disabled C0114,C0115,C0116,C0103,E0401,W1203,B101 in the github pylin…

…t action

.github/workflows/pylint.yml

@@ -20,4 +20,4 @@ jobs:
         pip install pylint
     - name: Analysing the code with pylint
       run: |
-        pylint $(git ls-files '*.py')
+        pylint $(git ls-files '*.py') --disable=C0114,C0115,C0116,C0103,E0401,W1203,B101,B311

.pre-commit-config.yaml

@@ -17,7 +17,8 @@ repos:
           [
             "-rn", # Only display messages
             "-sn", # Don't display the score
-            "--disable=pointless-statement,duplicate-code"  # do not warn on bit operator statements
+            "--disable=pointless-statement,duplicate-code,line-too-long,missing-module-docstring,missing-class-docstring"
+            # do not warn on bit operator statements
           ]
 
   - repo: https://github.com/DanielNoord/pydocstringformatter
@@ -87,3 +88,4 @@ repos:
     rev: '1.7.7'
     hooks:
       - id: bandit
+        args: ["--skip", "B101,B311"]

pyproject.toml

@@ -71,3 +71,6 @@ dev = [
 
 [tool.black]
 line-length = 100
+
+[tool.flake8]
+max-line-length = 100

src/cehrbert/data_generators/data_generator_base.py

@@ -275,9 +275,7 @@ def __init__(self, concept_tokenizer: ConceptTokenizer, *args, **kwargs):
 
     def _clean_dataframe(self):
         self._training_data = self._training_data[
-            self._training_data[self.default_required_column].apply(
-                lambda token_ids: len(token_ids)
-            )
+            self._training_data[self.default_required_column].apply(len)
             >= max(self.default_min_num_of_concepts, self._min_num_of_concepts)
         ]
 
@@ -330,9 +328,9 @@ def __init__(
         max_num_of_concepts: int,
         include_att_prediction: bool,
         include_visit_prediction: bool,
+        *args,
         min_num_of_concepts: int = 5,
         min_num_of_visits: int = 2,
-        *args,
         **kwargs,
     ):
 
@@ -341,7 +339,7 @@ def __init__(
         self._max_num_of_visits = max_num_of_visits
         self._max_num_of_concepts = max_num_of_concepts
 
-        super(HierarchicalBertDataGenerator, self).__init__(
+        super().__init__(
             concept_tokenizer=concept_tokenizer,
             visit_tokenizer=visit_tokenizer,
             max_num_of_visits=max_num_of_visits,
@@ -410,8 +408,7 @@ def __init__(
     ):
         self._include_readmission = include_readmission
         self._include_prolonged_length_stay = include_prolonged_length_stay
-
-        super(HierarchicalBertMultiTaskDataGenerator, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
 
     def _get_learning_objective_classes(self):