Format the entire repo with Black and iSort (#469)(patch)

### Fixed
- the formatting of all the Python files in the repository

cg_lims/EPPs/arnold/base.py

@@ -1,11 +1,10 @@
 #!/usr/bin/env python
 
 import click
-
+from cg_lims.EPPs.arnold.flow_cell import flow_cell
 from cg_lims.EPPs.arnold.prep import prep
 from cg_lims.EPPs.arnold.sample import sample
 from cg_lims.EPPs.arnold.sequencing import sequencing
-from cg_lims.EPPs.arnold.flow_cell import flow_cell
 
 
 @click.group(invoke_without_command=True)

cg_lims/EPPs/arnold/flow_cell.py

@@ -2,15 +2,12 @@
 from typing import List
 
 import click
-from genologics.lims import Process, Lims, Artifact
 import requests
-from requests import Response
-
 from cg_lims.exceptions import LimsError
 from cg_lims.get.artifacts import OutputGenerationType, OutputType, get_output_artifacts
-
 from cg_lims.models.arnold.flow_cell import FlowCell, Lane
-
+from genologics.lims import Artifact, Lims, Process
+from requests import Response
 
 LOG = logging.getLogger(__name__)
 

cg_lims/EPPs/arnold/prep.py

@@ -1,22 +1,20 @@
+import json
 import logging
 from typing import List, Literal
 
 import click
-from genologics.lims import Lims, Process, Sample
 import requests
-from requests import Response
-import json
-
 from cg_lims import options
 from cg_lims.exceptions import LimsError
 from cg_lims.get.samples import get_process_samples
 from cg_lims.models.arnold.base_step import BaseStep
 from cg_lims.models.arnold.prep.microbial_prep import build_microbial_step_documents
-from cg_lims.models.arnold.prep.wgs import build_wgs_documents
+from cg_lims.models.arnold.prep.rna import build_rna_documents
 from cg_lims.models.arnold.prep.sars_cov_2_prep import build_sars_cov_2_documents
 from cg_lims.models.arnold.prep.twist import build_twist_documents
-from cg_lims.models.arnold.prep.rna import build_rna_documents
-
+from cg_lims.models.arnold.prep.wgs import build_wgs_documents
+from genologics.lims import Lims, Process, Sample
+from requests import Response
 
 LOG = logging.getLogger(__name__)
 

cg_lims/EPPs/arnold/sample.py

@@ -1,14 +1,14 @@
+import json
 import logging
 from typing import List
 
 import click
-from genologics.lims import Process, Sample
 import requests
-from requests import Response
-import json
 from cg_lims.exceptions import LimsError
 from cg_lims.get.samples import get_process_samples
 from cg_lims.models.arnold.sample import ArnoldSample
+from genologics.lims import Process, Sample
+from requests import Response
 
 LOG = logging.getLogger(__name__)
 

cg_lims/EPPs/arnold/sequencing.py

@@ -1,19 +1,17 @@
+import json
 import logging
 from typing import List, Literal
 
 import click
-from genologics.lims import Lims, Process, Sample
 import requests
-from requests import Response
-import json
-
 from cg_lims import options
 from cg_lims.exceptions import LimsError
 from cg_lims.get.samples import get_process_samples
 from cg_lims.models.arnold.base_step import BaseStep
 from cg_lims.models.arnold.sequencing.novaseq_6000 import build_novaseq_6000_step_documents
 from cg_lims.models.arnold.sequencing.novaseq_x import build_novaseq_x_step_documents
-
+from genologics.lims import Lims, Process, Sample
+from requests import Response
 
 LOG = logging.getLogger(__name__)
 

cg_lims/EPPs/base.py

@@ -3,17 +3,16 @@
 import pathlib
 
 import click
-from genologics.entities import Process
-
 from cg_lims import options
+from cg_lims.EPPs.arnold import arnold_upload
 from cg_lims.EPPs.files import files
 
 # commands
 from cg_lims.EPPs.move import move
-from cg_lims.EPPs.udf import udf
 from cg_lims.EPPs.qc import qc
-from cg_lims.EPPs.arnold import arnold_upload
+from cg_lims.EPPs.udf import udf
 from cg_lims.get.files import get_log_content
+from genologics.entities import Process
 
 
 @click.group(invoke_without_command=True)

cg_lims/EPPs/files/barcode_tubes.py

@@ -1,22 +1,22 @@
-import re
 import logging
+import re
 import sys
-import click
-import pandas as pd
-
 from pathlib import Path
 from typing import List
-from genologics.lims import Artifact
+
+import click
+import pandas as pd
 from cg_lims import options
-from cg_lims.exceptions import LimsError, InvalidValueError, MissingValueError
+from cg_lims.exceptions import InvalidValueError, LimsError, MissingValueError
 from cg_lims.get.artifacts import get_artifacts
 from cg_lims.get.fields import get_barcode
-
+from genologics.lims import Artifact
 
