feat: Add SUPPORTED_DETECTION_MODES to parsers for auto-generated table (#1219)

## Summary
- PR #1209 manually added a "Supported Detection Modes" column to the
instruments table, but the table is auto-generated by `hatch run
scripts:update-instrument-table`
- This PR moves detection mode data into parser class attributes
(`SUPPORTED_DETECTION_MODES`) so the generation script produces the
column automatically
- Adds `SUPPORTED_DETECTION_MODES: str | None = None` to the
`VendorParser` base class
- Declares detection modes in all 53 parser classes (matching the values
from PR #1209)
- Updates `get_table_contents()` to render the 5th column

## Changes
- `vendor_parser.py`: New optional class attribute
- `parser_factory.py`: New `supported_detection_modes` property on
`Vendor`, updated table generation
- All 53 parser files: One-line addition of `SUPPORTED_DETECTION_MODES =
"..."` (or `None` for liquid handlers)

## Test plan
- [x] `test_table_contents` passes — generated output matches the
existing `.adoc` file
- [x] All 318 parser_factory and discover_vendor tests pass
- [x] Lint passes

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

---------

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

Author: nathan-stender

.claude/skills/parser-generator/scripts/create_parser.py

@@ -58,6 +58,7 @@ class {class_name}(VendorParser[Data, Model]):
     DISPLAY_NAME = "{display_name}"
     RELEASE_STATE = ReleaseState.WORKING_DRAFT
     SUPPORTED_EXTENSIONS = "{extension}"
+    SUPPORTED_DETECTION_MODES = None  # TODO: Set detection modes (e.g. "Absorbance, Fluorescence")
     SCHEMA_MAPPER = Mapper
 
     def create_data(self, named_file_contents: NamedFileContents) -> Data:
@@ -367,10 +368,11 @@ def main():
     print("\n📝 Next steps:")
     print(f"1. Edit {parser_name}_reader.py to implement file parsing")
     print(f"2. Edit {parser_name}_structure.py to map data to schema")
-    print(f"3. Add test data to {testdata_dir}")
-    print(f"4. Run tests: hatch run test:pytest tests/parsers/{parser_name}/")
-    print("5. Register parser in src/allotropy/parser_factory.py")
-    print("6. Update README.md with parser information")
+    print(f"3. Set SUPPORTED_DETECTION_MODES in {parser_name}_parser.py")
+    print(f"4. Add test data to {testdata_dir}")
+    print(f"5. Run tests: hatch run test:pytest tests/parsers/{parser_name}/")
+    print("6. Register parser in src/allotropy/parser_factory.py")
+    print("7. Run: hatch run scripts:update-instrument-table")
 
 
 if __name__ == "__main__":

.claude/skills/parser-generator/skill.md

@@ -68,9 +68,11 @@ The script dynamically scans your local allotropy repository for all available s
 Use the `create_parser.py` script to generate the complete parser:
 
 ```bash
-python scripts/create_parser.py <parser_name> <vendor_name> --example <example_file>
+python scripts/create_parser.py <parser_name> <schema_regex> --display_name "Vendor Instrument" --detection_modes "Absorbance, Fluorescence"
 ```
 
