# from metabolights_utils.common import CamelCaseModel
# from metabolights_utils.isatab import Reader, Writer
# from metabolights_utils.isatab.default.assay_file import DefaultAssayFileReader
# from metabolights_utils.isatab.default.assignment_file import (
#     DefaultAssignmentFileReader,
# )
# from metabolights_utils.isatab.default.factory import (
#     DefaultIsaTabReaderFactory,
#     DefaultIsaTabWriterFactory,
# )
# from metabolights_utils.isatab.default.investigation_file import (
#     DefaultInvestigationFileReader,
#     DefaultInvestigationFileWriter,
# )
# from metabolights_utils.isatab.default.parser.isa_table_parser import (
#     assay_file_expected_patterns,
#     samples_file_expected_patterns,
# )
# from metabolights_utils.isatab.default.sample_file import DefaultSampleFileReader
# from metabolights_utils.isatab.default.writer import DefaultIsaTableFileWriter
# from metabolights_utils.isatab.reader import (
#     InvestigationFileReader,
#     InvestigationFileReaderResult,
#     IsaTableFileReader,
#     IsaTableFileReaderResult,
#     IsaTabReaderFactory,
# )
# from metabolights_utils.isatab.writer import (
#     InvestigationFileWriter,
#     IsaTableFileWriter,
#     IsaTabWriterFactory,
# )
# from metabolights_utils.models.common import GenericMessage, MetabolightsBaseModel
# from metabolights_utils.models.enums import GenericMessageType
# from metabolights_utils.models.isa.assay_file import AssayFile
# from metabolights_utils.models.isa.assignment_file import AssignmentFile
# from metabolights_utils.models.isa.common import (
#     AssayTechnique,
#     Comment,
#     IsaAbstractModel,
#     IsaTable,
#     IsaTableColumn,
#     IsaTableFile,
#     NumericItem,
#     OntologyItem,
#     OrganismAndOrganismPartPair,
# )
# from metabolights_utils.models.isa.enums import (
#     ColumnsStructure,
#     IsaTableAdditionalColumn,
# )
# from metabolights_utils.models.isa.investigation_file import (
#     Assay,
#     BaseSection,
#     Factor,
#     Investigation,
#     InvestigationContacts,
#     InvestigationPublications,
#     OntologyAnnotation,
#     OntologySourceReference,
#     OntologySourceReferences,
#     Person,
#     Protocol,
#     Publication,
#     Study,
#     StudyAssays,
#     StudyContacts,
#     StudyFactors,
#     StudyProtocols,
#     StudyPublications,
#     ValueTypeAnnotation,
# )
# from metabolights_utils.models.metabolights.metabolights_study import (
#     BaseMetabolightsStudyModel,
# )
# from metabolights_utils.models.parser.common import ParserMessage, ParserReport
# from metabolights_utils.models.parser.enums import ParserMessageType
# from metabolights_utils.tsv.actions.add_column import AddColumnsTsvAction
# from metabolights_utils.tsv.actions.add_row import AddRowsTsvAction
# from metabolights_utils.tsv.actions.base import BaseTsvAction, TsvActionException
# from metabolights_utils.tsv.actions.copy_column import CopyColumnTsvAction
# from metabolights_utils.tsv.actions.copy_row import CopyRowTsvAction
# from metabolights_utils.tsv.actions.delete_column import DeleteColumnsTsvAction
# from metabolights_utils.tsv.actions.delete_row import DeleteRowsTsvAction
# from metabolights_utils.tsv.actions.move_column import MoveColumnTsvAction
# from metabolights_utils.tsv.actions.update_cell import UpdateCellsTsvAction
# from metabolights_utils.tsv.actions.update_column import UpdateColumnsTsvAction
# from metabolights_utils.tsv.actions.update_column_header import (
#     UpdateColumnHeadersTsvAction,
# )
# from metabolights_utils.tsv.actions.update_row import UpdateRowsTsvAction
# from metabolights_utils.tsv.filter import (
#     BetweenEqualCustomFilter,
#     ContainsFilter,
#     CustomFilter,
#     EmptyFilter,
#     EndsWithFilter,
#     EnumContainsCustomFilter,
#     Filter,
#     FilterDataType,
#     FilterOperation,
#     FilterRegistry,
#     GreaterEqualFilter,
#     GreaterFilter,
#     LessEqualFilter,
#     LessFilter,
#     RegexFilter,
#     StartsWithFilter,
#     TsvFileFilterOption,
#     TsvFilterException,
#     ValidDatetimeCustomFilter,
#     ValidNumberCustomFilter,
# )
# from metabolights_utils.tsv.model import (
#     TsvAction,
#     TsvActionReport,
#     TsvActionResult,
#     TsvActionType,
#     TsvAddColumnsAction,
#     TsvAddRowsAction,
#     TsvCellData,
#     TsvColumnData,
#     TsvCopyColumnAction,
#     TsvCopyRowAction,
#     TsvDeleteColumnsAction,
#     TsvDeleteRowsAction,
#     TsvMoveColumnAction,
#     TsvMoveRowAction,
#     TsvRowData,
#     TsvUpdateCellsAction,
#     TsvUpdateColumnHeaderAction,
#     TsvUpdateColumnsAction,
#     TsvUpdateRowsAction,
# )
# from metabolights_utils.tsv.sort import (
#     