isort fixed

sdrf_pipelines/maxquant/maxquant.py

@@ -8,7 +8,8 @@
 import re
 import time
 from datetime import datetime
-from xml.dom.minidom import Document, parse
+from xml.dom.minidom import Document
+from xml.dom.minidom import parse
 
 import numpy as np
 import pandas as pd

sdrf_pipelines/openms/openms.py

@@ -3,6 +3,7 @@
 from collections import Counter
 
 import pandas as pd
+
 from sdrf_pipelines.openms.unimod import UnimodDatabase
 
 # example: parse_sdrf convert-openms -s .\sdrf-pipelines\sdrf_pipelines\large_sdrf.tsv -c '[characteristics[biological replicate],characteristics[individual]]'

sdrf_pipelines/openms/unimod.py

@@ -1,6 +1,6 @@
 import re
-import defusedxml.ElementTree as et
 
+import defusedxml.ElementTree as et
 import pkg_resources
 
 

sdrf_pipelines/parse_sdrf.py

@@ -15,7 +15,9 @@
 from sdrf_pipelines.normalyzerde.normalyzerde import NormalyzerDE
 from sdrf_pipelines.openms.openms import OpenMS
 from sdrf_pipelines.sdrf.sdrf import SdrfDataFrame
-from sdrf_pipelines.sdrf.sdrf_schema import ALL_TEMPLATES, DEFAULT_TEMPLATE, MASS_SPECTROMETRY
+from sdrf_pipelines.sdrf.sdrf_schema import ALL_TEMPLATES
+from sdrf_pipelines.sdrf.sdrf_schema import DEFAULT_TEMPLATE
+from sdrf_pipelines.sdrf.sdrf_schema import MASS_SPECTROMETRY
 from sdrf_pipelines.utils.exceptions import AppConfigException
 
 CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])

sdrf_pipelines/sdrf/sdrf_schema.py

@@ -4,14 +4,14 @@
 from typing import Any
 
 import pandas as pd
-from pandas_schema import Column, Schema
-from pandas_schema.validation import (
-    LeadingWhitespaceValidation,
-    MatchesPatternValidation,
-    TrailingWhitespaceValidation,
-    _BaseValidation,
-    _SeriesValidation,
-)
+from pandas_schema import Column
+from pandas_schema import Schema
+from pandas_schema.validation import LeadingWhitespaceValidation
+from pandas_schema.validation import MatchesPatternValidation
+from pandas_schema.validation import TrailingWhitespaceValidation
+from pandas_schema.validation import _BaseValidation
+from pandas_schema.validation import _SeriesValidation
+
 from sdrf_pipelines.sdrf import sdrf
 from sdrf_pipelines.utils.exceptions import LogicError
 from sdrf_pipelines.zooma.ols import OlsClient

sdrf_pipelines/sdrf_merge/add_data_analysis_param.py

@@ -3,6 +3,7 @@
 
 import pandas as pd
 import yaml
+
 from sdrf_pipelines.openms.unimod import UnimodDatabase
 from sdrf_pipelines.sdrf.sdrf import SdrfDataFrame
 from sdrf_pipelines.zooma.zooma import OlsClient

sdrf_pipelines/tests/test_sdrfchecker.py

@@ -1,6 +1,8 @@
 from click.testing import CliRunner
+
 from sdrf_pipelines.parse_sdrf import cli
-from sdrf_pipelines.zooma.zooma import SlimOlsClient, Zooma
+from sdrf_pipelines.zooma.zooma import SlimOlsClient
+from sdrf_pipelines.zooma.zooma import Zooma
 
 
 def test_validate_srdf():

sdrf_pipelines/zooma/zooma.py

@@ -1,5 +1,6 @@
 import requests
 from requests import HTTPError
+
 from sdrf_pipelines.zooma.ols import OlsClient