OntodockerClient: Refactor query_df()

[mbruns91]

Refactor OntodockerClient.query_df() to re-use query_raw() instead of using its own Implementation.
This way, we also get rid of SPARQLWrapper as dependency.

[github-actions]

👈 Launch a binder notebook on branch pyiron/courier/refactor_query_df

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 89.97%. Comparing base (d8df495) to head (34da671).

Additional details and impacted files

@@                  Coverage Diff                  @@
##           ontodocker_client      #32      +/-   ##
=====================================================
- Coverage              90.20%   89.97%   -0.23%     
=====================================================
  Files                     17       17              
  Lines                    449      449              
=====================================================
- Hits                     405      404       -1     
- Misses                    44       45       +1     

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[Copilot]

Pull request overview

Refactors OntodockerClient.sparql.query_df() to reuse the internal HTTP-based query_raw() pathway (removing the prior SPARQLWrapper-based approach) and updates result-to-DataFrame compatibility behavior and tests accordingly.

Changes:

• Reimplemented SparqlResource.query_df() to call query_raw() and json.loads() the response.
• Updated _compat.make_dataframe() to build rows by requested columns and yield None for missing variables.
• Adjusted unit tests to assert HTTP GET usage/headers and the new missing-variable behavior.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

File	Description
courier/services/ontodocker/sparql.py	query_df() now reuses query_raw() and decodes SPARQL results JSON directly.
courier/services/ontodocker/_compat.py	DataFrame construction now follows requested column order and fills missing bindings with None.
tests/unit/test_ontodocker_client.py	Updates query_df() test to validate GET/params/Accept header behavior and token handling via session headers.
tests/unit/services/ontodocker/test_compat.py	Updates expectation for missing variables in bindings to yield None instead of raising.

Comments suppressed due to low confidence (1)

courier/services/ontodocker/_compat.py:123

• make_dataframe() now fills missing variables in a binding with None instead of raising due to row/column length mismatch. The docstring doesn't mention this behavioral change, which is important for callers interpreting missing data. Consider documenting that missing binding entries for requested columns yield None (or NA).

def make_dataframe(result: dict, columns: list[str]) -> pd.DataFrame:
    """Convert a SPARQL JSON result into a pandas DataFrame.

    Parameters
    ----------
    result
        SPARQL JSON result containing `result["results"]["bindings"]`.
    columns
        Column labels for the resulting DataFrame.

    Returns
    -------
    df
        DataFrame containing one row per binding.

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