fix: allow reordered subfamily member records

apps/cli/run_subfamily_confirm.py

@@ -118,7 +118,7 @@ def _atomic_promote_pair(curated_id: Path, curated_pep: Path, final_id: Path, fi
     tmp_pep.write_text(curated_pep.read_text(encoding="utf-8", errors="ignore"), encoding="utf-8")
     tmp_ids = _read_id_list(tmp_id)
     tmp_fasta_ids = _read_fasta_ids(tmp_pep)
-    if tmp_ids != tmp_fasta_ids:
+    if sorted(tmp_ids) != sorted(tmp_fasta_ids):
         tmp_id.unlink(missing_ok=True)
         tmp_pep.unlink(missing_ok=True)
         raise RuntimeError(f"Temporary final member validation failed for {final_id.stem}")
@@ -160,7 +160,7 @@ def _promote_curated_members_to_final(final_dir: Path, prefixes: Iterable[str],
         if not curated_ids:
             raise ValueError(f"Curated member ID file is empty: {curated_id}")
         fasta_ids = _read_fasta_ids(curated_pep)
-        if curated_ids != fasta_ids:
+        if sorted(curated_ids) != sorted(fasta_ids):
             raise ValueError(
                 f"Curated member ID/FASTA mismatch for {member_prefix}: "
                 f"{len(curated_ids)} IDs vs {len(fasta_ids)} FASTA records"
@@ -179,7 +179,7 @@ def _promote_curated_members_to_final(final_dir: Path, prefixes: Iterable[str],
 
         promoted_ids = _read_id_list(final_id)
         promoted_fasta_ids = _read_fasta_ids(final_pep)
-        if promoted_ids != curated_ids or promoted_fasta_ids != curated_ids:
+        if sorted(promoted_ids) != sorted(curated_ids) or sorted(promoted_fasta_ids) != sorted(curated_ids):
             raise RuntimeError(f"Post-promotion final member validation failed for {member_prefix}")
         promotions.append({
             "prefix": member_prefix,

gfa_core/mas/effective_members.py

@@ -259,7 +259,7 @@ def _build_result(
 
     id_list = _read_ids(path_id) if path_id else []
     pep_ids = _read_fasta_ids(path_pep) if path_pep else []
-    if path_id and path_pep and id_list != pep_ids:
+    if path_id and path_pep and sorted(id_list) != sorted(pep_ids):
         raise MemberResolutionError(f"Member ID/FASTA mismatch: {path_id} vs {path_pep}")
     member_count = len(id_list or pep_ids)
     warnings = []

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_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)