yaml library parses demes named "y" as booleans with the value TRUE

[grahamgower]

Four valid test cases from the demes-spec repo (listed below) cannot be parsed because they contain a deme with the name "y". The yaml library only supports yaml v1.1 (not v1.2), and thus interprets these deme names as being a boolean type with the value TRUE. See #9.

toplevel_defaults_deme_01.yaml
successors_predecessors_01.yaml
deme_end_time_01.yaml

[reedacartwright]

I believe that tags or strings can be use to override this behavior, and this should be noted in the documentation.

[IsabelMarleen]

Minor correction, unicode_deme_name_04.yaml could not be parsed in #9 because of an unrelated unicode issue, see #11.

I believe that tags or strings can be use to override this behavior, and this should be noted in the documentation.

Do you mean specifying a custom handling function in the yaml parser? Part of the issue is that the values are not quoted, so in the yaml file it just says - name: y. According to this issue vubiostat/r-yaml#122 on the yaml parsing library repo, the value being unquoted means that it cannot be fixed without compiler modifications.

[grahamgower]

Minor correction, unicode_deme_name_04.yaml could not be parsed in #9 because of an unrelated unicode issue, see #11.

Ah, yep, thanks. I removed it from the list.

I believe that tags or strings can be use to override this behavior, and this should be noted in the documentation.

Do you mean specifying a custom handling function in the yaml parser? Part of the issue is that the values are not quoted, so in the yaml file it just says - name: y. According to this issue vubiostat/r-yaml#122 on the yaml parsing library repo, the value being unquoted means that it cannot be fixed without compiler modifications.

No, I think Reed means that one can write !!str in the yaml file to force the type to be a string. E.g.

time_units: generations
demes:
 - name: !!str y
   epochs:
    - start_size: 1000

It would be nice if we could make this work by somehow telling the yaml parser that the name field of a deme is always a string, but I'm not sure that's possible. Maybe the handler arg to the yaml.load() function could be used somehow?

[reedacartwright]

Given that y can be interpreted in the standard as a boolean, and name is supposed to be a string, it seems to me that the input test file is the problem, not the library. The demes file should look something like this:

time_units: generations
demes:
 - name: "y"
   epochs:
    - start_size: 1000

[grahamgower]

Given that y can be interpreted in the standard as a boolean, and name is supposed to be a string, it seems to me that the input test file is the problem, not the library.

Yes I think you're right that we should fix the test files. It's a shame that YAML 1.2 parsers are not widespread, given that it's now 14 years old.

[IsabelMarleen]

Alright, then I'll implement a custom handling function for "n" and "y", so that it works when the test files have changed, and then I'll close this issue.

Thank you both for your help!

[grahamgower]

Oh, you shouldn't need to have a custom handler. When the source file has the y in quotes, like name: "y", this will be interpreted as a string in YAML v1.1.

[grahamgower]

These test files have now been fixed in the spec repository. Updating to use the latest spec test files here should close this issue.

[IsabelMarleen]

I just updated to the latest spec test files in Pull Request #13 and will close this issue now.