Allotropy

Changed

- AppBio QuantStudio Design & Analysis - redefine stage number as optional

Added

- Thermo Fisher Scientific Qubit 4 - initial implementation
- Roche Cedex HiRes - initial implementation

Fixed

- Internal - update the `structure_custom_information_document` function to create dataclasses with default field values set to `None`. This change ensures that custom keys are omitted as they are not required keys.
- Internal - fix encoding issues while reading units.json file in schemas.py script
- Internal - fix encoding issues while reading test json files in testing/utils.py script

Changed

- Internal - update NON_UNIQUE_IDENTIFIERS to have "group identifier" field

Added

- Documentation - add electrophoresis and spectrophotometry parser requirement templates

Fixed

- Beckman Vi-Cell XR - catch and raise AllotropeConversionError when missing date header
- Internal - fix get_model_class_from_schema work with Windows style path
- Agilent Gen5 - support non-numeric emission values for luminescence

Changed

- AppBio QuantStudio Design & Analysis - allow missing target DNA reference
- Global - standardize use of "N/A" for strings where a non-applicable value is necessary
- Global - update `None` filtering to preserve required keys when converting model to dictionary
- Global - update ASM converter name field to specify the parser name instead of just "allotropy", this is intended to give better granularity on the adapter that did the conversion and not just the library version
- Internal - upgrade pydantic to pull in fix for ForwardRef._evaluate() issue (https://github.com/pydantic/pydantic/issues/9637)
- Agilent Gen5 - update non-numeric emission related values to NaN instead of removing them from ASM

Added

- Agilent TapeStation Analysis - initial implementation
- Internal - add utility to add both dict and dataclass custom information document to an ASM model

- Added Solution Analyzer BENCHLING/2024/03 schema with the extension of the Data System Document.
Fixed

- Internal - updated schema cleaner to handle utf-8 characters in unit schema urls
- Internal - updated schema cleaner to handle object schemas with no properties
- Documentation - updated Beckman Vi-Cell XR requirements doc to reflect support for .txt files
- Global - handle dashes and slashes in custom information document key names
- Mabtech Apex - updated fields to support LED Filter

Added
- Mabtech Apex - initial implementation
- Beckman Vi-Cell XR - add support for parsing txt files
- Electrophoresis - add electrophoresis/BENCHLING/2024/06 schema
- Agilent TapeStation Analysis - add test files
- Documentation - add requirements for remaining parsers to /docs
- Agilent Gen5 - add Alphalisa assay support
- Spectrophotometry - add fluorescence point detection measurement extension to spectrophotometry/BENCHLING/2023/12 schema

Changed

- AppBio QuantStudio RT-PCR - redefine plate well count as optional

Added

- Luminex xPONENT - add ability to parse tabular CSV files

Fixed

- AppBio QuantStudio Design & Analysis - improved way of infer reference sample and DNA target
- CTL ImmunoSpot - fix model number and device id

Deprecated
- Roche Cedex Bioht - remove sample role type