refactor: file formats are updated with isort and black.

metabolights_utils/__init__.py

@@ -157,16 +157,8 @@
 #     MetabolightsHashUtils,
 # )
 # from metabolights_utils.utils.search_utils import MetabolightsSearchUtils
-from metabolights_utils import (
-    isatab,
-    commands,
-    models,
-    provider,
-    tsv,
-    utils,
-    common,
-    isa_file_utils,
-)
+from metabolights_utils import (commands, common, isa_file_utils, isatab,
+                                models, provider, tsv, utils)
 
 __VERSION__ = "1.3.7"
 

metabolights_utils/commands/cli.py

@@ -3,7 +3,8 @@
 from metabolights_utils import __VERSION__
 from metabolights_utils.commands.model.model_cli import model_cli
 from metabolights_utils.commands.public.public_cli import public_cli
-from metabolights_utils.commands.submission.submission_cli import submission_cli
+from metabolights_utils.commands.submission.submission_cli import \
+    submission_cli
 
 
 @click.group()

metabolights_utils/commands/public/public_describe.py

@@ -6,7 +6,8 @@
 from metabolights_utils.commands.utils import print_study_model_summary
 from metabolights_utils.models.parser.enums import ParserMessageType
 from metabolights_utils.provider import definitions
-from metabolights_utils.provider.ftp_repository import MetabolightsFtpRepository
+from metabolights_utils.provider.ftp_repository import \
+    MetabolightsFtpRepository
 
 
 @click.command(no_args_is_help=True, name="describe")

metabolights_utils/commands/public/public_download.py

@@ -5,7 +5,8 @@
 
 from metabolights_utils.provider import definitions
 from metabolights_utils.provider.ftp.model import LocalDirectory
-from metabolights_utils.provider.ftp_repository import MetabolightsFtpRepository
+from metabolights_utils.provider.ftp_repository import \
+    MetabolightsFtpRepository
 from metabolights_utils.provider.utils import is_metadata_filename_pattern
 
 

metabolights_utils/commands/public/public_list.py

@@ -7,7 +7,8 @@
 from metabolights_utils.common import sort_by_study_id
 from metabolights_utils.models.enums import GenericMessageType
 from metabolights_utils.provider import definitions
-from metabolights_utils.provider.ftp_repository import MetabolightsFtpRepository
+from metabolights_utils.provider.ftp_repository import \
+    MetabolightsFtpRepository
 
 
 @click.command(name="list")

metabolights_utils/commands/public/public_search.py

@@ -3,7 +3,8 @@
 
 import click
 
-from metabolights_utils.commands.utils import convert_html_to_plain_text, split_to_lines
+from metabolights_utils.commands.utils import (convert_html_to_plain_text,
+                                               split_to_lines)
 from metabolights_utils.provider import definitions
 from metabolights_utils.provider.utils import rest_api_post
 

metabolights_utils/commands/submission/submission_cli.py

@@ -2,24 +2,22 @@
 
 import click
 
-from metabolights_utils.commands.submission.submission_create_assay import (
-    submission_create_assay,
-)
-from metabolights_utils.commands.submission.submission_delete_assay import (
-    submission_delete_assay,
-)
-from metabolights_utils.commands.submission.submission_describe import (
-    submission_describe,
-)
-from metabolights_utils.commands.submission.submission_download import (
-    submission_download,
-)
-from metabolights_utils.commands.submission.submission_list import submission_list
-from metabolights_utils.commands.submission.submission_login import submission_login
-from metabolights_utils.commands.submission.submission_upload import submission_upload
-from metabolights_utils.commands.submission.submission_validate import (
-    submission_validate,
-)
+from metabolights_utils.commands.submission.submission_create_assay import \
+    submission_create_assay
+from metabolights_utils.commands.submission.submission_delete_assay import \
+    submission_delete_assay
+from metabolights_utils.commands.submission.submission_describe import \
+    submission_describe
+from metabolights_utils.commands.submission.submission_download import \
+    submission_download
+from metabolights_utils.commands.submission.submission_list import \
+    submission_list
+from metabolights_utils.commands.submission.submission_login import \
+    submission_login
+from metabolights_utils.commands.submission.submission_upload import \
+    submission_upload
+from metabolights_utils.commands.submission.submission_validate import \
+    submission_validate
 
