Fix pylint warnings and add typehints

metagenopolis · Aug 22, 2024 · 0da7851 · 0da7851
1 parent af20bf7
commit 0da7851
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/crocodeel/__init__.py b/crocodeel/__init__.py
@@ -1,3 +1,3 @@
 import os
 # Disable implicit parallelism in numpy
-os.environ["OMP_NUM_THREADS"] = "1"
+os.environ["OMP_NUM_THREADS"] = "1"
diff --git a/crocodeel/conta_event.py b/crocodeel/conta_event.py
@@ -77,7 +77,7 @@ def write_tsv(conta_events: list[ContaminationEvent], fh: TextIO) -> None:
                 ),
                 file=fh,
             )
-        
+
         logging.info(
             "Contamination events saved in %s",
             Path(fh.name).resolve(),

diff --git a/crocodeel/search_conta.py b/crocodeel/search_conta.py
@@ -57,7 +57,7 @@ def __init__(self, species_ab_table, rf_classifier):
         self.species_ab_table = species_ab_table
         self.rf_classifier = rf_classifier
 
-    def classify_sample_pair(self, sample_pair):
+    def classify_sample_pair(self, sample_pair) -> ContaminationEvent:
         source, target = sample_pair
 
         if source == target:
@@ -128,7 +128,7 @@ def __init__(
         self.num_sample_pairs = num_sample_pairs
         self.nproc = nproc
 
-    def search_contamination(self):
+    def search_contamination(self) -> list[ContaminationEvent]:
         rf_classifier = RandomForestModel.load()
         worker = ContaminationSearcherWorker(self.species_ab_table, rf_classifier)