chore: Clean up VendorParser class now that all parsers are migrated to schema mappers

docs/tutorial.md

@@ -166,7 +166,7 @@ and *must* define set `DISPLAY_NAME`, `RELEASE_STATE`, and `SCHEMA_MAPPER` and i
 `create_data` that takes a `NamedFileContents` objects as input and produces an instance of (something derived from) `Data` as a result:
 
 ```python
-class ExampleWeylandYutaniParser(MapperVendorParser[Data, Model]):
+class ExampleWeylandYutaniParser(VendorParser[Data, Model]):
     DISPLAY_NAME = DISPLAY_NAME
     RELEASE_STATE = ReleaseState.WORKING_DRAFT
     SCHEMA_MAPPER = Mapper

scripts/templates/parser_template

@@ -16,10 +16,10 @@ from allotropy.parsers.$PARSER_NAME$.$PARSER_NAME$_structure import (
     create_metadata,
 )
 from allotropy.parsers.utils.pandas import map_rows
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class $CLASS_NAME_PREFIX$Parser(MapperVendorParser[Data, Model]):
+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

src/allotropy/parser_factory.py

@@ -2,6 +2,7 @@
 from datetime import tzinfo
 from enum import Enum
 from pathlib import Path
+from typing import Any
 
 from allotropy.allotrope.schema_parser.path_util import ROOT_DIR
 from allotropy.parsers.agilent_gen5.agilent_gen5_parser import AgilentGen5Parser
@@ -137,12 +138,14 @@ def supported_extensions(self) -> list[str]:
             ext.strip() for ext in self.get_parser().SUPPORTED_EXTENSIONS.split(",")
         ]
 
-    def get_parser(self, default_timezone: tzinfo | None = None) -> VendorParser:
+    def get_parser(
+        self, default_timezone: tzinfo | None = None
+    ) -> VendorParser[Any, Any]:
         timestamp_parser = TimestampParser(default_timezone)
         return _VENDOR_TO_PARSER[self](timestamp_parser)
 
 
-_VENDOR_TO_PARSER: dict[Vendor, type[VendorParser]] = {
+_VENDOR_TO_PARSER: dict[Vendor, type[VendorParser[Any, Any]]] = {
     Vendor.AGILENT_GEN5: AgilentGen5Parser,
     Vendor.AGILENT_GEN5_IMAGE: AgilentGen5ImageParser,
     Vendor.AGILENT_TAPESTATION_ANALYSIS: AgilentTapestationAnalysisParser,

src/allotropy/parsers/agilent_gen5/agilent_gen5_parser.py

@@ -24,10 +24,10 @@
     NO_MEASUREMENTS_ERROR,
 )
 from allotropy.parsers.release_state import ReleaseState
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class AgilentGen5Parser(MapperVendorParser[Data, Model]):
+class AgilentGen5Parser(VendorParser[Data, Model]):
     DISPLAY_NAME = "Agilent Gen5"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = AgilentGen5Reader.SUPPORTED_EXTENSIONS

src/allotropy/parsers/agilent_gen5_image/agilent_gen5_image_parser.py

@@ -17,10 +17,10 @@
     ReadData,
 )
 from allotropy.parsers.release_state import ReleaseState
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class AgilentGen5ImageParser(MapperVendorParser[Data, Model]):
+class AgilentGen5ImageParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "Agilent Gen5 Image"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = AgilentGen5Reader.SUPPORTED_EXTENSIONS

src/allotropy/parsers/agilent_tapestation_analysis/agilent_tapestation_analysis_parser.py

@@ -14,10 +14,10 @@
     create_metadata,
 )
 from allotropy.parsers.release_state import ReleaseState
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class AgilentTapestationAnalysisParser(MapperVendorParser[Data, Model]):
+class AgilentTapestationAnalysisParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "Agilent TapeStation Analysis"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = "xml"

src/allotropy/parsers/appbio_absolute_q/appbio_absolute_q_parser.py

@@ -15,10 +15,10 @@
 )
 from allotropy.parsers.release_state import ReleaseState
 from allotropy.parsers.utils.pandas import read_csv
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class AppbioAbsoluteQParser(MapperVendorParser[Data, Model]):
+class AppbioAbsoluteQParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "AppBio AbsoluteQ"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = "csv"

src/allotropy/parsers/appbio_quantstudio/appbio_quantstudio_parser.py

@@ -23,10 +23,10 @@
 )
 from allotropy.parsers.lines_reader import LinesReader
 from allotropy.parsers.release_state import ReleaseState
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class AppBioQuantStudioParser(MapperVendorParser[Data, Model]):
+class AppBioQuantStudioParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "AppBio QuantStudio RT-PCR"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = "txt"

src/allotropy/parsers/appbio_quantstudio_designandanalysis/appbio_quantstudio_designandanalysis_parser.py

@@ -14,10 +14,10 @@
     DesignQuantstudioReader,
 )
 from allotropy.parsers.release_state import ReleaseState
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class AppBioQuantStudioDesignandanalysisParser(MapperVendorParser[Data, Model]):
+class AppBioQuantStudioDesignandanalysisParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "AppBio QuantStudio Design & Analysis"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = DesignQuantstudioReader.SUPPORTED_EXTENSIONS