 LOG = logging.getLogger(__name__)
 
+
 def get_data_and_write(
-    artifacts: List[Artifact], 
+    artifacts: List[Artifact],
     file: str,
 ):
     """Making a barcode csv file with sample names as barcode."""
@@ -31,59 +31,55 @@ def get_data_and_write(
             art_container_type = artifact.container.type.name
 
             if art_container_type.lower() != "tube":
-
                 LOG.info(
-                    f"Sample {barcode} does not have container type \"Tube\" therefore excluded."
+                    f'Sample {barcode} does not have container type "Tube" therefore excluded.'
                 )
                 continue
-
-
-            #Function to get project nr and sample id
-            f=lambda x: re.findall(r'\d+',x)
-
+
+            # Function to get project nr and sample id
+            f = lambda x: re.findall(r"\d+", x)
+
             file_rows.append([barcode, f(barcode)[0], int(f(barcode)[1])])
             #                           ^^^^^          ^^^^^^
-            #  e.g.     ACC10001A1 =    10001             1 
-        
+            #  e.g.     ACC10001A1 =    10001             1
+
         except:
-            unexpected_container_type = + 1
+            unexpected_container_type = +1
             failed_samples.append(artifact.samples[0].id)
 
     if unexpected_container_type:
         failed_message = " ".join(map(str, failed_samples))
         raise InvalidValueError(
-            f"The following samples are missing a container: {failed_message} of type \"Tube\"."
+            f'The following samples are missing a container: {failed_message} of type "Tube".'
         )
 
     if file_rows == []:
-        raise MissingValueError(
-            f"Missing samples with container type \"Tube\"."
-        )
+        raise MissingValueError(f'Missing samples with container type "Tube".')
 
     # Sort and create csv file.
     unfiltered_df = pd.DataFrame(
-        data=file_rows, 
-        index = None, 
-        columns = [
+        data=file_rows,
+        index=None,
+        columns=[
             "Barcode",
             "Project",
             "id",
-        ]
-        ).sort_values(by=["Project","id"])
-    
+        ],
+    ).sort_values(by=["Project", "id"])
+
     # Filter off unwanted columns
     out = unfiltered_df["Barcode"]
     out.to_csv(Path(file), index=False)
-
-
 
 
 @click.command()
 @options.file_placeholder(help="Barcode Tubes")
 @options.input()
 @click.pass_context
 def make_barcode_csv(
-    ctx: click.Context, file: str, input: bool,
+    ctx: click.Context,
+    file: str,
+    input: bool,
 ):
     """Script to make barcode for tubes"""
 

cg_lims/EPPs/files/base.py

@@ -1,15 +1,15 @@
 #!/usr/bin/env python
 import click
+from cg_lims.EPPs.files.barcode_tubes import make_barcode_csv
+from cg_lims.EPPs.files.csv_for_kapa_truble_shooting.csv_for_kapa_debug import trouble_shoot_kapa
 
 # commands
 from cg_lims.EPPs.files.file_to_udf import csv_well_to_udf
 from cg_lims.EPPs.files.hamilton.base import hamilton
-from cg_lims.EPPs.files.xml_to_udf import parse_run_parameters
-from cg_lims.EPPs.files.pooling_map.make_pooling_map import pool_map
 from cg_lims.EPPs.files.placement_map.make_96well_placement_map import placement_map
-from cg_lims.EPPs.files.csv_for_kapa_truble_shooting.csv_for_kapa_debug import trouble_shoot_kapa
-from cg_lims.EPPs.files.barcode_tubes import make_barcode_csv
+from cg_lims.EPPs.files.pooling_map.make_pooling_map import pool_map
 from cg_lims.EPPs.files.sample_sheet.create_sample_sheet import create_sample_sheet
+from cg_lims.EPPs.files.xml_to_udf import parse_run_parameters
 
 
 @click.group(invoke_without_command=True)

cg_lims/EPPs/files/csv_for_kapa_truble_shooting/csv_for_kapa_debug.py

@@ -1,26 +1,25 @@
 import csv
+import logging
 import sys
 from pathlib import Path
 from typing import List
 
 import click
-import logging
-from genologics.lims import Lims
-
 from cg_lims import options
-from cg_lims.EPPs.files.csv_for_kapa_truble_shooting.models import DebugKapaCSV, HEADERS
+from cg_lims.EPPs.files.csv_for_kapa_truble_shooting.models import HEADERS, DebugKapaCSV
+from cg_lims.exceptions import FileError, LimsError
+from cg_lims.get.artifacts import get_artifact_by_name
+from cg_lims.get.files import get_file_path
 from cg_lims.models.api.master_steps import (
-    HybridizeLibraryTWIST,
     AliquotsamplesforenzymaticfragmentationTWIST,
-    KAPALibraryPreparation,
-    PoolsamplesforhybridizationTWIST,
-    CaptureandWashTWIST,
     BeadPurificationTWIST,
     BufferExchange,
+    CaptureandWashTWIST,
+    HybridizeLibraryTWIST,
+    KAPALibraryPreparation,
+    PoolsamplesforhybridizationTWIST,
 )
-from cg_lims.exceptions import LimsError, FileError
-from cg_lims.get.artifacts import get_artifact_by_name
-from cg_lims.get.files import get_file_path
+from genologics.lims import Lims
 
