LVP bug fixes

[dosumis]

Fixes for master reports, bubble plots.

[Copilot]

Pull request overview

This pull request implements bug fixes for master reports and bubble plots in the LangPA validation tools. The changes primarily address visualization improvements, dependency updates, and system prompt handling in the DeepSearch service.

Key Changes

• Updated bubble plot visualization to use program indices on axes with overlap-count-based bubble sizing, replacing the previous gene Jaccard/name similarity scatter plot approach
• Added overlap_count field to SimilarityScores model to track the number of overlapping genes between matched programs
• Upgraded url2ref dependency from v1.0-beta to v1.2-beta and added citeproc-py dependencies for citation processing
• Improved path handling in master report generation with _safe_relpath() helper function to handle cross-drive scenarios
• Added explicit system prompt resolution in DeepSearchService with validation and warnings for model-prompt incompatibilities
• Changed default use_pydantic parameter to True in process_and_save_structured_output()

Reviewed changes

Copilot reviewed 16 out of 17 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
uv.lock	Updated url2ref dependency and added citeproc-py packages for citation handling
langpa/pyproject.toml	Added citeproc-py dependency declaration
langpa_validation_tools/src/langpa_validation_tools/visualization/heatmaps.py	Refactored bubble plot to use program indices as axes with overlap-based sizing; added return_fig parameter
langpa_validation_tools/src/langpa_validation_tools/reporting/master_report.py	Added _safe_relpath() helper to handle relative path calculation across drives
langpa_validation_tools/src/langpa_validation_tools/comparison/models.py	Added overlap_count field to SimilarityScores model
langpa_validation_tools/src/langpa_validation_tools/comparison/matching.py	Updated to calculate and store overlap_count in similarity scores
langpa_validation_tools/src/langpa_validation_tools/analysis/run_comparison.py	Added genes_a_count and genes_b_count to output DataFrame
langpa_validation_tools/tests/unit/test_*.py	Updated tests to include new overlap_count, genes_a_count, genes_b_count fields
langpa/src/langpa/services/deepsearch_service.py	Added cache_config parameter, _resolve_system_prompt() method with validation and warnings
langpa/src/langpa/services/deepsearch_prompts.py	Clarified output format instructions for schema_embedded template
langpa/src/langpa/services/deepsearch_configs.py	Added explicit system prompt constants
langpa/src/langpa/services/output_manager.py	Changed use_pydantic default from False to True
20251212_121027/	Runtime output files that should not be in version control

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[Copilot]

@dosumis I've opened a new pull request, #21, to work on those changes. Once the pull request is ready, I'll request review from you.

[Copilot]

@dosumis I've opened a new pull request, #22, to work on those changes. Once the pull request is ready, I'll request review from you.