Declarative YAML test coverage for gxformat2.cytoscape

[jmchilton]

Summary

• Add gxformat2/examples/expectations/cytoscape.yml with 13 declarative cases covering cytoscape_elements output (group counts, input node shape, tool step shape, edge shape, int input step type, subworkflow classes, subworkflow edges with named output, multi-data inputs, real-workflow repo_link from tool_shed_repository, and a real-workflow node-id smoke). Consumed by the existing DeclarativeTestSuite harness so downstream ports (TypeScript galaxy-tool-util) can sync and reuse them.
• Register cytoscape_elements_to_list, cytoscape_node_ids, cytoscape_edge_ids in tests/test_interop_tests.py OPERATIONS. The two _ids variants return list-of-string for value_set / value_any_contains assertions; _to_list returns the canonical flat list-of-dicts.
• Fixtures reuse existing synthetic-* / real-* files — no new workflow fixtures.
• Thin tests/test_cytoscape.py retained for things that aren't a pure function of (workflow dict) → result: CLI JSON/HTML output modes, render_html, _input_type_str on a string[] input, and the Java interop generator.
• Fix latent test pollution: test_interop_generation was leaking a tmp*.gxwf.yml / tmp*.gxwf.cytoscape.json pair into tests/examples/cytoscape/ on each run because write_cytoscape_elements_for_string named its staging file via tempfile.NamedTemporaryFile. Now takes an explicit filename arg (with_report.gxwf.yml); write_cytoscape_elements skips its self-copy when src == dst.

Mirrors #194 (mermaid) one-for-one.

Test plan

• pytest tests/ — 642 passed, 8 skipped (no regressions; 13 new declarative cases × 2 = 28 over the previous 631 + 1 thinned-out test ≈ 642)
• Re-run leaves tests/examples/cytoscape/ with exactly 4 deterministic files (no new tmp* accumulation)
• TypeScript port consumes cytoscape.yml via make sync-workflow-expectations (will land alongside the TS cytoscape port, see WF_VIZ_1)

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 41.03%. Comparing base (06e8536) to head (b1839f7).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #196   +/-   ##
=======================================
  Coverage   41.03%   41.03%           
=======================================
  Files          51       51           
  Lines        1974     1974           
  Branches      441      441           
=======================================
  Hits          810      810           
  Misses       1047     1047           
  Partials      117      117           

Flag	Coverage Δ
unittests	41.03% <ø> (ø)

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