PESummary not working with python 3.11
A quick investigation suggests that inspect.getargspec
does not exist anymore in python 3.11. I think replacing it with getargs
(as suggested by the error message) or getfullargspec
should work here.
Traceback (most recent call last):
File "/scratch/elise.sanger/envs/tgrflow-dev/bin/summarypages", line 8, in <module>
sys.exit(main())
^^^^^^
File "/scratch/elise.sanger/envs/tgrflow-dev/lib/python3.11/site-packages/pesummary/cli/summarypages.py", line 201, in main
_parser.add_all_groups_to_parser()
File "/scratch/elise.sanger/envs/tgrflow-dev/lib/python3.11/site-packages/pesummary/gw/cli/parser.py", line 346, in add_all_groups_to_parser
super(ArgumentParser, self).add_all_groups_to_parser()
File "/scratch/elise.sanger/envs/tgrflow-dev/lib/python3.11/site-packages/pesummary/core/cli/parser.py", line 550, in add_all_groups_to_parser
self.add_core_group()
File "/scratch/elise.sanger/envs/tgrflow-dev/lib/python3.11/site-packages/pesummary/core/cli/parser.py", line 503, in add_core_group
return self.add_known_options_to_parser_from_key(core_group, "core")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/scratch/elise.sanger/envs/tgrflow-dev/lib/python3.11/site-packages/pesummary/core/cli/parser.py", line 496, in add_known_options_to_parser_from_key
return self.add_known_options_to_parser(options, parser=parser)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/scratch/elise.sanger/envs/tgrflow-dev/lib/python3.11/site-packages/pesummary/core/cli/parser.py", line 616, in add_known_options_to_parser
return self.add_additional_options_to_parser(_options, parser=parser)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/scratch/elise.sanger/envs/tgrflow-dev/lib/python3.11/site-packages/pesummary/core/cli/parser.py", line 592, in add_additional_options_to_parser
arglist = inspect.getargspec(action_class).args
^^^^^^^^^^^^^^^^^^
AttributeError: module 'inspect' has no attribute 'getargspec'. Did you mean: 'getargs'?