 
 @click.group(name="submission")

metabolights_utils/commands/submission/submission_create_assay.py

@@ -4,9 +4,8 @@
 import click
 
 from metabolights_utils.provider import definitions
-from metabolights_utils.provider.submission_repository import (
-    MetabolightsSubmissionRepository,
-)
+from metabolights_utils.provider.submission_repository import \
+    MetabolightsSubmissionRepository
 
 VALID_PARAMETERS = {
     "LC-MS": (
@@ -82,9 +81,9 @@ def submission_create_assay(
     study_id: MetaboLights study accession number (MTBLSxxxx).
     assay_technique: Valid assay techniques:  NMR, LC-MS, LC-DAD, GC-MS, GCxGC-MS, GC-FID, DI-MS, FIA-MS, CE-MS, MALDI-MS, MSImaging
 
-    Acronyms: Diode array detection (LC-DAD), Tandem MS (GCxGC-MS), Flame ionisation detector (GC-FID), 
+    Acronyms: Diode array detection (LC-DAD), Tandem MS (GCxGC-MS), Flame ionisation detector (GC-FID),
     Direct infusion (DI-MS), Flow injection analysis (FIA-MS), Capillary electrophoresis (CE-MS),
-    Matrix-assisted laser desorption-ionisation imaging mass spectrometry (MALDI-MS), 
+    Matrix-assisted laser desorption-ionisation imaging mass spectrometry (MALDI-MS),
     Nuclear magnetic resonance (NMR), Mass spec spectrometry (MSImaging)
 
 

metabolights_utils/commands/submission/submission_delete_assay.py

@@ -4,9 +4,8 @@
 import click
 
 from metabolights_utils.provider import definitions
-from metabolights_utils.provider.submission_repository import (
-    MetabolightsSubmissionRepository,
-)
+from metabolights_utils.provider.submission_repository import \
+    MetabolightsSubmissionRepository
 
 
 @click.command(no_args_is_help=True, name="delete-assay")

metabolights_utils/commands/submission/submission_describe.py

@@ -5,9 +5,8 @@
 
 from metabolights_utils.commands.utils import print_study_model_summary
 from metabolights_utils.provider import definitions
-from metabolights_utils.provider.submission_repository import (
-    MetabolightsSubmissionRepository,
-)
+from metabolights_utils.provider.submission_repository import \
+    MetabolightsSubmissionRepository
 
 
 @click.command(no_args_is_help=True, name="describe")

metabolights_utils/commands/submission/submission_download.py

@@ -4,9 +4,8 @@
 import click
 
 from metabolights_utils.provider import definitions
-from metabolights_utils.provider.submission_repository import (
-    MetabolightsSubmissionRepository,
-)
+from metabolights_utils.provider.submission_repository import \
+    MetabolightsSubmissionRepository
 
 
 @click.command(no_args_is_help=True, name="download")

metabolights_utils/commands/submission/submission_list.py

@@ -3,14 +3,12 @@
 import click
 
 from metabolights_utils.commands.submission.model import (
-    StudyResponse,
-    SubmittedStudySummary,
-)
-from metabolights_utils.commands.utils import convert_html_to_plain_text, split_to_lines
+    StudyResponse, SubmittedStudySummary)
+from metabolights_utils.commands.utils import (convert_html_to_plain_text,
+                                               split_to_lines)
 from metabolights_utils.provider import definitions
-from metabolights_utils.provider.submission_repository import (
-    MetabolightsSubmissionRepository,
-)
+from metabolights_utils.provider.submission_repository import \
+    MetabolightsSubmissionRepository
 
 
 def print_submitted_study(study: SubmittedStudySummary, log):

metabolights_utils/commands/submission/submission_login.py

@@ -4,11 +4,9 @@
 
 import click
 
-from metabolights_utils.commands.submission.model import (
-    FtpLoginCredentials,
-    LoginCredentials,
-    RestApiCredentials,
-)
+from metabolights_utils.commands.submission.model import (FtpLoginCredentials,
+                                                          LoginCredentials,
+                                                          RestApiCredentials)
 from metabolights_utils.provider import definitions
 