+The `--detection_modes` flag sets the `SUPPORTED_DETECTION_MODES` class attribute, which populates the instruments table. Use comma-separated values for multiple modes (e.g. `"Absorbance, Fluorescence, Luminescence"`). Omit for instruments without detection (liquid handlers).
+
 ### Parser Structure Created
 
 ```
@@ -122,6 +124,7 @@ Generate `VendorParser` subclass with:
 - `DISPLAY_NAME` - User-friendly instrument name
 - `RELEASE_STATE` - Start with `ReleaseState.WORKING_DRAFT`
 - `SUPPORTED_EXTENSIONS` - File extensions (from analysis)
+- `SUPPORTED_DETECTION_MODES` - Detection modes the parser supports (e.g. `"Absorbance, Fluorescence"`) or `None` for instruments without detection (e.g. liquid handlers). This populates the "Supported Detection Modes" column in the supported instruments table.
 - `SCHEMA_MAPPER` - Reference to schema mapper
 - `create_data()` - Orchestrate reader + structure → Data
 
@@ -196,10 +199,11 @@ _VENDOR_TO_PARSER: dict[Vendor, type[VendorParser]] = {
 - [ ] Confirm or select schema with `list_schemas.py`
 - [ ] Generate parser using `create_parser.py`
 - [ ] Review and adjust generated code
+- [ ] Set `SUPPORTED_DETECTION_MODES` to the correct value for the instrument
 - [ ] Add example test data to `testdata/`
 - [ ] Run tests and validate output
 - [ ] Register parser in `parser_factory.py`
-- [ ] Update README with parser info
+- [ ] Run `hatch run scripts:update-instrument-table` to regenerate the supported instruments table
 - [ ] Update `RELEASE_STATE` when stable
 
 ## Key Design Principles

scripts/create_parser.py

@@ -61,7 +61,10 @@ def add_to_parser_factory(parser_name: str, enum_name: str, class_name: str) ->
 
 
 def create_parser(
-    name: str, schema_path: Path, display_name: str | None = None
+    name: str,
+    schema_path: Path,
+    display_name: str | None = None,
+    detection_modes: str | None = None,
 ) -> None:
     name = name.replace(" ", "_").replace("-", "_").lower()
     enum_name = name.upper()
@@ -84,6 +87,8 @@ def create_parser(
     Path(tests_dir, "__init__.py").touch()
     Path(tests_dir, "testdata").mkdir()
 
+    detection_modes_value = f'"{detection_modes}"' if detection_modes else "None"
+
     template_replacements = {
         "PARSER_NAME": name,
         "CLASS_NAME_PREFIX": class_name_prefix,
@@ -92,6 +97,7 @@ def create_parser(
         "MODEL_IMPORT_PATH": import_path,
         "MAPPER_IMPORT_PATH": import_path.replace("models", "schema_mappers"),
         "MANIFEST": manifest,
+        "SUPPORTED_DETECTION_MODES": detection_modes_value,
     }
     write_template_files(
         parser_dir,
@@ -119,8 +125,15 @@ def create_parser(
 @click.option(
     "--display_name", help="Display name for parser, defaults to title case of NAME"
 )
+@click.option(
+    "--detection_modes",
+    help="Comma-separated detection modes (e.g. 'Absorbance, Fluorescence')",
+)
 def _create_parser(
-    name: str, schema_regex: str, display_name: str | None = None
+    name: str,
+    schema_regex: str,
+    display_name: str | None = None,
+    detection_modes: str | None = None,
 ) -> None:
     """Create parser with name NAME for schema found with SCHEMA_REGEX."""
     if "parser" in name.lower():
@@ -135,7 +148,7 @@ def _create_parser(
         msg = f"Found more than one schema with schema regex, please narrow down: {[str(p) for p in schema_paths]}"
         raise ValueError(msg)
 
-    create_parser(name, schema_paths[0], display_name)
+    create_parser(name, schema_paths[0], display_name, detection_modes)
 
     from allotropy.parser_factory import update_supported_instruments
 

scripts/templates/parser_template

@@ -23,6 +23,7 @@ class $CLASS_NAME_PREFIX$Parser(VendorParser[Data, Model]):
     DISPLAY_NAME = DISPLAY_NAME
     RELEASE_STATE = ReleaseState.WORKING_DRAFT