src/allotropy/parsers/beckman_pharmspec/beckman_pharmspec_parser.py

@@ -17,10 +17,10 @@
     Header,
 )
 from allotropy.parsers.release_state import ReleaseState
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class PharmSpecParser(MapperVendorParser[Data, Model]):
+class PharmSpecParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "Beckman PharmSpec"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = BeckmanPharmspecReader.SUPPORTED_EXTENSIONS

src/allotropy/parsers/beckman_vi_cell_blu/vi_cell_blu_parser.py

@@ -15,10 +15,10 @@
 )
 from allotropy.parsers.release_state import ReleaseState
 from allotropy.parsers.utils.pandas import map_rows
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class ViCellBluParser(MapperVendorParser[Data, Model]):
+class ViCellBluParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "Beckman Vi-Cell BLU"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = ViCellBluReader.SUPPORTED_EXTENSIONS

src/allotropy/parsers/beckman_vi_cell_xr/vi_cell_xr_parser.py

@@ -15,10 +15,10 @@
     create_metadata,
 )
 from allotropy.parsers.release_state import ReleaseState
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class ViCellXRParser(MapperVendorParser[Data, Model]):
+class ViCellXRParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "Beckman Vi-Cell XR"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = "txt,xls,xlsx"

src/allotropy/parsers/biorad_bioplex_manager/biorad_bioplex_manager_parser.py

@@ -19,10 +19,10 @@
     Well,
 )
 from allotropy.parsers.release_state import ReleaseState
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class BioradBioplexParser(MapperVendorParser[Data, Model]):
+class BioradBioplexParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "Bio-Rad Bio-Plex Manager"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = "xml"

src/allotropy/parsers/bmg_mars/bmg_mars_parser.py

@@ -15,10 +15,10 @@
     Header,
 )
 from allotropy.parsers.release_state import ReleaseState
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class BmgMarsParser(MapperVendorParser[Data, Model]):
+class BmgMarsParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "BMG MARS"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = "csv"

src/allotropy/parsers/chemometec_nc_view/chemometec_nc_view_parser.py

@@ -16,10 +16,10 @@
 from allotropy.parsers.chemometec_nc_view.constants import DISPLAY_NAME
 from allotropy.parsers.release_state import ReleaseState
 from allotropy.parsers.utils.pandas import map_rows
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class ChemometecNcViewParser(MapperVendorParser[Data, Model]):
+class ChemometecNcViewParser(VendorParser[Data, Model]):
     DISPLAY_NAME = DISPLAY_NAME
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = ChemometecNcViewReader.SUPPORTED_EXTENSIONS

src/allotropy/parsers/chemometec_nucleoview/nucleoview_parser.py

@@ -13,10 +13,10 @@
 )
 from allotropy.parsers.release_state import ReleaseState
 from allotropy.parsers.utils.pandas import df_to_series_data, map_rows
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class ChemometecNucleoviewParser(MapperVendorParser[Data, Model]):
+class ChemometecNucleoviewParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "ChemoMetec Nucleoview"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = NucleoviewReader.SUPPORTED_EXTENSIONS

src/allotropy/parsers/ctl_immunospot/ctl_immunospot_parser.py

@@ -14,10 +14,10 @@
 )
 from allotropy.parsers.lines_reader import LinesReader
 from allotropy.parsers.release_state import ReleaseState
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class CtlImmunospotParser(MapperVendorParser[Data, Model]):
+class CtlImmunospotParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "CTL ImmunoSpot"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = "txt"

src/allotropy/parsers/example_weyland_yutani/example_weyland_yutani_parser.py

@@ -18,10 +18,10 @@
     Plate,
 )
 from allotropy.parsers.release_state import ReleaseState
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class ExampleWeylandYutaniParser(MapperVendorParser[Data, Model]):
+class ExampleWeylandYutaniParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "Example Weyland Yutani"
     RELEASE_STATE = ReleaseState.WORKING_DRAFT
     SUPPORTED_EXTENSIONS = ExampleWeylandYutaniReader.SUPPORTED_EXTENSIONS

src/allotropy/parsers/luminex_xponent/luminex_xponent_parser.py

@@ -15,10 +15,10 @@
     Data,
 )
 from allotropy.parsers.release_state import ReleaseState
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class LuminexXponentParser(MapperVendorParser[MapperData, Model]):
+class LuminexXponentParser(VendorParser[MapperData, Model]):
     DISPLAY_NAME = "Luminex xPONENT"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = LuminexXponentReader.SUPPORTED_EXTENSIONS

src/allotropy/parsers/mabtech_apex/mabtech_apex_parser.py