 

metabolights_utils/commands/submission/submission_upload.py

@@ -3,9 +3,8 @@
 import click
 
 from metabolights_utils.provider import definitions
-from metabolights_utils.provider.submission_repository import (
-    MetabolightsSubmissionRepository,
-)
+from metabolights_utils.provider.submission_repository import \
+    MetabolightsSubmissionRepository
 
 
 @click.command(no_args_is_help=True, name="upload")

metabolights_utils/commands/submission/submission_validate.py

@@ -4,9 +4,8 @@
 import click
 
 from metabolights_utils.provider import definitions
-from metabolights_utils.provider.submission_repository import (
-    MetabolightsSubmissionRepository,
-)
+from metabolights_utils.provider.submission_repository import \
+    MetabolightsSubmissionRepository
 
 
 @click.command(no_args_is_help=True, name="validate")

metabolights_utils/commands/submission/utils.py

@@ -2,11 +2,9 @@
 import os
 from typing import Union
 
-from metabolights_utils.commands.submission.model import (
-    FtpLoginCredentials,
-    LoginCredentials,
-    RestApiCredentials,
-)
+from metabolights_utils.commands.submission.model import (FtpLoginCredentials,
+                                                          LoginCredentials,
+                                                          RestApiCredentials)
 
 
 def get_submission_private_ftp_credentials(

metabolights_utils/isa_file_utils.py

@@ -3,9 +3,10 @@
 from typing import Any, List, Tuple, Union
 
 from metabolights_utils.isatab import Writer
-from metabolights_utils.models.metabolights.model import MetabolightsStudyModel
-from metabolights_utils.models.isa.common import IsaTable, IsaTableColumn, IsaTableFile
+from metabolights_utils.models.isa.common import (IsaTable, IsaTableColumn,
+                                                  IsaTableFile)
 from metabolights_utils.models.isa.enums import ColumnsStructure
+from metabolights_utils.models.metabolights.model import MetabolightsStudyModel
 
 logger = logging.getLogger(__name__)
 

metabolights_utils/isatab/__init__.py

@@ -1,21 +1,14 @@
 from functools import lru_cache
 
-from metabolights_utils.isatab.default.factory import (
-    DefaultIsaTabReaderFactory,
-    DefaultIsaTabWriterFactory,
-)
-from metabolights_utils.isatab.reader import (
-    InvestigationFileReader,
-    IsaTableFileReader,
-    IsaTabReaderFactory,
-)
-from metabolights_utils.isatab.writer import (
-    InvestigationFileWriter,
-    IsaTableFileWriter,
-    IsaTabWriterFactory,
-)
-
 from metabolights_utils.isatab import default, reader, writer
+from metabolights_utils.isatab.default.factory import (
+    DefaultIsaTabReaderFactory, DefaultIsaTabWriterFactory)
+from metabolights_utils.isatab.reader import (InvestigationFileReader,
+                                              IsaTableFileReader,
+                                              IsaTabReaderFactory)
+from metabolights_utils.isatab.writer import (InvestigationFileWriter,
+                                              IsaTableFileWriter,
+                                              IsaTabWriterFactory)
 
 
 @lru_cache

metabolights_utils/isatab/default/__init__.py

@@ -1,14 +1,8 @@
-from metabolights_utils.isatab.default import (
-    parser,
-    assay_file,
-    assignment_file,
-    base_isa_table_file,
-    base_isa_file,
-    factory,
-    investigation_file,
-    sample_file,
-    writer,
-)
+from metabolights_utils.isatab.default import (assay_file, assignment_file,
+                                               base_isa_file,
+                                               base_isa_table_file, factory,
+                                               investigation_file, parser,
+                                               sample_file, writer)
 
