Merge pull request #334 from MannLabs/linitin-rule-I

Linitin rule i

.pre-commit-config.yaml

@@ -8,10 +8,11 @@ repos:
     - id: end-of-file-fixer
     - id: trailing-whitespace
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.4.0
+  rev: v0.6.6
   hooks:
     - id: ruff-format
-#    - id: ruff
+    - id: ruff
+      args: ['--fix']
 -   repo: https://github.com/Yelp/detect-secrets
     rev: v1.5.0
     hooks:

alphastats/DataSet.py

@@ -1,26 +1,24 @@
-from typing import List, Union, Dict, Optional, Tuple
-
-import pandas as pd
-import numpy as np
 import logging
 import warnings
+from typing import Dict, List, Optional, Tuple, Union
+
+import numpy as np
+import pandas as pd
 import plotly
 import scipy
 
 from alphastats import BaseLoader
-
-
+from alphastats.dataset_factory import DataSetFactory
 from alphastats.DataSet_Plot import Plot
 from alphastats.DataSet_Preprocess import Preprocess
 from alphastats.DataSet_Statistics import Statistics
-from alphastats.utils import LoaderError, check_for_missing_values, ignore_warning
-from alphastats.statistics.tukey_test import tukey_test
 from alphastats.plots.ClusterMap import ClusterMap
 from alphastats.plots.DimensionalityReduction import DimensionalityReduction
 from alphastats.plots.IntensityPlot import IntensityPlot
 from alphastats.plots.SampleHistogram import SampleHistogram
 from alphastats.plots.VolcanoPlot import VolcanoPlot
-from alphastats.dataset_factory import DataSetFactory
+from alphastats.statistics.tukey_test import tukey_test
+from alphastats.utils import LoaderError, check_for_missing_values, ignore_warning
 
 plotly.io.templates["alphastats_colors"] = plotly.graph_objects.layout.Template(
     layout=plotly.graph_objects.Layout(

alphastats/DataSet_Pathway.py

@@ -1,13 +1,14 @@
 # TODO this whole module is unused
 #  Check if this can be merged with the enrichment code accessible through the p'interpreter
-import plotly.express as px
-import requests
-import pandas as pd
 from io import StringIO
+
 import numpy as np
+import pandas as pd
+import plotly.express as px
+import requests
 
 from alphastats import AlphaPeptLoader
-from alphastats.utils import check_internetconnection, check_if_df_empty
+from alphastats.utils import check_if_df_empty, check_internetconnection
 
 
 class enrichment_df(pd.DataFrame):

alphastats/DataSet_Plot.py

@@ -1,15 +1,15 @@
-import plotly.express as px
-import plotly
-import scipy
+from typing import Dict
 
-import plotly.graph_objects as go
-import seaborn as sns
 import pandas as pd
+import plotly
+import plotly.express as px
 import plotly.figure_factory
-from typing import Dict
+import plotly.graph_objects as go
+import scipy
+import seaborn as sns
 
-from alphastats.utils import check_for_missing_values
 from alphastats.plots.PlotUtils import PlotUtils
+from alphastats.utils import check_for_missing_values
 
 
 class plotly_object(plotly.graph_objs._figure.Figure):

alphastats/DataSet_Preprocess.py

@@ -1,13 +1,12 @@
 import logging
-from typing import Tuple, Dict, List, Union
+from typing import Dict, List, Tuple, Union
 
 import numpy as np
 import pandas as pd
 import sklearn
 import sklearn.ensemble
 import sklearn.impute
 import streamlit as st
-
 from sklearn.experimental import enable_iterative_imputer  # noqa
 
 from alphastats.utils import ignore_warning

alphastats/DataSet_Statistics.py

@@ -1,17 +1,17 @@
-import pandas as pd
+from functools import lru_cache
+from typing import Dict, Union
+
 import numpy as np
+import pandas as pd
 import pingouin
 
