feat: Add Diomni v4.2/4.3 file support to QuantStudio Design & Analysis parser (#1224)

## Summary
- Adds support for files exported by Diomni software (v4.2/4.3), which
use `Primary_result` sheet instead of `Results`, alphanumeric well
identifiers (A01 format), separate `Software name`/`Software version`
header fields, and multicomponent data with partial dye columns
- Normalizes alphanumeric wells to numeric IDs with a stable sorted
mapping across all sheets, preserving well position as a separate column
- Gracefully handles missing reporter/passive dye columns in
multicomponent data instead of raising an error

## Test plan
- [x] New test file:
`appbio_quantstudio_designandanalysis_Diomni_v4.3_Presence_Absence.xlsx`
with expected JSON output
- [x] All 29 parser tests pass (28 existing + 1 new)
- [x] All 316 discover_vendor tests pass (no sniff conflicts)
- [x] Lint clean (ruff, black, mypy)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Author: nathan-stender

src/allotropy/parsers/appbio_quantstudio_designandanalysis/appbio_quantstudio_designandanalysis_data_creator.py

@@ -166,13 +166,22 @@ def _create_melt_curve_data_cube(
 
 def _create_measurement(well: Well, well_item: WellItem, data: Data) -> Measurement:
     header = data.header
+    multicomponent = well.multicomponent_data
+    reporter_dye = well_item.reporter_dye_setting
+    passive_dye = header.passive_reference_dye_setting
+    # Only request dye columns that actually exist in multicomponent data
+    if multicomponent is not None:
+        if reporter_dye is not None and reporter_dye not in multicomponent.columns:
+            reporter_dye = None
+        if passive_dye is not None and passive_dye not in multicomponent.columns:
+            passive_dye = None
     (
         reporter_dye_data_cube,
         passive_reference_dye_data_cube,
     ) = _create_multicomponent_data_cubes(
-        well.multicomponent_data,
-        well_item.reporter_dye_setting,
-        header.passive_reference_dye_setting,
+        multicomponent,
+        reporter_dye,
+        passive_dye,
     )
     return Measurement(
         identifier=well_item.uuid,

src/allotropy/parsers/appbio_quantstudio_designandanalysis/appbio_quantstudio_designandanalysis_parser.py

@@ -41,7 +41,7 @@ def sniff(cls, named_file_contents: NamedFileContents) -> bool:
             )
             sheet_names = set(wb.sheetnames)
             wb.close()
-            return "Results" in sheet_names
+            return "Results" in sheet_names or "Primary_result" in sheet_names
         except Exception:
             return False
 

src/allotropy/parsers/appbio_quantstudio_designandanalysis/appbio_quantstudio_designandanalysis_reader.py

@@ -16,6 +16,9 @@
     assert_not_none,
 )
 
+RESULTS_SHEET = "Results"
+PRIMARY_RESULT_SHEET = "Primary_result"
+
 
 class DesignQuantstudioReader:
     SUPPORTED_EXTENSIONS = "xlsx,xls"
@@ -36,12 +39,14 @@ def create(named_file_contents: NamedFileContents) -> DesignQuantstudioReader:
 
     def __init__(self, contents: dict[str, pd.DataFrame]) -> None:
         self.contents = contents
+        if PRIMARY_RESULT_SHEET in contents and RESULTS_SHEET not in contents:
+            contents[RESULTS_SHEET] = contents.pop(PRIMARY_RESULT_SHEET)
         self.header = self._get_header(contents)
         self.data = self._get_data(contents)
 
     def _get_header(self, contents: dict[str, pd.DataFrame]) -> SeriesData:
         sheet = assert_not_none(
-            contents.get("Results"),
+            contents.get(RESULTS_SHEET),
             msg="Unable to find 'Results' sheet.",
         )
         df, _ = split_header_and_data(sheet, lambda row: row[0] is None)
@@ -52,8 +57,29 @@ def _get_data(self, contents: dict[str, pd.DataFrame]) -> dict[str, pd.DataFrame
         for name, sheet in contents.items():
             _, data = split_header_and_data(sheet, lambda row: row[0] is None)
             data_structure[name] = parse_header_row(data.replace(np.nan, None))
+        self._normalize_well_columns(data_structure)
         return data_structure
 
+    def _normalize_well_columns(self, data_structure: dict[str, pd.DataFrame]) -> None:
+        results = data_structure.get(RESULTS_SHEET)
+        if results is None or "Well" not in results.columns:
+            return
+        first_well = results["Well"].iloc[0] if not results.empty else None
+        if first_well is None or isinstance(first_well, int | float):
+            return
+        # Alphanumeric wells — build a stable numeric mapping and add Well Position
+        all_wells: list[str] = []
+        for df in data_structure.values():
+            if "Well" in df.columns:
+                all_wells.extend(df["Well"].dropna().unique().tolist())
+        unique_wells = sorted({str(w) for w in all_wells})
+        well_to_id = {well: idx + 1 for idx, well in enumerate(unique_wells)}
+        for df in data_structure.values():
+            if "Well" in df.columns:
+                if "Well Position" not in df.columns:
+                    df.insert(1, "Well Position", df["Well"].astype(str))
+                df["Well"] = df["Well"].map(well_to_id)
+
     def has_sheet(self, sheet_name: str) -> bool:
         return sheet_name in self.data
 

src/allotropy/parsers/appbio_quantstudio_designandanalysis/structure/generic/structure.py

@@ -107,7 +107,10 @@ def create(header: SeriesData) -> Header:
         software_name, software_version = (
             (software_info.group(1), software_info.group(2))
             if software_info
-            else (None, None)
+            else (
+                header.get(str, "Software name"),
+                header.get(str, "Software version"),
+            )
         )
 
         stage_number_raw = header.get(str, "PCR Stage/Step Number", "")