feat: ranking for biolink:statistical_significance_qualifier

[SkyeAv]

Adds ranking boosts for biolink:statistical_significance_qualifier (biolink/biolink-model#1766) across all Shepherd ARAs, modeled on the equivalent ARAX implementation (RTXteam/RTX#2859). Closes #134.

Note: the Shepherd-side edge filter from earlier revisions of this PR was removed per #136 — implicit filtering for this qualifier belongs in Gandalf, not Shepherd; Shepherd ranks/scores only. The TRAPI override standard for the default significance cutoff is coordinated in BioPack-team/retriever#198; Gandalf-side filtering and the Retriever pass-through (retriever#197) are tracked in their respective repos.

Shared module

• shepherd_utils/statistical_significance_qualifier.py (NEW): single source of truth for SIGNIFICANCE_BAND_SCORES (0.70…0.0), SIGNIFICANCE_SOURCE_WEIGHT (0.5), and get_statistical_significance(edge) — a qualifiers-only lookup that strips any biolink: prefix. Reused by both rankers below.

Ranking — aragorn_score (Aragorn + BTE)

• workers/aragorn_score/worker.py: extracts the qualifier in get_edge_values() via the shared helper (the attribute loop only walks edge["attributes"]; the qualifier lives in edge["qualifiers"]). Adds it as a scored property feeding the graph-Laplacian: band_score × 0.5 → admittance -1/log(weight). Max effective weight 0.35 → bounded boost.
• Covers both ARAs: aragorn_score is the shared Aragorn + BTE ranker (both workflows run aragorn.score); one change updates both. There is no separate BTE ranker.
• No penalty: not_significant and qualifier-less edges are unchanged (property_w > 0 guard, also avoids log(0)).

Ranking — arax_rank (ARAX dict port)

• workers/arax_rank/ranker.py: categorical-bypass injection in _calculate_edge_confidence() — the qualifier is looked up separately from the numeric attribute normalizer (the enum string would otherwise hit float() → ValueError). Appends band_score × SIGNIFICANCE_SOURCE_WEIGHT to edge_attribute_score_list. Works even for attribute-less edges (injected at method level, not nested inside if edge.get("attributes")).
• Mirrors RTX post-refactor: trust weight is a standalone constant, not in known_attributes_to_trust (RTX moved it out in the same refactor).

Design

• Qualifier-only placement: reads edge["qualifiers"] exclusively — the qualifier is_a: statement_qualifier, so BMT/Retriever route it there. Matches ARAX (qualifier-only as of RTX#2859; its defensive edge.attributes lookup was removed). A one-line fallback in the shared helper covers a KP ever sending it as an attribute.
• No penalty for qualifier-less edges: rollout is incremental across KGs; penalizing non-adopters would be unfair. Ranking is boost-only.
• Conservative heuristics: band scores (0.70…0.0) and trust (0.5) match RTX exactly. These are starting points, not empirically validated. Deferred: revisit post-rollout.
• Deferred: significance-aware path scoring in score_paths (currently purely structural); edge.attributes fallback; per-ARA threshold tuning.
• Inert until retriever#197 ships: no edges carry the qualifier yet, so the boost applies to zero edges today and auto-activates when qualifier data starts flowing.

Testing

• Full CI-equivalent suite: tox (py312 + coverage envs) → both envs OK, 502 passed (down from 511 with the filter: 8 filter tests removed with the feature, 1 ordinal-table test removed with the now-dead SIGNIFICANCE_ORDINAL constant).
• Unit suite: pytest tests/unit -q → 502 passed, 9 warnings.
• Targeted qualifier/ranker tests: pytest tests/unit -k "significance or arax_rank or aragorn_score" -v → 74 passed, 428 deselected (15 new tests: 6 shared-helper, 4 aragorn_score, 5 arax_rank).
• Coverage (tox coverage env, .coveragerc, branch coverage; gate 10%): total 56.66%; touched files — statistical_significance_qualifier.py 95%, aragorn_score/worker.py 93%, aragorn/worker.py / bte/worker.py 73% each, shared.py 79%, arax_rank/ranker.py 23% (large legacy port file; qualifier path covered by the targeted tests).
• Verification: git grep filter_edges_by_statistical_significance / git grep SIGNIFICANCE_ORDINAL / git grep minimum_significance → 0 hits; compose.yml YAML parse valid; black --check clean on the touched files.

[SkyeAv]

Decisions on where statistical significance filtering lives (Gandalf, not Shepherd) are now recorded in #136 — filtering portion of this PR to be removed per that issue.

[SkyeAv]

Removed the Shepherd-side edge filter per #136 (filtering belongs in Gandalf). The branch was rewritten to drop the filter commit entirely, so this PR now contains only the ranking/scoring work (aragorn_score + arax_rank) and the shared qualifier helpers.