 __all__ = [
     "parser",

metabolights_utils/isatab/default/assay_file.py

@@ -1,6 +1,7 @@
 from typing import List
 
-from metabolights_utils.isatab.default.base_isa_table_file import BaseIsaTableFileReader
+from metabolights_utils.isatab.default.base_isa_table_file import \
+    BaseIsaTableFileReader
 
 
 class DefaultAssayFileReader(BaseIsaTableFileReader):

metabolights_utils/isatab/default/assignment_file.py

@@ -1,6 +1,7 @@
 from typing import List
 
-from metabolights_utils.isatab.default.base_isa_table_file import BaseIsaTableFileReader
+from metabolights_utils.isatab.default.base_isa_table_file import \
+    BaseIsaTableFileReader
 
 
 class DefaultAssignmentFileReader(BaseIsaTableFileReader):

metabolights_utils/isatab/default/base_isa_table_file.py

@@ -6,17 +6,17 @@
 from typing import List, Union
 
 from metabolights_utils.isatab.default.base_isa_file import BaseIsaFile
-from metabolights_utils.isatab.default.parser.isa_table_parser import get_isa_table_file
-from metabolights_utils.isatab.reader import (
-    IsaTableFileReader,
-    IsaTableFileReaderResult,
-)
+from metabolights_utils.isatab.default.parser.isa_table_parser import \
+    get_isa_table_file
+from metabolights_utils.isatab.reader import (IsaTableFileReader,
+                                              IsaTableFileReaderResult)
 from metabolights_utils.models.isa.common import IsaTable, IsaTableFile
 from metabolights_utils.models.parser.common import ParserMessage, ParserReport
 from metabolights_utils.models.parser.enums import ParserMessageType
 from metabolights_utils.tsv.filter import TsvFileFilterOption
 from metabolights_utils.tsv.sort import TsvFileSortOption
-from metabolights_utils.utils.hash_utils import MetabolightsHashUtils as HashUtils
+from metabolights_utils.utils.hash_utils import \
+    MetabolightsHashUtils as HashUtils
 
 logger = logging.getLogger(__name__)
 

metabolights_utils/isatab/default/factory.py

@@ -1,25 +1,19 @@
 import logging
 
 from metabolights_utils.isatab.default.assay_file import DefaultAssayFileReader
-from metabolights_utils.isatab.default.assignment_file import (
-    DefaultAssignmentFileReader,
-)
+from metabolights_utils.isatab.default.assignment_file import \
+    DefaultAssignmentFileReader
 from metabolights_utils.isatab.default.investigation_file import (
-    DefaultInvestigationFileReader,
-    DefaultInvestigationFileWriter,
-)
-from metabolights_utils.isatab.default.sample_file import DefaultSampleFileReader
+    DefaultInvestigationFileReader, DefaultInvestigationFileWriter)
+from metabolights_utils.isatab.default.sample_file import \
+    DefaultSampleFileReader
 from metabolights_utils.isatab.default.writer import DefaultIsaTableFileWriter
-from metabolights_utils.isatab.reader import (
-    InvestigationFileReader,
-    IsaTableFileReader,
-    IsaTabReaderFactory,
-)
-from metabolights_utils.isatab.writer import (
-    InvestigationFileWriter,
-    IsaTableFileWriter,
-    IsaTabWriterFactory,
-)
+from metabolights_utils.isatab.reader import (InvestigationFileReader,
+                                              IsaTableFileReader,
+                                              IsaTabReaderFactory)
+from metabolights_utils.isatab.writer import (InvestigationFileWriter,
+                                              IsaTableFileWriter,
+                                              IsaTabWriterFactory)
 
 logger = logging.getLogger(__name__)