 from alphastats.DataSet_Preprocess import PreprocessingStateKeys
-from alphastats.utils import ignore_warning
-from functools import lru_cache
-from typing import Union, Dict
-
-from alphastats.statistics.MultiCovaAnalysis import MultiCovaAnalysis
+from alphastats.statistics.Anova import Anova
 from alphastats.statistics.DifferentialExpressionAnalysis import (
     DifferentialExpressionAnalysis,
 )
-from alphastats.statistics.Anova import Anova
+from alphastats.statistics.MultiCovaAnalysis import MultiCovaAnalysis
+from alphastats.utils import ignore_warning
 
 
 class Statistics:

alphastats/__init__.py

@@ -40,10 +40,11 @@
 }
 
 # TODO get rid of these imports
+import alphastats.gui
+
+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 *
-import alphastats.gui

alphastats/dataset_factory.py

@@ -1,9 +1,9 @@
-from typing import List, Union, Dict, Optional, Tuple
-
-import pandas as pd
-import numpy as np
 import logging
 import warnings
+from typing import Dict, List, Optional, Tuple, Union
+
+import numpy as np
+import pandas as pd
 
 
 class DataSetFactory:

alphastats/gui/AlphaPeptStats.py

@@ -1,11 +1,11 @@
 import os
-import streamlit as st
 
+import streamlit as st
 
 from alphastats.gui.utils.ui_helper import (
-    sidebar_info,
     img_to_bytes,
     init_session_state,
+    sidebar_info,
 )
 
 st.set_page_config(layout="wide")

alphastats/gui/gui.py

@@ -1,5 +1,6 @@
 import os
 import sys
+
 from streamlit.web import cli as stcli
 
 

alphastats/gui/pages/02_Import Data.py

@@ -2,24 +2,23 @@
 
 import streamlit as st
 
-from alphastats.DataSet import DataSet
 from alphastats import BaseLoader
-from alphastats.gui.utils.options import SOFTWARE_OPTIONS
-
+from alphastats.DataSet import DataSet
 from alphastats.gui.utils.import_helper import (
     load_example_data,
-    uploaded_file_to_df,
-    show_loader_columns_selection,
-    load_proteomics_data,
     load_options,
-    show_select_sample_column_for_metadata,
+    load_proteomics_data,
     show_button_download_metadata_template_file,
+    show_loader_columns_selection,
+    show_select_sample_column_for_metadata,
+    uploaded_file_to_df,
 )
+from alphastats.gui.utils.options import SOFTWARE_OPTIONS
 from alphastats.gui.utils.ui_helper import (
-    sidebar_info,
+    StateKeys,
     empty_session_state,
     init_session_state,
-    StateKeys,
+    sidebar_info,
 )
 
 

alphastats/gui/pages/03_Data Overview.py

@@ -1,13 +1,13 @@
 import streamlit as st
 
 from alphastats.gui.utils.overview_helper import (
+    display_loaded_dataset,
     display_matrix,
     get_intensity_distribution_processed,
-    get_sample_histogram_matrix,
     get_intensity_distribution_unprocessed,
-    display_loaded_dataset,
+    get_sample_histogram_matrix,
 )
-from alphastats.gui.utils.ui_helper import sidebar_info, init_session_state, StateKeys
+from alphastats.gui.utils.ui_helper import StateKeys, init_session_state, sidebar_info
 
 init_session_state()
 sidebar_info()

alphastats/gui/pages/03_Preprocessing.py

@@ -1,17 +1,16 @@
-import streamlit as st
 import pandas as pd
-
+import streamlit as st
 
 from alphastats.gui.utils.preprocessing_helper import (
-    draw_workflow,
+    PREPROCESSING_STEPS,
     configure_preprocessing,
     display_preprocessing_info,
-    update_workflow,
-    run_preprocessing,
+    draw_workflow,
     reset_preprocessing,
-    PREPROCESSING_STEPS,
+    run_preprocessing,
+    update_workflow,
 )
-from alphastats.gui.utils.ui_helper import sidebar_info, init_session_state, StateKeys
+from alphastats.gui.utils.ui_helper import StateKeys, init_session_state, sidebar_info
 
