OpenFermion-PySCF
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Set parse_arg option of pyscf.gto.mole.Mole.build to False
pyscf.gto.mole.Mole.build method has parse_arg option, which specifies whether pyscf should parse command line arguments or not:
https://sunqm.github.io/pyscf/gto.html#pyscf.gto.mole.Mole.build
The default value of the option is True and it sometimes results in a conflict with command line arguments parsed by a user script.
cf. pyscf/pyscf#470
I think the root problem is on pyscf side (they should set the default value to False), but I think it is good to specify the argument explicitly in OpenFermion-PySCF; for example here:
https://github.com/quantumlib/OpenFermion-PySCF/blob/b1081b90a372afc68ee8b265d7585afdcbe94c7b/openfermionpyscf/_run_pyscf.py#L43