diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 20d94e7f..b6806c8c 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pycqa/isort
-    rev: 5.11.2
+    rev: 5.11.3
     hooks:
       - id: isort
         args: ["--settings-path", "pyproject.toml", "--check"]
@@ -10,6 +10,11 @@ repos:
     hooks:
       - id: black
         args: ["--config", "pyproject.toml", "--check"]
+  - repo: https://github.com/hadialqattan/pycln
+    rev: v2.1.2 # Possible releases: https://github.com/hadialqattan/pycln/releases
+    hooks:
+      - id: pycln
+        args: ["--config", "pyproject.toml"]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v2.3.0
     hooks:
diff --git a/pyproject.toml b/pyproject.toml
index f2a639e8..ad84c5f3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -37,6 +37,7 @@ exclude = '''
   | build
   | dist
   | .*venv*
+  | __init__.py
 )/
 '''
 
@@ -56,6 +57,6 @@ extend_skip =  '''
   | _build
   | build
   | dist
-  | .*venv*
 )/
 '''
+skip_glob = ["**/__init__.py", "*venv"]
\ No newline at end of file
diff --git a/src/funman/model/__init__.py b/src/funman/model/__init__.py
index f888fb8f..4f749bbe 100644
--- a/src/funman/model/__init__.py
+++ b/src/funman/model/__init__.py
@@ -2,9 +2,8 @@
 This submodule contains class definitions used to represent and interact with
 models in FUNMAN.
 """
-
+from .model import *
+from .query import *
 from .bilayer import *
 from .encoded import *
 from .gromet import *
-from .model import *
-from .query import *
diff --git a/src/funman/scenario/__init__.py b/src/funman/scenario/__init__.py
index 7134da2d..daab8204 100644
--- a/src/funman/scenario/__init__.py
+++ b/src/funman/scenario/__init__.py
@@ -3,6 +3,6 @@
 is capable of solving.
 """
 
+from .scenario import *
 from .consistency import *
 from .parameter_synthesis import *
-from .scenario import *
diff --git a/src/funman/search/__init__.py b/src/funman/search/__init__.py
index 9426aaf6..cd793a2c 100644
--- a/src/funman/search/__init__.py
+++ b/src/funman/search/__init__.py
@@ -2,8 +2,8 @@
 This subpackage contains the search algorithms used to run FUNMAN. It also defines the representations for episodes (single executions) of one of the search algorithms supported by FUNMAN.
 """
 
-from .box_search import *
 from .handlers import *
 from .representation import *
 from .search import *
+from .box_search import *
 from .smt_check import *
diff --git a/src/funman/translate/__init__.py b/src/funman/translate/__init__.py
index 264fa7fd..ba79ebd4 100644
--- a/src/funman/translate/__init__.py
+++ b/src/funman/translate/__init__.py
@@ -1,4 +1,4 @@
+from .translate import *
 from .bilayer import *
 from .encoded import *
 from .gromet import *
-from .translate import *
diff --git a/src/funman/translate/gromet.py b/src/funman/translate/gromet.py
index a781b743..6735602b 100644
--- a/src/funman/translate/gromet.py
+++ b/src/funman/translate/gromet.py
@@ -28,7 +28,7 @@
 )
 from pysmt.typing import BOOL, INT, REAL
 
-from funman.model import GrometModel, Model
+from funman.model import Model
 from funman.translate import Encoder, EncodingOptions
 
 # TODO more descriptive name