 init_session_state()
 sidebar_info()

alphastats/gui/pages/04_Analysis.py

@@ -1,19 +1,19 @@
 import streamlit as st
 
-from alphastats.gui.utils.ui_helper import (
-    sidebar_info,
-    init_session_state,
-    convert_df,
-    StateKeys,
-)
 from alphastats.gui.utils.analysis_helper import (
-    get_analysis,
-    load_options,
+    display_df,
     display_figure,
-    save_plot_to_session_state,
     download_figure,
-    display_df,
     download_preprocessing_info,
+    get_analysis,
+    load_options,
+    save_plot_to_session_state,
+)
+from alphastats.gui.utils.ui_helper import (
+    StateKeys,
+    convert_df,
+    init_session_state,
+    sidebar_info,
 )
 
 

alphastats/gui/pages/05_LLM.py

@@ -1,27 +1,28 @@
 import os
-import streamlit as st
+
 import pandas as pd
+import streamlit as st
 from openai import AuthenticationError
 
 from alphastats.gui.utils.analysis_helper import (
     check_if_options_are_loaded,
     display_figure,
-    save_plot_to_session_state,
     gui_volcano_plot_differential_expression_analysis,
     helper_compare_two_groups,
+    save_plot_to_session_state,
 )
 from alphastats.gui.utils.gpt_helper import (
-    get_assistant_functions,
     display_proteins,
-    get_subgroups_for_each_group,
+    get_assistant_functions,
     get_general_assistant_functions,
+    get_subgroups_for_each_group,
 )
+from alphastats.gui.utils.ollama_utils import LLMIntegration
 from alphastats.gui.utils.openai_utils import (
     set_api_key,
 )
-from alphastats.gui.utils.ollama_utils import LLMIntegration
 from alphastats.gui.utils.options import interpretation_options
-from alphastats.gui.utils.ui_helper import sidebar_info, init_session_state, StateKeys
+from alphastats.gui.utils.ui_helper import StateKeys, init_session_state, sidebar_info
 
 init_session_state()
 sidebar_info()

alphastats/gui/pages/06_Results.py

@@ -1,12 +1,13 @@
-import streamlit as st
-import pandas as pd
 import io
 
+import pandas as pd
+import streamlit as st
+
 from alphastats.gui.utils.ui_helper import (
-    sidebar_info,
-    init_session_state,
-    convert_df,
     StateKeys,
+    convert_df,
+    init_session_state,
+    sidebar_info,
 )
 
 

alphastats/gui/utils/analysis_helper.py

@@ -1,8 +1,9 @@
+import io
+
 import pandas as pd
 import streamlit as st
-import io
 
-from alphastats.gui.utils.ui_helper import convert_df, StateKeys
+from alphastats.gui.utils.ui_helper import StateKeys, convert_df
 from alphastats.plots.VolcanoPlot import VolcanoPlot
 
 

alphastats/gui/utils/enrichment_analysis.py

@@ -1,10 +1,8 @@
 from typing import List
-import requests
-
-
-from gprofiler import GProfiler
 
 import pandas as pd
+import requests
+from gprofiler import GProfiler
 
 
 def _get_functional_annotation_string(identifier, species_id="9606") -> pd.DataFrame:

alphastats/gui/utils/gpt_helper.py

@@ -1,15 +1,15 @@
 import copy
-from typing import Union, List, Dict
-
 import json
-
-from Bio import Entrez
+from typing import Dict, List, Union
 
 import pandas as pd
+import requests
 import streamlit as st
+from Bio import Entrez
+from gprofiler import GProfiler
 
-from alphastats.plots.DimensionalityReduction import DimensionalityReduction
 from alphastats.gui.utils.ui_helper import StateKeys
+from alphastats.plots.DimensionalityReduction import DimensionalityReduction
 
 Entrez.email = "[email protected]"  # Always provide your email address when using NCBI services.