[codex] refactor: rename ligand receptor workflow to cci

[hutaobo]

Summary

This PR performs the intentional breaking rename from the ligand-receptor workflow to the CCI/TopoLink-CCI workflow across source, tests, docs, tutorials, benchmark scaffolding, and tracked topology artifacts.

What changed

• Replaces the public API with pyXenium.cci.cci_topology_analysis and removes the old public pyXenium.ligand_receptor package.
• Renames user-facing score/output language from LR_score to CCI_score, and renames the input argument from lr_pairs to interaction_pairs while preserving biological ligand/receptor table columns for CCI LR-resource mode.
• Renames the Atera benchmark workflow from atera-lr / lr_2026_atera to atera-cci / cci_2026_atera, including env names, runner utilities, CLI docs, and scaffold files.
• Updates RTD/API/tutorial navigation to publish pyXenium.cci, cci.html, and cci_benchmarking.html instead of the old ligand-receptor pages.
• Updates tracked manuscript/topology artifacts and GMI/contour references to use CCI terminology where they expose pyXenium-generated interaction summaries.

Breaking change

Old public imports and CLI names are intentionally not retained:

• pyXenium.ligand_receptor is removed.
• ligand_receptor_topology_analysis is removed from the public API.
• pyxenium benchmark atera-lr ... is replaced by pyxenium benchmark atera-cci ....

Third-party API names such as Squidpy ligrec, COMMOT ligand-receptor database calls, and R package argument names are kept where required by external packages.

Validation

• python -m compileall src\pyXenium benchmarking\cci_2026_atera\scripts benchmarking\cci_2026_atera\runners\python
• python -m pytest tests/test_topology_analysis.py tests/test_cci_benchmarking.py tests/test_cci_benchmark_cli.py tests/test_pdc_benchmark_scripts.py tests/test_validation_module.py -q
• python -m pytest tests/test_cli.py tests/test_contour_boundary_ecology.py tests/test_gmi_pdc_plan.py -q
• Import check: from pyXenium.cci import cci_topology_analysis passes.
• Old import check: from pyXenium.ligand_receptor import ligand_receptor_topology_analysis raises ModuleNotFoundError.
• Clean staged-tree Sphinx build: python -m sphinx -b html docs docs\_build\html.
• Grep gate confirms no old public API strings remain in the committed tree: pyXenium.ligand_receptor, ligand_receptor_topology_analysis, atera-lr, lr_2026_atera, LR_score, lr_pairs, pyx-lr, r-lr.

Notes

The local working tree still contains unrelated unstaged WIP and generated benchmark outputs. They were intentionally excluded from this PR.

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[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Export the renamed cervical CCI panel constant

pyXenium.validation now advertises DEFAULT_ATERA_WTA_CERVICAL_LR_PANEL, but atera_wta_cervical_end_to_end.py only defines DEFAULT_ATERA_WTA_CERVICAL_CCI_PANEL. Because __getattr__ resolves this mapping dynamically, any code that imports or accesses DEFAULT_ATERA_WTA_CERVICAL_LR_PANEL (including from pyXenium.validation import * via __all__) will raise AttributeError at runtime instead of returning the panel constant.

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