id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4460 Python script on startup command-line, QTimer errors Tom Goddard Eric Pettersen "If I start ChimeraX from a shell with a Python script argument and the Python script raises an error I get a hard to follow traceback where the actual error is listed followed by about 6 QTimer errors and ChimeraX fails to start. Should give just the error that actually occurred in the script, and also ChimeraX should probably remain running. Here's my example Python test.py script. ChimeraX apparently does not keep the __file__ variable in the script global namespace so it raises an error. print ('starting test.py with __file__ = ', __file__) $ ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/MacOS/ChimeraX"" test.py ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/MacOS/ChimeraX"" test.py Traceback (most recent call last): File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py"", line 813, in init commands.run(sess, 'open %s' % StringArg.unparse(arg)) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/open_command/cmd.py"", line 179, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/open_command/cmd.py"", line 404, in collated_open return func(*func_args, **func_kw) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core_formats/__init__.py"", line 48, in open return open_python_script(session, data, file_name) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/scripting.py"", line 82, in open_python_script _exec_python(session, code, argv) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/scripting.py"", line 59, in _exec_python exec(code, sandbox.__dict__) File ""test.py"", line 1, in print ('starting test.py with __file__ = ', __file__) NameError: name '__file__' is not defined Error in sys.excepthook: Traceback (most recent call last): File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py"", line 297, in ehook self.session.ui.thread_safe(self.report_exception, exc_info=exc_info) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 363, in thread_safe func(*args, **kw) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py"", line 443, in report_exception self.info(tb_msg, is_html=True) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py"", line 388, in info self._log(Log.LEVEL_INFO, msg, add_newline, image, is_html, File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py"", line 498, in _log if log.log(*args): File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py"", line 340, in log self.show_page_source() File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py"", line 344, in show_page_source self.session.ui.thread_safe(self._show) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 363, in thread_safe func(*args, **kw) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py"", line 348, in _show self.regulating_timer.start(100) RuntimeError: wrapped C/C++ object of type QTimer has been deleted Original exception was: Traceback (most recent call last): File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 202, in cx_qt_msg_handler self.session.logger.method_map[log_level](msg_string) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py"", line 465, in warning self._log(Log.LEVEL_WARNING, msg, add_newline, image, is_html, File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py"", line 498, in _log if log.log(*args): File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py"", line 340, in log self.show_page_source() File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py"", line 344, in show_page_source self.session.ui.thread_safe(self._show) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 363, in thread_safe func(*args, **kw) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py"", line 348, in _show self.regulating_timer.start(100) RuntimeError: wrapped C/C++ object of type QTimer has been deleted Error in sys.excepthook: Traceback (most recent call last): File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py"", line 297, in ehook self.session.ui.thread_safe(self.report_exception, exc_info=exc_info) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 363, in thread_safe func(*args, **kw) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py"", line 443, in report_exception self.info(tb_msg, is_html=True) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py"", line 388, in info self._log(Log.LEVEL_INFO, msg, add_newline, image, is_html, File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py"", line 498, in _log if log.log(*args): File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py"", line 340, in log self.show_page_source() File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py"", line 344, in show_page_source self.session.ui.thread_safe(self._show) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 363, in thread_safe func(*args, **kw) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py"", line 348, in _show self.regulating_timer.start(100) RuntimeError: wrapped C/C++ object of type QTimer has been deleted Original exception was: Traceback (most recent call last): File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 202, in cx_qt_msg_handler self.session.logger.method_map[log_level](msg_string) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py"", line 465, in warning self._log(Log.LEVEL_WARNING, msg, add_newline, image, is_html, File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py"", line 498, in _log if log.log(*args): File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py"", line 340, in log self.show_page_source() File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py"", line 344, in show_page_source self.session.ui.thread_safe(self._show) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 363, in thread_safe func(*args, **kw) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py"", line 348, in _show self.regulating_timer.start(100) RuntimeError: wrapped C/C++ object of type QTimer has been deleted Error in sys.excepthook: Traceback (most recent call last): File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py"", line 297, in ehook self.session.ui.thread_safe(self.report_exception, exc_info=exc_info) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 363, in thread_safe func(*args, **kw) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py"", line 443, in report_exception self.info(tb_msg, is_html=True) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py"", line 388, in info self._log(Log.LEVEL_INFO, msg, add_newline, image, is_html, File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py"", line 498, in _log if log.log(*args): File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py"", line 340, in log self.show_page_source() File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py"", line 344, in show_page_source self.session.ui.thread_safe(self._show) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 363, in thread_safe func(*args, **kw) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py"", line 348, in _show self.regulating_timer.start(100) RuntimeError: wrapped C/C++ object of type QTimer has been deleted Original exception was: Traceback (most recent call last): File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 202, in cx_qt_msg_handler self.session.logger.method_map[log_level](msg_string) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py"", line 465, in warning self._log(Log.LEVEL_WARNING, msg, add_newline, image, is_html, File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/logger.py"", line 498, in _log if log.log(*args): File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py"", line 340, in log self.show_page_source() File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py"", line 344, in show_page_source self.session.ui.thread_safe(self._show) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 363, in thread_safe func(*args, **kw) File ""/Users/goddard/Desktop/ChimeraX April 1 2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/log/tool.py"", line 348, in _show self.regulating_timer.start(100) RuntimeError: wrapped C/C++ object of type QTimer has been deleted " defect closed moderate Logging fixed all ChimeraX