add fix for JSON passing into query method, add tests

[sierra-moxon]

build_query was defaulting to return_json=True, returning a JSON string. But query() passes its input directly to requests, which expects a dict. This changes build_query to default to return_json=False and updates query()'s type hint from str to dict to match what it needs. The return_json=True option still works if you need a JSON string for something else.

Added tests covering the default return type, query structure, and that build_query's output type matches query's expected input.

[Copilot]

Pull request overview

This PR fixes a mismatch between build_query()’s default return type and what query() passes to requests.post(..., json=...), by making the default query payload a Python dict instead of a JSON string.

Changes:

• Changed build_query(..., return_json=...) default to False so it returns a dict by default.
• Updated query()’s parameter type hint and docstring to reflect that it expects a dict.

Comments suppressed due to low confidence (1)

TCT/trapi.py:50

• The build_query docstring now says the default return is a dict, but the example still shows (and quotes) a JSON/string-like return. Please update the example to either show a dict return value or call build_query(..., return_json=True) so the docs match the new default behavior.

    A dict (default) or json string if return_json=True

    Examples
    --------
    In this example, we want all genes that physically interact with gene 3845.
    >>> build_query(['NCBIGene:3845'], ['biolink:Gene'], ['biolink:physically_interacts_with'])

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