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.._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 (.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.._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 (.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.._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..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..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' -> : 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