     SUPPORTED_EXTENSIONS = $CLASS_NAME_PREFIX$Reader.SUPPORTED_EXTENSIONS
+    SUPPORTED_DETECTION_MODES = $SUPPORTED_DETECTION_MODES$
     SCHEMA_MAPPER = Mapper
 
     def create_data(self, named_file_contents: NamedFileContents) -> Data:

src/allotropy/parser_factory.py

@@ -207,6 +207,10 @@ def supported_extensions(self) -> list[str]:
             for ext in self.get_parser().SUPPORTED_EXTENSIONS.split(",")
         ]
 
+    @property
+    def supported_detection_modes(self) -> str | None:
+        return self.get_parser().SUPPORTED_DETECTION_MODES
+
     @property
     def manifests(self) -> list[str]:
         # NOTE: this is a list because eventually parsers will support multiple schemas as they are upgraded.
@@ -355,16 +359,16 @@ def get_table_contents() -> str:
             continue
         table_data[vendor.technique].append(vendor)
 
-    contents += '[cols="4*^.^"]\n'
+    contents += '[cols="5*^.^"]\n'
     contents += "|===\n"
-    contents += (
-        "|Instrument Category|Instrument Software|Release Status|Exported ASM Schema\n"
-    )
+    contents += "|Instrument Category|Instrument Software|Release Status|Exported ASM Schema|Supported Detection Modes\n"
     for technique in sorted(table_data):
         vendors = table_data[technique]
-        contents += f".{len(vendors)}+|{technique}|{vendors[0].display_name}|{vendors[0].release_state}|{vendors[0].asm_versions[0]}\n"
+        modes = vendors[0].supported_detection_modes or "N/A"
+        contents += f".{len(vendors)}+|{technique}|{vendors[0].display_name}|{vendors[0].release_state}|{vendors[0].asm_versions[0]}|{modes}\n"
         for vendor in vendors[1:]:
-            contents += f"|{vendor.display_name}|{vendor.release_state}|{vendor.asm_versions[0]}\n"
+            modes = vendor.supported_detection_modes or "N/A"
+            contents += f"|{vendor.display_name}|{vendor.release_state}|{vendor.asm_versions[0]}|{modes}\n"
     contents += "|==="
 
     return contents

src/allotropy/parsers/agilent_gen5/agilent_gen5_parser.py

@@ -19,6 +19,7 @@ class AgilentGen5Parser(VendorParser[Data, Model]):
     DISPLAY_NAME = "Agilent Gen5"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = AgilentGen5Reader.SUPPORTED_EXTENSIONS
+    SUPPORTED_DETECTION_MODES = "Absorbance, Fluorescence, Luminescence"
     SCHEMA_MAPPER = Mapper
 
     @classmethod

src/allotropy/parsers/agilent_gen5_image/agilent_gen5_image_parser.py

@@ -24,6 +24,7 @@ class AgilentGen5ImageParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "Agilent Gen5 Image"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = AgilentGen5Reader.SUPPORTED_EXTENSIONS
+    SUPPORTED_DETECTION_MODES = "Optical Imaging"
     SCHEMA_MAPPER = Mapper
 
     @classmethod

src/allotropy/parsers/agilent_openlab_cds/agilent_openlab_cds_parser.py

@@ -23,6 +23,7 @@ class AgilentOpenLabCDSParser(VendorParser[Data, Model]):
     DISPLAY_NAME = constants.DISPLAY_NAME
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = "rslt"
+    SUPPORTED_DETECTION_MODES = "Absorbance, Fluorescence"
     SCHEMA_MAPPER = Mapper
 
     @classmethod

src/allotropy/parsers/agilent_tapestation_analysis/agilent_tapestation_analysis_parser.py

@@ -21,6 +21,7 @@ class AgilentTapestationAnalysisParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "Agilent TapeStation Analysis"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = "xml"
+    SUPPORTED_DETECTION_MODES = "Fluorescence"
     SCHEMA_MAPPER = Mapper
 
     @classmethod

src/allotropy/parsers/appbio_absolute_q/appbio_absolute_q_parser.py

@@ -26,6 +26,7 @@ class AppbioAbsoluteQParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "AppBio AbsoluteQ"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = AppbioAbsoluteQReader.SUPPORTED_EXTENSIONS
+    SUPPORTED_DETECTION_MODES = "Fluorescence"
     SCHEMA_MAPPER = Mapper
 
     @classmethod