 LOG = logging.getLogger(__name__)
 

cg_lims/EPPs/files/csv_for_kapa_truble_shooting/models.py

@@ -1,6 +1,5 @@
-from pydantic.v1 import BaseModel, Field
-
 from cg_lims.models.api.master_steps import HybridizeLibraryTWIST
+from pydantic.v1 import BaseModel, Field
 
 
 class DebugKapaCSV(BaseModel):

cg_lims/EPPs/files/file_to_udf.py

@@ -1,17 +1,16 @@
 #!/usr/bin/env python
 
+import csv
 import logging
 import sys
-import csv
 from pathlib import Path
 
 import click
-from genologics.entities import Artifact
-
 from cg_lims import options
 from cg_lims.exceptions import LimsError, MissingArtifactError, MissingFileError
 from cg_lims.get.artifacts import get_artifact_by_name
 from cg_lims.get.files import get_file_path
+from genologics.entities import Artifact
 
 LOG = logging.getLogger(__name__)
 
@@ -53,7 +52,7 @@ def set_udfs(well_field: str, value_field: str, udf: str, well_dict: dict, resul
                 continue
             art = well_dict[well]
             try:
-            	art.udf[udf] = str(value)
+                art.udf[udf] = str(value)
             except:
                 art.udf[udf] = float(value)
             art.put()
@@ -62,7 +61,7 @@ def set_udfs(well_field: str, value_field: str, udf: str, well_dict: dict, resul
     if passed_arts < len(well_dict.keys()):
         error_msg.append("Some samples in the step were not represented in the file.")
 
-    error_string = ' '.join(list(set(error_msg)))
+    error_string = " ".join(list(set(error_msg)))
     if error_msg:
         raise MissingArtifactError(error_string)
 

cg_lims/EPPs/files/hamilton/base.py

@@ -1,10 +1,10 @@
 import click
+from cg_lims.EPPs.files.hamilton.buffer_exchange_twist_file import buffer_exchange_twist_file
+from cg_lims.EPPs.files.hamilton.make_kapa_csv import make_kapa_csv
 
 # commands
 from cg_lims.EPPs.files.hamilton.normalization_file import barcode_file
-from cg_lims.EPPs.files.hamilton.make_kapa_csv import make_kapa_csv
 from cg_lims.EPPs.files.hamilton.sars_cov2_prep_file import sars_cov2_prep_file
-from cg_lims.EPPs.files.hamilton.buffer_exchange_twist_file import buffer_exchange_twist_file
 
 
 @click.group(invoke_without_command=True)

cg_lims/EPPs/files/hamilton/buffer_exchange_twist_file.py

@@ -2,17 +2,16 @@
 
 import logging
 import sys
-
-import click
 from typing import List
-from genologics.entities import Artifact
 
+import click
 from cg_lims import options
 from cg_lims.exceptions import LimsError, MissingUDFsError
 from cg_lims.files.manage_csv_files import make_plate_file
 from cg_lims.get.artifacts import get_artifacts
 from cg_lims.get.fields import get_artifact_well
 from cg_lims.get.samples import get_one_sample_from_artifact
+from genologics.entities import Artifact
 
 LOG = logging.getLogger(__name__)
 

cg_lims/EPPs/files/hamilton/make_kapa_csv.py

@@ -4,13 +4,12 @@
 import sys
 
 import click
-from genologics.lims import Lims
-
 from cg_lims import options
 from cg_lims.exceptions import LimsError, MissingUDFsError
 from cg_lims.files.manage_csv_files import make_plate_file
 from cg_lims.get.artifacts import get_artifacts, get_latest_analyte
 from cg_lims.get.fields import get_index_well
+from genologics.lims import Lims
 
 LOG = logging.getLogger(__name__)
 

cg_lims/EPPs/files/hamilton/normalization_file.py

@@ -5,13 +5,12 @@
 from typing import List
 
 import click
-from genologics.lims import Artifact
-
 from cg_lims import options
 from cg_lims.EPPs.files.hamilton.models import BarcodeFileRow
 from cg_lims.exceptions import LimsError, MissingUDFsError
 from cg_lims.files.manage_csv_files import build_csv, sort_csv_plate_and_tube
 from cg_lims.get.artifacts import get_artifacts
+from genologics.lims import Artifact
 
 LOG = logging.getLogger(__name__)