AbstractSorter,
#     CustomSorter,
#     DateTimeSorter,
#     EnumSorter,
#     FloatSorter,
#     IntegerSorter,
#     Sorter,
#     SorterRegistry,
#     SortType,
#     SortValueClassification,
#     StringSorter,
#     TsvFileSortOption,
#     TsvFileSortValueOrder,
#     TsvSortException,
# )
# from metabolights_utils.tsv.tsv_file_updater import TSV_FILE_ACTIONS, TsvFileUpdater
# from metabolights_utils.utils.audit_utils import MetabolightsAuditUtils
# from metabolights_utils.utils.filename_utils import MetabolightsFileNameUtils
# from metabolights_utils.utils.hash_utils import (
#     EMPTY_FILE_HASH,
#     IsaMetadataFolderHash,
#     MetabolightsHashUtils,
# )
# from metabolights_utils.utils.search_utils import MetabolightsSearchUtils
from metabolights_utils import (
    commands,
    common,
    isa_file_utils,
    isatab,
    models,
    provider,
    tsv,
    utils,
)

__VERSION__ = "1.4.2"

__all__ = [
    "commands",
    "isatab",
    "models",
    "provider",
    "tsv",
    "utils",
    "common",
    "isa_file_utils",
    # "Assay",
    # "BaseSection",
    # "Factor",
    # "Investigation",
    # "InvestigationContacts",
    # "InvestigationPublications",
    # "OntologyAnnotation",
    # "OntologySourceReference",
    # "OntologySourceReferences",
    # "Person",
    # "Protocol",
    # "Publication",
    # "Study",
    # "StudyAssays",
    # "StudyContacts",
    # "StudyFactors",
    # "StudyProtocols",
    # "StudyPublications",
    # "ValueTypeAnnotation",
    # "ColumnsStructure",
    # "IsaTableAdditionalColumn",
    # "IsaAbstractModel",
    # "NumericItem",
    # "AssayFile",
    # "AssignmentFile",
    # "GenericMessage",
    # "GenericMessageType",
    # "MetabolightsBaseModel",
    # "CamelCaseModel",
    # "AssayTechnique",
    # "Comment",
    # "IsaTable",
    # "IsaTableColumn",
    # "IsaTableFile",
    # "OntologyItem",
    # "OrganismAndOrganismPartPair",
    # "BaseMetabolightsStudyModel",
    # "ParserMessage",
    # "ParserMessageType",
    # "ParserReport",
    # "Reader",
    # "DefaultAssayFileReader",
    # "InvestigationFileReader",
    # "DefaultAssignmentFileReader",
    # "IsaTableFileReader",
    # "InvestigationFileReaderResult",
    # "IsaTableFileReaderResult",
    # "DefaultIsaTabReaderFactory",
    # "DefaultIsaTabWriterFactory",
    # "DefaultInvestigationFileReader",
    # "DefaultInvestigationFileWriter",
    # "assay_file_expected_patterns",
    # "samples_file_expected_patterns",
    # "DefaultSampleFileReader",
    # "DefaultIsaTableFileWriter",
    # "IsaTabReaderFactory",
    # "Writer",
    # "InvestigationFileWriter",
    # "IsaTableFileWriter",
    # "IsaTabWriterFactory",
    # # TSV
    # "TsvAction",
    # "TsvActionReport",
    # "TsvActionResult",
    # "TsvActionType",
    # "TsvAddColumnsAction",
    # "TsvAddRowsAction",
    # "TsvCellData",
    # "TsvColumnData",
    # "TsvCopyColumnAction",
    # "TsvCopyRowAction",
    # "TsvDeleteColumnsAction",
    # "TsvDeleteRowsAction",
    # "TsvMoveColumnAction",
    # "TsvMoveRowAction",
    # "TsvRowData",
    # "TsvUpdateCellsAction",
    # "TsvUpdateColumnHeaderAction",
    # "TsvUpdateColumnsAction",
    # "TsvUpdateRowsAction",
    # "Filter",
    # "FilterDataType",
    # "FilterOperation",
    # "TsvFileFilterOption",
    # "TsvFilterException",
    # "CustomFilter",
    # "FilterRegistry",
    # "ContainsFilter",
    # "StartsWithFilter",
    # "EndsWithFilter",
    # "GreaterFilter",
    # "GreaterEqualFilter",
    # "LessFilter",
    # "LessEqualFilter",
    # "EmptyFilter",
    # "RegexFilter",
    # "ValidNumberCustomFilter",
    # "ValidDatetimeCustomFilter",
    # "EnumContainsCustomFilter",
    # "BetweenEqualCustomFilter",
    # "AbstractSorter",
    # "CustomSorter",
    # "DateTimeSorter",
    # "EnumSorter",
    # "FloatSorter",
    # "IntegerSorter",
    # "Sorter",
    # "SorterRegistry",
    # "SortType",
    # "SortValueClassification",
    # "StringSorter",
    # "TsvFileSortOption",
    # "TsvFileSortValueOrder",
    # "TsvSortException",
    # "TSV_FILE_ACTIONS",
    # "TsvFileUpdater",
    # "TsvActionException",
    # "BaseTsvAction",
    # "AddColumnsTsvAction",
    # "AddRowsTsvAction",
    # "CopyColumnTsvAction",
    # "CopyRowTsvAction",
    # "DeleteColumnsTsvAction",
    # "DeleteRowsTsvAction",
    # "MoveColumnTsvAction",
    # "UpdateCellsTsvAction",
    # "UpdateColumnsTsvAction",
    # "UpdateColumnHeadersTsvAction",
    # "UpdateRowsTsvAction",
    # # utils
    # "MetabolightsAuditUtils",
    # "MetabolightsSearchUtils",
    # "MetabolightsFileNameUtils",
    # # hash utils
    # "MetabolightsHashUtils",
    # "IsaMetadataFolderHash",
    # "EMPTY_FILE_HASH",
]
