from metabolights_utils import common as metabolights_common
from metabolights_utils.isatab import Reader, Writer, reader, writer
from metabolights_utils.isatab.default import assay_file as default_assay_file_reader
from metabolights_utils.isatab.default import (
    assignment_file as default_assignment_file_reader,
)
from metabolights_utils.isatab.default import base_isa_file, base_isa_table_file
from metabolights_utils.isatab.default import factory as default_factory
from metabolights_utils.isatab.default import (
    investigation_file as default_investigation_file_operations,
)
from metabolights_utils.isatab.default import sample_file as default_sample_file_reader
from metabolights_utils.isatab.default import writer as default_isa_writer
from metabolights_utils.isatab.default.parser import common as default_parser_commons
from metabolights_utils.isatab.default.parser import (
    investigation_parser,
    isa_table_parser,
)
from metabolights_utils.models import common as models_common
from metabolights_utils.models import enums as models_enum
from metabolights_utils.models.isa import assay_file, assignment_file
from metabolights_utils.models.isa import common as isa_commons
from metabolights_utils.models.isa import enums as isa_enums
from metabolights_utils.models.isa import investigation_file, samples_file
from metabolights_utils.models.metabolights import metabolights_study
from metabolights_utils.models.parser import common as parser_common
from metabolights_utils.models.parser import enums as parser_enums
from metabolights_utils.tsv import filter as tsv_filter
from metabolights_utils.tsv import model as tsv_model
from metabolights_utils.tsv import sort as tsv_sort
from metabolights_utils.tsv import tsv_file_updater
from metabolights_utils.tsv import utils as tsv_utils
from metabolights_utils.tsv.actions import add_column, add_row
from metabolights_utils.tsv.actions import base as tsv_actions_base
from metabolights_utils.tsv.actions import (
    copy_column,
    copy_row,
    delete_column,
    delete_row,
    move_column,
    move_row,
    update_cell,
    update_column,
    update_column_header,
    update_row,
)
from metabolights_utils.utils import (
    audit_utils,
    filename_utils,
    hash_utils,
    search_utils,
)
from metabolights_utils.utils.audit_utils import create_audit_folder
from metabolights_utils.utils.hash_utils import (
    get_isa_metadata_folder_hash,
    sha256sum,
    IsaMetadataFolderHash,
    EMPTY_FILE_HASH,
)

__all__ = [
    "Reader",
    "Writer",
    "metabolights_common",
    "metabolights_study",
    "parser_common",
    "parser_enums",
    "models_common",
    "models_enum",
    "assay_file",
    "assignment_file",
    "isa_commons",
    "isa_enums",
    "investigation_file",
    "samples_file",
    "reader",
    "writer",
    "default_assay_file_reader",
    "default_assignment_file_reader",
    "base_isa_file",
    "base_isa_table_file",
    "default_factory",
    "default_investigation_file_operations",
    "default_sample_file_reader",
    "default_isa_writer",
    "default_parser_commons",
    "investigation_parser",
    "isa_table_parser",
    # TSV
    "tsv_filter",
    "tsv_model",
    "tsv_sort",
    "tsv_file_updater",
    "tsv_utils",
    "add_column",
    "add_row",
    "tsv_actions_base",
    "copy_column",
    "copy_row",
    "delete_column",
    "delete_row",
    "move_column",
    "move_row",
    "update_cell",
    "update_column_header",
    "update_column",
    "update_row",
    # UTILS
    "audit_utils",
    "hash_utils",
    "filename_utils",
    "search_utils",
    # audit utils
    "create_audit_folder"
    # hash utils
    "get_isa_metadata_folder_hash",
    "sha256sum",
    "IsaMetadataFolderHash",
    "EMPTY_FILE_HASH",
]
