common/naming.py: a GraphQL-encoded name can begin with the reserved '__' prefix, and the warning reports the unencoded name #65

NameCompatibility with the GraphQL profile can produce names that begin with __, a prefix GraphQL reserves for introspection (October 2021, §2.1.9). Two paths in packages/linkml/src/linkml/generators/common/naming.py do it:

• _no_heading_digits prefixes a digit-leading name with __, giving __0, __1, __3_prime_utr.
• _only_alphanum_underscore / _transform_char replaces a character that is not alphanumeric with its Unicode name wrapped in __. When that character is first, the name begins with __: __PLUS_SIGN__, __HYPHEN_MINUS__, __FULL_STOP__, __QUESTION_MARK__.

Both reach the biolink reference snapshot. After #63 the snapshot parses, and these are nine of its remaining validation errors:

Name '__0' must not begin with '__', which is reserved by GraphQL introspection.
Name '__PLUS_SIGN__' must not begin with '__', which is reserved by GraphQL introspection.

Note the substitution is only a problem at the start of a name: an enum value such as AD-02 encodes to AD__HYPHEN_MINUS__02, which is legal.

A separate cosmetic bug belongs with this one. Both functions log output before the encoding is assigned to it, so the warning reports the unencoded name as the encoded one:

WARNING:root:Name 'AD-02' contains a character illegal in GraphQL, the resulting encoded name is AD-02

That makes the warning useless for diagnosing exactly the names this issue is about, and it is noisy: a single run over a schema with ISO 3166-2 region codes emits it thousands of times.

NameCompatibility is used only by graphqlgen (grep-verified), so a fix is contained and cannot disturb another generator. Upstream linkml/linkml has since added Python-keyword helpers to this module but has not touched either path.