From ed26e48f01e8a89fef456afdd0bd1adc8041c7c0 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Fri, 18 Oct 2024 10:15:50 +0200
Subject: [PATCH] manual fixes for rule F

---
 alphastats/__init__.py                        | 14 +++++++-------
 alphastats/gui/__init__.py                    |  2 +-
 alphastats/load_data.py                       |  4 ++--
 pyproject.toml                                |  2 +-
 release/pyinstaller/alphastats_pyinstaller.py |  2 +-
 5 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/alphastats/__init__.py b/alphastats/__init__.py
index d25740ed..f8025997 100644
--- a/alphastats/__init__.py
+++ b/alphastats/__init__.py
@@ -40,11 +40,11 @@
 }
 
 # TODO get rid of these imports
-import alphastats.gui
+import alphastats.gui  # noqa: F401
 
-from .cli import *
-from .loader.AlphaPeptLoader import *
-from .loader.DIANNLoader import *
-from .loader.FragPipeLoader import *
-from .loader.MaxQuantLoader import *
-from .loader.SpectronautLoader import *
+from .cli import *  # noqa: F403
+from .loader.AlphaPeptLoader import *  # noqa: F403
+from .loader.DIANNLoader import *  # noqa: F403
+from .loader.FragPipeLoader import *  # noqa: F403
+from .loader.MaxQuantLoader import *  # noqa: F403
+from .loader.SpectronautLoader import *  # noqa: F403
diff --git a/alphastats/gui/__init__.py b/alphastats/gui/__init__.py
index dcaea0ee..a4589819 100644
--- a/alphastats/gui/__init__.py
+++ b/alphastats/gui/__init__.py
@@ -1 +1 @@
-from .gui import run
+from .gui import run  # noqa: F401 TODO: check if necessary
diff --git a/alphastats/load_data.py b/alphastats/load_data.py
index 19d9dee3..6afa01a4 100644
--- a/alphastats/load_data.py
+++ b/alphastats/load_data.py
@@ -1,10 +1,10 @@
+from alphastats import MaxQuantLoader
 from alphastats.loader.AlphaPeptLoader import AlphaPeptLoader
 from alphastats.loader.DIANNLoader import DIANNLoader
 from alphastats.loader.FragPipeLoader import FragPipeLoader
-from alphastats.loader.MaxQuantLoader import *
 
 
-# TODO: Currenlty only used by tests, but should maybe be used more widely
+# TODO: Currently only used by tests, but should maybe be used more widely
 def load_data(file, type, **kwargs):
     type = type.lower()
     if type == "maxquant":
diff --git a/pyproject.toml b/pyproject.toml
index 6d12c81a..356baa19 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,7 @@ extend-exclude = [".bumpversion.cfg", ".secrets.baseline"]
 #    # pycodestyle
 #    "E",
 #    # Pyflakes
-#    "F",
+    "F",
     # pyupgrade
     "UP",
 #    # flake8-bugbear
diff --git a/release/pyinstaller/alphastats_pyinstaller.py b/release/pyinstaller/alphastats_pyinstaller.py
index 1be7c73a..91a5ad73 100644
--- a/release/pyinstaller/alphastats_pyinstaller.py
+++ b/release/pyinstaller/alphastats_pyinstaller.py
@@ -2,7 +2,7 @@
     try:
         import multiprocessing
 
-        import alphastats
+        import alphastats  # noqa: F401 TODO check if this can be removed
 
         multiprocessing.freeze_support()