Deprecate CifParser init support of filename as StringIO

[DanielYang59]

Summary

• Move CIF parsing logics from __init__ of CifParser to from_str
• Revert accidentally removed filename as TextIOWrapper support (though this may not be intended) in Improve type annotations and comments for io.cif #3820, add a deprecation warning reverted, guess this was not intended, also doesn't agree with type/docstring
• Currently the filename of CifParser constructor could also be the string for the CIF file itself (StringIO), it's a bit confusing (cc @ka-sarthak) but I guess this was intended to support from_str. After this refactoring this could be deprecated I guess

[ka-sarthak]

Thanks, @DanielYang59, for taking this up. My initial confusion was whether using a file handler is supported in the filename parameter, like:

cif = 'my_path.cif'
with open(cif) as file:
    parser = CifParser(filename=file) 

# output: "TypeError: Unsupported file format."

I think this used to work at some point, even though it might not have been intended. It's more of my negligence to misinterpret the interface.

I like that you make the error statement explicit now, as Unsupported file format alone is confusing, given that the file format (.cif) is correct.