Fix pylint warnings

crocodeel/easy_wf.py

@@ -1,5 +1,5 @@
 from typing import Any
-import crocodeel.ab_table_utils as ab_table_utils
+from crocodeel import ab_table_utils
 from crocodeel.search_conta import run_search_conta
 from crocodeel.plot_conta import run_plot_conta, Defaults as plot_conta_defaults
 
@@ -16,6 +16,3 @@ def run_easy_wf(args: dict[str,Any]):
     args["no_conta_line"] = False
     args["color_conta_species"] = False
     run_plot_conta(args)
-
-
-

crocodeel/plot_conta.py

@@ -1,14 +1,14 @@
 from typing import BinaryIO, Any, Final
 from functools import partial
+import logging
+from time import perf_counter
 from matplotlib.backends.backend_pdf import PdfPages
 import matplotlib.pyplot as plt
 import pandas as pd
 import numpy as np
 import tqdm
-import logging
-from time import perf_counter
 from crocodeel.conta_event import ContaminationEvent, ContaminationEventIO
-import crocodeel.ab_table_utils as ab_table_utils
+from crocodeel import ab_table_utils
 
 
 def run_plot_conta(args: dict[str, Any]):

crocodeel/rf_model.py

@@ -12,7 +12,7 @@ def get_path() -> Path:
             Path(__file__).resolve().parent / "models" / "crocodeel_rf_Mar2023.joblib"
         )
         return model_path
-    
+
     @staticmethod
     def load() -> RandomForestClassifier:
         return joblib.load(RandomForestModel.get_path())

crocodeel/search_conta.py

@@ -1,17 +1,17 @@
 from multiprocessing import Pool
 from functools import partial
 from itertools import product
-import numpy as np
-import pandas as pd
-import tqdm
 import logging
 from time import perf_counter
 from typing import Final, Any
+import numpy as np
+import pandas as pd
+import tqdm
 from sklearn.linear_model import RANSACRegressor, LinearRegression
 from sklearn.metrics import mean_squared_error
 from sklearn.neighbors import NearestNeighbors
 from scipy.stats import spearmanr
-import crocodeel.ab_table_utils as ab_table_utils
+from crocodeel import ab_table_utils
 from crocodeel.conta_event import ContaminationEvent, ContaminationEventIO
 from crocodeel.rf_model import RandomForestModel
 
@@ -39,7 +39,10 @@ def run_search_conta(args: dict[str,Any]):
 
     conta_events.sort(key=lambda e: e.rate, reverse=True)
     ContaminationEventIO.write_tsv(conta_events, args['conta_events_fh'])
-    logging.info("Contamination events sorted by decreasing contamination rate saved in %s", args['conta_events_fh'].name)
+    logging.info(
+        "Contamination events sorted by decreasing contamination rate saved in %s",
+        args["conta_events_fh"].name,
+    )
     if args["conta_events_fh"].mode == 'w':
         args["conta_events_fh"].close()
 

crocodeel/test_install.py

@@ -19,12 +19,20 @@ class TestData:
 
 def run_test_install(keep_results: bool) -> None:
     with (
-        open(TestData.SPECIES_ABUNDANCE_TABLE, "r") as species_ab_table_fh,
+        open(TestData.SPECIES_ABUNDANCE_TABLE, "r", encoding="utf-8") as species_ab_table_fh,
         NamedTemporaryFile(
-            mode="w+", prefix="contamination_events_", suffix=".tsv", delete = not keep_results, delete_on_close=False
+            mode="w+",
+            prefix="contamination_events_",
+            suffix=".tsv",
+            delete=not keep_results,
+            delete_on_close=False,
         ) as conta_events_fh,
         NamedTemporaryFile(
-            mode="wb", prefix="contamination_events_", suffix=".pdf", delete = not keep_results, delete_on_close=False
+            mode="wb",
+            prefix="contamination_events_",
+            suffix=".pdf",
+            delete=not keep_results,
+            delete_on_close=False,
         ) as pdf_report_fh,
     ):
         easy_wf_args = {