fix: Handle trailing tabs and quoted fields in Agilent Gen5 parser

Some Gen5 exports (e.g. Synergy H1) produce files with trailing tabs on
every line, leading tabs on data sections, and quoted fields containing
commas. This caused multiple parse failures: header DataFrame had extra
rows, section names were quoted, kinetic/results data had shifted columns,
and non-UTF-8 encoding wasn't detected.

Fixes:
- Add chardet encoding detection for non-UTF-8 files
- Strip trailing tabs from all lines at read time
- Strip quotes from procedure detail lines in DeviceControlData
- Extract section names from first non-empty tab field (handles leading tabs)
- Detect and strip extra leading tab from data sections
- Merge section data when a blank line separates header from content

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: nathan-stender

src/allotropy/parsers/agilent_gen5/agilent_gen5_parser.py

@@ -5,6 +5,7 @@
     Data,
     Mapper,
 )
+from allotropy.constants import CHARDET_ENCODING
 from allotropy.named_file_contents import NamedFileContents
 from allotropy.parsers.agilent_gen5.agilent_gen5_reader import AgilentGen5Reader
 from allotropy.parsers.agilent_gen5.agilent_gen5_structure import (
@@ -35,6 +36,12 @@ def sniff(cls, named_file_contents: NamedFileContents) -> bool:
             return False
 
     def create_data(self, named_file_contents: NamedFileContents) -> Data:
+        if named_file_contents.encoding is None:
+            named_file_contents = NamedFileContents(
+                named_file_contents.contents,
+                named_file_contents.original_file_path,
+                CHARDET_ENCODING,
+            )
         reader = AgilentGen5Reader(named_file_contents)
         context = reader.extract_data_context(named_file_contents.original_file_path)
 

src/allotropy/parsers/agilent_gen5/agilent_gen5_reader.py

@@ -20,7 +20,7 @@
     MULTIPLATE_FILE_ERROR,
     NO_PLATE_DATA_ERROR,
 )
-from allotropy.parsers.lines_reader import SectionLinesReader
+from allotropy.parsers.lines_reader import read_to_lines, SectionLinesReader
 from allotropy.parsers.utils.pandas import df_to_series_data, read_csv, SeriesData
 from allotropy.parsers.utils.values import assert_not_none
 
@@ -31,7 +31,8 @@ class AgilentGen5Reader:
     SUPPORTED_EXTENSIONS = "txt"
 
     def __init__(self, named_file_contents: NamedFileContents) -> None:
-        reader = SectionLinesReader.create(named_file_contents)
+        lines = [line.rstrip("\t") for line in read_to_lines(named_file_contents)]
+        reader = SectionLinesReader(lines)
 
         plate_readers = list(reader.iter_sections("^Software Version"))
         if not plate_readers:
@@ -75,7 +76,14 @@ def __init__(self, named_file_contents: NamedFileContents) -> None:
         last_read_label: str | None = None
 
         while lines := list(plate_reader.pop_until_empty()):
-            section_name = lines[0].split("\t")[0].strip(":")
+            section_name = self._get_section_name(lines[0])
+
+            # Check if this is a single-line section header with data in the next block
+            if len(lines) == 1 and section_name in ("Layout", "Results"):
+                plate_reader.drop_empty()
+                next_lines = list(plate_reader.pop_until_empty())
+                if next_lines:
+                    lines = [lines[0], *next_lines]
 
             # Check if this is a "Read X:label" section (single line, starts with "Read ")
             # If so, store the label and immediately read the next section
@@ -87,27 +95,50 @@ def __init__(self, named_file_contents: NamedFileContents) -> None:
                 if not lines:
                     # No data section after the label, just continue
                     continue
-                section_name = lines[0].split("\t")[0].strip(":")
+                section_name = self._get_section_name(lines[0])
 
             # If this is a Time section, associate it with a read label if we have one
             if section_name == "Time":
                 if last_read_label:
                     # Format: "Read X:label" -> Time section
-                    self.kinetic_sections[last_read_label] = lines
+                    self.kinetic_sections[last_read_label] = self._strip_leading_tab(
+                        lines
+                    )
                     last_read_label = None
                 elif last_section_name:
                     # Format: "{label}" section followed by Time section
                     # Store with just the label as key for kinetic files
-                    self.kinetic_sections[last_section_name] = lines
+                    self.kinetic_sections[last_section_name] = self._strip_leading_tab(
+                        lines
+                    )
                 else:
                     # Standalone Time section (shouldn't happen, but store it anyway)
-                    self.sections[section_name] = lines
+                    self.sections[section_name] = self._strip_leading_tab(lines)
             else:
-                self.sections[section_name] = lines
+                self.sections[section_name] = self._strip_leading_tab(lines)
                 last_section_name = section_name
 
             plate_reader.drop_empty()
 
+    @staticmethod
+    def _get_section_name(line: str) -> str:
+        fields = line.split("\t")
+        for field in fields:
+            name = field.strip('"').strip(":")
+            if name:
+                return name
+        return ""
+
+    @staticmethod
+    def _strip_leading_tab(lines: list[str]) -> list[str]:
+        if len(lines) < 2:
+            return lines
+        non_header = lines[1:] if not lines[0].startswith("\t") else lines
+        non_empty = [line for line in non_header if line.strip()]
+        if non_empty and all(line.startswith("\t") for line in non_empty):
+            return [line[1:] if line.startswith("\t") else line for line in lines]
+        return lines
+
     def get_required_section(self, section_name: str) -> list[str]:
         """Get a required section, raises error if not found."""
         section = self.sections.get(section_name)

src/allotropy/parsers/agilent_gen5/agilent_gen5_structure.py

@@ -240,7 +240,7 @@ def create(cls, lines: list[str], read_mode: ReadMode) -> DeviceControlData:
         device_control_data = DeviceControlData()
 
         for line in lines:
-            strp_line = str(line.strip())
+            strp_line = str(line.strip().strip('"').strip())
             if strp_line == "Fluorescence Polarization":
                 device_control_data.is_polarization = True
                 continue