Merge origin/master before analysis handoff push

tests/unit/test_effective_member_resolver.py

@@ -116,6 +116,49 @@ def test_pre_confirm_prefers_curated_before_identified(tmp_path: Path):
     assert result.member_count == 2
 
 
+def test_pre_confirm_accepts_same_curated_members_in_different_order(tmp_path: Path):
+    ws = tmp_path / "workspace" / "job1"
+    final_dir = ws / "final"
+    input_dir = tmp_path / "input" / "job1"
+    prefix = "Target.Sl.GRAS"
+
+    _write(final_dir / f"{prefix}.curated_members.id", "gene1\ngene2\n")
+    _write(final_dir / f"{prefix}.curated_members.pep.fa", _pep(["gene2", "gene1"]))
+
+    result = resolve_effective_members(
+        workspace=ws,
+        final_dir=final_dir,
+        input_dir=input_dir,
+        prefix=prefix,
+        phase="pre_confirm",
+        require="pair",
+    )
+
+    assert result.member_count == 2
+    assert result.path_id == final_dir / f"{prefix}.curated_members.id"
+    assert result.path_pep == final_dir / f"{prefix}.curated_members.pep.fa"
+
+
+def test_pre_confirm_rejects_different_curated_members_with_equal_counts(tmp_path: Path):
+    ws = tmp_path / "workspace" / "job1"
+    final_dir = ws / "final"
+    input_dir = tmp_path / "input" / "job1"
+    prefix = "Target.Sl.GRAS"
+
+    _write(final_dir / f"{prefix}.curated_members.id", "gene1\ngene2\n")
+    _write(final_dir / f"{prefix}.curated_members.pep.fa", _pep(["gene1", "gene3"]))
+
+    with pytest.raises(MemberResolutionError, match="ID/FASTA mismatch"):
+        resolve_effective_members(
+            workspace=ws,
+            final_dir=final_dir,
+            input_dir=input_dir,
+            prefix=prefix,
+            phase="pre_confirm",
+            require="pair",
+        )
+
+
 def test_subfamily_evidence_required_rejects_unreviewed_identified_members(tmp_path: Path):
     ws = tmp_path / "workspace" / "job1"
     final_dir = ws / "final"

tests/unit/test_intent_species_roles.py

@@ -1,3 +1,6 @@
+import pytest
+
+from gfa_core.mas.agents.intent_v2 import IntentAgentV2
 from gfa_core.mas.utils.intent_parser import (
     parse_explicit_species_role_mentions,
     parse_gene_family_scope_selection,
@@ -30,3 +33,58 @@ def test_explicit_role_parser_keeps_unassigned_mentions_separate() -> None:
         "comparativeSpecies": [],
         "unassigned": ["Ppy"],
     }
+
+
+@pytest.mark.parametrize("species", ["Gm", "Br", "Pt", "Sb"])
+def test_scope_parser_preserves_species_supported_by_legacy_intent(species: str) -> None:
+    scope = parse_gene_family_scope_selection(f"分析 {species} 的 SPL 基因家族")
+
+    assert scope["targetSpecies"] == [species]
+
+
+def test_scope_parser_accepts_explicit_role_bound_custom_species_code() -> None:
+    scope = parse_gene_family_scope_selection("目标物种 Sv；参考物种 At")
+
+    assert scope["targetSpecies"] == ["Sv"]
+    assert scope["referenceSpecies"] == ["At"]
+
+
+def test_scope_parser_does_not_treat_gene_family_as_species() -> None:
+    scope = parse_gene_family_scope_selection("目标物种 Ft；分析 SPL 基因家族")
+
+    assert scope["targetSpecies"] == ["Ft"]
+
+
+def test_scope_parser_does_not_bind_custom_code_to_generic_goal_word() -> None:
+    scope = parse_gene_family_scope_selection("分析目标 SPL 基因家族")
+
+    assert scope["targetSpecies"] == []
+
+
+def test_intent_validation_keeps_confirmed_target_and_reference_separate() -> None:
+    agent = object.__new__(IntentAgentV2)
+
+    intent = agent._validate_intent(
+        {"gene_family": "SPL", "stages": ["identify"], "params": {}},
+        (
+            "请按照你规划的步骤来帮我执行\n"
+            "已确认上下文：基因家族 SPL；目标物种 Ft；参考物种 At。"
+        ),
+    )
+
+    assert intent["target_species"] == ["Ft"]
+    assert intent["reference_species"] == ["At"]
+    assert intent["species"] == "Ft"
+
+
+def test_intent_validation_preserves_unlabelled_multi_target_request() -> None:
+    agent = object.__new__(IntentAgentV2)
+
+    intent = agent._validate_intent(
+        {"gene_family": "SPL", "stages": ["identify"], "params": {}},
+        "分析 Ft 和 Os 的 SPL 基因家族",
+    )
+
+    assert intent["target_species"] == ["Ft", "Os"]
+    assert intent["reference_species"] == []
+    assert intent["species"] == "Multi"

tests/unit/test_subfamily_confirm_member_promotion.py

@@ -1,5 +1,7 @@
 from pathlib import Path
 
+import pytest
+
 from apps.cli.run_subfamily_confirm import _promote_curated_members_to_final
 
