_args['log'] = log
   2896 try:
-> 2897     result = ci.function(session, **kw_args)
   2898 except CancelOperation:
   2899     if not self._ci.self_logging:

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/cmd.py:75, in cmd_save(session, file_name, rest_of_line, log)
     73         session.logger.info(more_log_info, is_html=True)
     74     raise
---> 75 Command(session, registry=registry).run(provider_cmd_text, log=log)

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py:2897, in Command.run(self, text, log, log_only, return_json, _used_aliases)
   2895     kw_args['log'] = log
   2896 try:
-> 2897     result = ci.function(session, **kw_args)
   2898 except CancelOperation:
   2899     if not self._ci.self_logging:

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/cmd.py:90, in provider_save(session, file_name, format, **provider_kw)
     88 try:
     89     saver_info = provider_info.bundle_info.run_provider(session, provider_info.format_name, mgr)
---> 90     saver_info.save(session, path, **provider_kw)
     91 except (IOError, PermissionError, OSError) as e:
     92     raise UserError("Cannot save '%s': %s" % (file_name, e))

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core_formats/__init__.py:84, in _SessionAPI.run_provider.<locals>.Info.save(self, session, path, **kw)
     82 def save(self, session, path, **kw):
     83     from chimerax.core.session import save as cxs_save
---> 84     return cxs_save(session, path, **kw)

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py:901, in save(session, path, version, compress, include_maps)
    899 session.session_file_path = path
    900 try:
--> 901     session.save(output, version=version, include_maps=include_maps)
    902 except Exception:
    903     if open_func is not None:

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py:625, in Session.save(self, stream, version, include_maps)
    621 fserialize(stream, metadata)
    622 # guarantee that bundles are serialized first, so on restoration,
    623 # all of the related code will be loaded before the rest of the
    624 # session is restored
--> 625 mgr.discovery(self._state_containers)
    626 fserialize(stream, mgr.bundle_infos())
    627 # TODO: collect OrderDAGError exceptions from walk and analyze

File /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py:266, in _SaveManager.discovery(self, containers)
    264     raise	# For example map size is larger than 4 Gbyte msgpack limit.
    265 except Exception as e:
--> 266     raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
    267 self.graph[key] = self._found_objs

ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at 0x7f71a2b0a690>: Unable to restore objects of NewerVersionQuery class in ChimeraX-Core bundle because the class name is not listed in the name to class table for session restore