[Patch] Implement Ontodocker Client

[mbruns91]

Implement the Ontodocker service client via porting from branch "refactor_project_structure":

• filled previously empty courier/services/ontodocker/* modules with the full implementation (client wiring + endpoints/datasets/SPARQL resources + models).
• Updated Ontodocker internals to match the new transport layout (e.g. courier.transport.url.join_url) and fixed minor upload_graph Turtle serialization/file-writing behavior.
• add unit tests for OntodockerClient: tests client wiring plus resource behavior/validation: URL construction and request dispatch for endpoints/datasets/SPARQL (incl. legacy endpoint parsing/rectification and token header propagation), using a fake session instead of real HTTP.
• rewrite ontodocker.pyas a compatibility wrapper around courier.services.ontodocker.OntodockerClient and _compat helpers.
  • Each legacy entry point calls _warn_deprecated(...) (emits DeprecationWarning, stacklevel=2).
  • Re-exported legacy helpers via _compat (rectify_endpoints, extract_dataset_names, make_dataframe).
  • add tests/unit/test_ontodocker_legacy_shim.py to verify delegation to OntodockerClient and expected warnings/behaviors.
• courier/__init__.py
  • Now also exports OntodockerClient at top level: courier.OntodockerClient.
• notebooks:
  • add notebooks to demonstrate basic usage of HttpClient and OntodockerClient. Uses mock-ups to avoid relying on actually running services.

[github-actions]

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

[codecov]

Codecov Report

❌ Patch coverage is 91.28205% with 17 lines in your changes missing coverage. Please review.
✅ Project coverage is 89.30%. Comparing base (dc52d39) to head (edc3c80).

Files with missing lines	Patch %	Lines
courier/ontodocker.py	68.88%	14 Missing ⚠️
courier/services/ontodocker/sparql.py	91.42%	3 Missing ⚠️

Additional details and impacted files

@@               Coverage Diff                @@
##           base_client      #29       +/-   ##
================================================
+ Coverage        50.00%   89.30%   +39.30%     
================================================
  Files               10       17        +7     
  Lines              396      449       +53     
================================================
+ Hits               198      401      +203     
+ Misses             198       48      -150     

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[mbruns91]

Sorry, I rebased the branch onto the updated base (base_client), which rewrote the commit history (same changes, new commit hashes). That makes the update a non-fast-forward, so a normal push is rejected. I used --force-with-lease to safely update the remote to the rebased history while refusing to overwrite any unexpected new remote commits.

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[mbruns91]

Closed because too hard too read. We reach the same result by merging #31 #32 and #33.