black and isort

cg_lims/EPPs/files/base.py

@@ -2,6 +2,7 @@
 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
+from cg_lims.EPPs.files.femtopulse_csv import make_femtopulse_csv
 
 # commands
 from cg_lims.EPPs.files.file_to_udf import csv_well_to_udf
@@ -14,7 +15,6 @@
 from cg_lims.EPPs.files.smrt_link.run_design import create_smrtlink_run_design
 from cg_lims.EPPs.files.smrt_link.sample_setup import create_smrtlink_sample_setup
 from cg_lims.EPPs.files.xml_to_udf import parse_run_parameters
-from cg_lims.EPPs.files.femtopulse_csv import make_femtopulse_csv
 
 
 @click.group(invoke_without_command=True)

cg_lims/EPPs/files/femtopulse_csv.py

@@ -5,17 +5,16 @@
 
 import click
 import pandas as pd
-from genologics.lims import Artifact
-
 from cg_lims import options
 from cg_lims.exceptions import InvalidValueError, LimsError
 from cg_lims.get.artifacts import get_artifacts
+from genologics.lims import Artifact
 
 LOG = logging.getLogger(__name__)
 
-ROWS = list(range(1,13)) # List numbered 1 to 12
-WELL_POSITIONS = [f"A{i}" for i in range(1,13)] # List with well positions A1-A12
-SAMPLE_NAMES = [""] * 12 # List with twelve empty positions for sample names
+ROWS = list(range(1, 13))  # List numbered 1 to 12
+WELL_POSITIONS = [f"A{i}" for i in range(1, 13)]  # List with well positions A1-A12
+SAMPLE_NAMES = [""] * 12  # List with twelve empty positions for sample names
 
 
 def parse_well(artifact_position: str) -> str:
@@ -27,12 +26,9 @@ def parse_well(artifact_position: str) -> str:
         return None
 
 
-def get_data_and_write(
-        artifacts: List[Artifact],
-        file: str
-):
-    """Make a csv file for a Femtopulse run start with three columns: 
-    one numbered 1-12, one with the sample position/well for the run and 
+def get_data_and_write(artifacts: List[Artifact], file: str):
+    """Make a csv file for a Femtopulse run start with three columns:
+    one numbered 1-12, one with the sample position/well for the run and
     a column with the sample name or ladder (in the 12th position)."""
 
     failed_samples: list = []
@@ -52,35 +48,41 @@ def get_data_and_write(
             if index < 11:
                 SAMPLE_NAMES[index] = artifact_name
             else:
-                failed_samples.append({"artifact_name": artifact_name, 
-                                       "parsed_well": parsed_well, 
-                                       "error": "This position is reserved for the ladder."})
+                failed_samples.append(
+                    {
+                        "artifact_name": artifact_name,
+                        "parsed_well": parsed_well,
+                        "error": "This position is reserved for the ladder.",
+                    }
+                )
         else:
-            failed_samples.append({"artifact_name": artifact_name, 
-                                "parsed_well": parsed_well, 
-                                "error": "Position is not possible for the run."})
+            failed_samples.append(
+                {
+                    "artifact_name": artifact_name,
+                    "parsed_well": parsed_well,
+                    "error": "Position is not possible for the run.",
+                }
+            )
 
     # Prints out error message(s)
     if failed_samples:
         error_index: int = 0
         for sample in failed_samples:
-            error_message: str = f"Sample {sample['artifact_name']} in position {sample['parsed_well']}: {sample['error']}"
+            error_message: str = (
+                f"Sample {sample['artifact_name']} in position {sample['parsed_well']}: {sample['error']}"
+            )
             if error_index < 1:
                 all_errors: str = error_message
-                error_index =+ 1
+                error_index = +1
             else:
-                all_errors = all_errors + ' ' + error_message
+                all_errors = all_errors + " " + error_message
         raise InvalidValueError(f"Errors found: {all_errors}")
 
     # The ladder will always be in well A12
     SAMPLE_NAMES[-1] = "ladder"
 
     # Create the csv file
-    df = pd.DataFrame({
-        0: ROWS,
-        1: WELL_POSITIONS,
-        2: SAMPLE_NAMES
-    })
+    df = pd.DataFrame({0: ROWS, 1: WELL_POSITIONS, 2: SAMPLE_NAMES})
     df.to_csv(Path(file), index=False, header=False)
 
 
@@ -106,4 +108,4 @@ def make_femtopulse_csv(
         )
         click.echo("The file was successfully generated.")
     except LimsError as e:
-        sys.exit(e.message)
+        sys.exit(e.message)