 
@@ -25,3 +27,37 @@ def test_promote_curated_members_to_final_records_checksums(tmp_path: Path):
     assert promotion["source_curated_id_checksum"]
     assert (final_dir / f"{prefix}.final_members.id").read_text(encoding="utf-8").splitlines() == curated_ids
     assert (final_dir / f"{prefix}.final_members.pep.fa").exists()
+
+
+def test_promote_curated_members_accepts_same_members_in_different_order(tmp_path: Path):
+    final_dir = tmp_path / "final"
+    final_dir.mkdir()
+    prefix = "Target.Sl.GRAS"
+    (final_dir / f"{prefix}.curated_members.id").write_text("gene1\ngene2\n", encoding="utf-8")
+    curated_pep = ">gene2\nMT\n>gene1\nMA\n"
+    (final_dir / f"{prefix}.curated_members.pep.fa").write_text(curated_pep, encoding="utf-8")
+    labels = {
+        "gene1": {"confirmed_subfamily": "GRAS-a"},
+        "gene2": {"confirmed_subfamily": "GRAS-b"},
+    }
+
+    promotions = _promote_curated_members_to_final(final_dir, [prefix], labels)
+
+    assert promotions[0]["count"] == 2
+    assert (final_dir / f"{prefix}.final_members.id").read_text(encoding="utf-8") == "gene1\ngene2\n"
+    assert (final_dir / f"{prefix}.final_members.pep.fa").read_text(encoding="utf-8") == curated_pep
+
+
+def test_promote_curated_members_rejects_different_members_with_equal_counts(tmp_path: Path):
+    final_dir = tmp_path / "final"
+    final_dir.mkdir()
+    prefix = "Target.Sl.GRAS"
+    (final_dir / f"{prefix}.curated_members.id").write_text("gene1\ngene2\n", encoding="utf-8")
+    (final_dir / f"{prefix}.curated_members.pep.fa").write_text(">gene1\nMA\n>gene3\nMT\n", encoding="utf-8")
+    labels = {
+        "gene1": {"confirmed_subfamily": "GRAS-a"},
+        "gene2": {"confirmed_subfamily": "GRAS-b"},
+    }
+
+    with pytest.raises(ValueError, match="ID/FASTA mismatch"):
+        _promote_curated_members_to_final(final_dir, [prefix], labels)

tests/unit/test_subfamily_prediction_plan.py

@@ -426,6 +426,64 @@ def test_confirmed_multi_species_roles_remain_separate(monkeypatch):
     assert resolved["classification_species"] == ["Ft", "Ppy"]
 
 
+def test_confirmation_ack_normalizes_structured_role_drift(monkeypatch):
+    main = _load_vue3_main()
+    monkeypatch.setattr(
+        main,
+        "_confirmed_config_species_scope",
+        lambda _job_id: {
+            "targetSpecies": ["Ft"],
+            "referenceSpecies": ["At"],
+            "comparativeSpecies": [],
+        },
+    )
+
+    resolved = main._reconcile_confirmed_gene_family_species(
+        "job-confirmed-ack",
+        "是",
+        {
+            "gene_family": "SPL",
+            "stages": ["identify"],
+            "target_species": ["Ft", "At"],
+            "params": {"targetSpecies": ["Ft", "At"]},
+        },
+    )
+
+    assert resolved["conflicts"] == []
+    assert resolved["target_species"] == ["Ft"]
+    assert resolved["reference_species"] == ["At"]
+
+
+def test_unassigned_reference_species_analysis_request_remains_blocked(monkeypatch):
+    main = _load_vue3_main()
+    monkeypatch.setattr(
+        main,
+        "_confirmed_config_species_scope",
+        lambda _job_id: {
+            "targetSpecies": ["Ft"],
+            "referenceSpecies": ["At"],
+            "comparativeSpecies": [],
+        },
+    )
+
+    resolved = main._reconcile_confirmed_gene_family_species(
+        "job-unassigned-reference",
+        "分析 At 的 SPL 基因家族",
+        {
+            "gene_family": "SPL",
+            "stages": ["identify"],
+            "target_species": ["At"],
+            "params": {"targetSpecies": ["At"]},
+        },
+    )
+
+    assert any(
+        conflict["code"] == "analysis_target_config_role_conflict"
+        and conflict["species"] == "At"
+        for conflict in resolved["conflicts"]
+    )
+
+
 def test_confirmed_config_duplicate_roles_are_blocked(monkeypatch):
     main = _load_vue3_main()
     monkeypatch.setattr(