@@ -17,10 +17,10 @@
 from allotropy.parsers.utils.pandas import (
     SeriesData,
 )
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class MabtechApexParser(MapperVendorParser[Data, Model]):
+class MabtechApexParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "Mabtech Apex"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = MabtechApexReader.SUPPORTED_EXTENSIONS

src/allotropy/parsers/methodical_mind/methodical_mind_parser.py

@@ -18,10 +18,10 @@
     PlateData,
 )
 from allotropy.parsers.release_state import ReleaseState
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class MethodicalMindParser(MapperVendorParser[Data, Model]):
+class MethodicalMindParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "Methodical Mind"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = "txt"

src/allotropy/parsers/moldev_softmax_pro/softmax_pro_parser.py

@@ -14,10 +14,10 @@
     StructureData,
 )
 from allotropy.parsers.release_state import ReleaseState
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class SoftmaxproParser(MapperVendorParser[Data, Model]):
+class SoftmaxproParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "Molecular Devices SoftMax Pro"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = "txt"

src/allotropy/parsers/novabio_flex2/novabio_flex2_parser.py

@@ -16,10 +16,10 @@
 )
 from allotropy.parsers.release_state import ReleaseState
 from allotropy.parsers.utils.pandas import read_csv
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class NovaBioFlexParser(MapperVendorParser[Data, Model]):
+class NovaBioFlexParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "NovaBio Flex2"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = "csv"

src/allotropy/parsers/perkin_elmer_envision/perkin_elmer_envision_parser.py

@@ -14,10 +14,10 @@
     Data as StructureData,
 )
 from allotropy.parsers.release_state import ReleaseState
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class PerkinElmerEnvisionParser(MapperVendorParser[Data, Model]):
+class PerkinElmerEnvisionParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "PerkinElmer Envision"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = "csv"

src/allotropy/parsers/qiacuity_dpcr/qiacuity_dpcr_parser.py

@@ -14,10 +14,10 @@
 )
 from allotropy.parsers.release_state import ReleaseState
 from allotropy.parsers.utils.pandas import map_rows
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class QiacuitydPCRParser(MapperVendorParser[Data, Model]):
+class QiacuitydPCRParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "Qiacuity dPCR"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = QiacuitydPCRReader.SUPPORTED_EXTENSIONS

src/allotropy/parsers/revvity_kaleido/kaleido_parser.py

@@ -13,10 +13,10 @@
     create_measurement_groups,
     create_metadata,
 )
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class KaleidoParser(MapperVendorParser[Data, Model]):
+class KaleidoParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "Revvity Kaleido"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SCHEMA_MAPPER = Mapper

src/allotropy/parsers/revvity_matrix/revvity_matrix_parser.py

@@ -16,10 +16,10 @@
     create_metadata,
 )
 from allotropy.parsers.utils.pandas import map_rows
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class RevvityMatrixParser(MapperVendorParser[Data, Model]):
+class RevvityMatrixParser(VendorParser[Data, Model]):
     DISPLAY_NAME = DISPLAY_NAME
     RELEASE_STATE = ReleaseState.WORKING_DRAFT
     SUPPORTED_EXTENSIONS = RevvityMatrixReader.SUPPORTED_EXTENSIONS

src/allotropy/parsers/roche_cedex_bioht/roche_cedex_bioht_parser.py

@@ -16,10 +16,10 @@
     Sample,
     Title,
 )
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class RocheCedexBiohtParser(MapperVendorParser[Data, Model]):
+class RocheCedexBiohtParser(VendorParser[Data, Model]):
     DISPLAY_NAME = "Roche Cedex BioHT"
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = RocheCedexBiohtReader.SUPPORTED_EXTENSIONS

src/allotropy/parsers/roche_cedex_hires/roche_cedex_hires_parser.py

@@ -16,10 +16,10 @@
     create_metadata,
 )
 from allotropy.parsers.utils.pandas import map_rows
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class RocheCedexHiResParser(MapperVendorParser[Data, Model]):
+class RocheCedexHiResParser(VendorParser[Data, Model]):
     DISPLAY_NAME = DISPLAY_NAME
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = RocheCedexHiResReader.SUPPORTED_EXTENSIONS

src/allotropy/parsers/thermo_fisher_genesys30/thermo_fisher_genesys30_parser.py

@@ -15,10 +15,10 @@
     create_measurement_groups,
     create_metadata,
 )
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class ThermoFisherGenesys30Parser(MapperVendorParser[Data, Model]):
+class ThermoFisherGenesys30Parser(VendorParser[Data, Model]):
     DISPLAY_NAME = DISPLAY_NAME
     RELEASE_STATE = ReleaseState.RECOMMENDED
     SUPPORTED_EXTENSIONS = ThermoFisherGenesys30Reader.SUPPORTED_EXTENSIONS