Merge branch 'main' into felipenarv/qiacuity_dpcr_get_unread

Author: felipenarv

CHANGELOG.md

@@ -5,6 +5,18 @@ All notable changes to this packages will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.1.107] - 2025-10-09
+
+### Added
+
+- Thermo Fisher Scientific Genesys30 - add unread data (#1093)
+- Mabtech Apex - support files with different plate info (#1099)
+- Cytiva Biacore T200 Evaluation Module - initial implementation (#1075)
+
+### Fixed
+
+- Thermo Fisher Scientific Qubit Flex - added handling for sep header (#1101)
+
 ## [0.1.106] - 2025-09-30
 
 ### Added

src/allotropy/__about__.py

@@ -1 +1 @@
-__version__ = "0.1.106"
+__version__ = "0.1.107"

src/allotropy/parsers/thermo_fisher_qubit_flex/thermo_fisher_qubit_flex_reader.py

@@ -3,9 +3,10 @@
 import numpy as np
 import pandas as pd
 
-from allotropy.constants import DEFAULT_ENCODING
+from allotropy.exceptions import AllotropeConversionError
 from allotropy.named_file_contents import NamedFileContents
-from allotropy.parsers.utils.pandas import read_csv, read_excel
+from allotropy.parsers.lines_reader import CsvReader
+from allotropy.parsers.utils.pandas import read_excel
 
 
 class ThermoFisherQubitFlexReader:
@@ -27,11 +28,14 @@ def read(cls, named_file_contents: NamedFileContents) -> pd.DataFrame:
         AllotropeConversionError: If the file format is not supported.
         """
         if named_file_contents.extension == "csv":
-            df = read_csv(
-                named_file_contents.contents,
-                index_col=False,
-                encoding=DEFAULT_ENCODING,
-            )
+            csv_reader = CsvReader.create(named_file_contents)
+            # Skip lines until we find the "Run ID" header
+            csv_reader.drop_until(r"Test Date")
+            # Read the CSV block starting from the header
+            df = csv_reader.pop_csv_block_as_df(index_col=False, header=0)
+            if df is None:
+                msg = "Unable to find 'Run ID' header in CSV file"
+                raise AllotropeConversionError(msg)
         else:
             df = read_excel(named_file_contents.contents)
         df = df.replace(np.nan, None)

tests/parsers/thermo_fisher_qubit_flex/testdata/thermo_fisher_qubit_flex_example_sep_header.csv

@@ -0,0 +1,8 @@
+sep=,
+Run ID,Test Date,Assay Name,Sample Name,Original Sample Conc.,Original sample conc. units,Qubit Tube Conc.,Qubit tube conc. units,Sample Volume (uL),Dilution Factor,Extended Low Range,Core Range,Extended High Range,Excitation,Std 1 RFU,Std 2 RFU,Std 3 RFU,Sample RFU,Last Read Standards,Reagent Lot#,Plate Barcode,Well,Sample ID,Tags,Calibrated Tubes,Software Version,Selected Samples
+131222-164034,13/12/2022 04:41:09 PM,RNA BR,S1,528,ng/uL,2.64,ug/mL,1,200,10.0-20.0,20.0-1000,1000-1200,RED,3.19791240277,45.4272739973,,26.8,13/12/2022 04:40:57 PM,,,,,,6,1.5.0,6
+131222-164034,13/12/2022 04:41:09 PM,RNA BR,S2,610,ng/uL,3.05,ug/mL,1,200,10.0-20.0,20.0-1000,1000-1200,RED,2.94017020913,42.6888518933,,28.4,13/12/2022 04:40:57 PM,,,,,,6,1.5.0,6
+131222-164034,13/12/2022 04:41:09 PM,RNA BR,S3,534,ng/uL,2.67,ug/mL,1,200,10.0-20.0,20.0-1000,1000-1200,RED,2.74925006568,40.589712998,,24.2,13/12/2022 04:40:57 PM,,,,,,6,1.5.0,6
+131222-164034,13/12/2022 04:41:09 PM,RNA BR,S4,372,ng/uL,1.86,ug/mL,1,200,10.0-20.0,20.0-1000,1000-1200,RED,2.987900245,43.0991381318,,18.9,13/12/2022 04:40:57 PM,,,,,,6,1.5.0,6
+131222-164034,13/12/2022 04:41:09 PM,RNA BR,S5,546,ng/uL,2.73,ug/mL,1,200,10.0-20.0,20.0-1000,1000-1200,RED,2.8447101374,41.381660854,,25.1,13/12/2022 04:40:57 PM,,,,,,6,1.5.0,6
+131222-164034,13/12/2022 04:41:09 PM,RNA BR,S6,486,ng/uL,2.43,ug/mL,1,200,10.0-20.0,20.0-1000,1000-1200,RED,2.82561812305,40.2748421637,,22.2,13/12/2022 04:40:57 PM,,,,,,6,1.5.0,6