apply linting agian on merged code

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/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/ollama_utils.py

@@ -1,22 +1,22 @@
+import json
 import logging
+from typing import Any, Dict, List, Optional, Tuple
 
-from openai import OpenAI
-from typing import List, Dict, Any, Optional, Tuple
-import json
-import streamlit as st
 import pandas as pd
-from IPython.display import display, Markdown, HTML
 import plotly.io as pio
+import streamlit as st
+from IPython.display import HTML, Markdown, display
+from openai import OpenAI
+
+from alphastats.gui.utils.enrichment_analysis import get_enrichment_data
 from alphastats.gui.utils.gpt_helper import (
-    perform_dimensionality_reduction,
     get_general_assistant_functions,
+    perform_dimensionality_reduction,
 )
+from alphastats.gui.utils.ui_helper import StateKeys
 
 # from alphastats.gui.utils.artefacts import ArtifactManager
 from alphastats.gui.utils.uniprot_utils import get_gene_function
-from alphastats.gui.utils.enrichment_analysis import get_enrichment_data
-from alphastats.gui.utils.ui_helper import StateKeys
-
 
 logger = logging.getLogger(__name__)
 

alphastats/gui/utils/openai_utils.py

@@ -1,9 +1,7 @@
-from typing import Optional, List
-from pathlib import Path
-
-import time
 import json
-
+import time
+from pathlib import Path
+from typing import List, Optional
 
 import openai
 import streamlit as st
@@ -22,12 +20,12 @@
     from utils.gpt_helper import (
         turn_args_to_float,
     )
-    from utils.uniprot_utils import (
-        get_gene_function,
-    )
     from utils.openai_utils import (
         wait_for_run_completion,
     )
+    from utils.uniprot_utils import (
+        get_gene_function,
+    )
 
 
 def wait_for_run_completion(

alphastats/gui/utils/uniprot_utils.py

@@ -1,7 +1,6 @@
-from typing import Union, List, Dict
-import requests
-
+from typing import Dict, List, Union
 
+import requests
 import streamlit as st
 
 from alphastats.gui.utils.ui_helper import StateKeys

tests/gui/conftest.py

@@ -1,8 +1,10 @@
-from streamlit.testing.v1 import AppTest
-from alphastats.load_data import load_data
+from io import BytesIO
 from pathlib import Path
+
+from streamlit.testing.v1 import AppTest
+
 from alphastats.DataSet import DataSet
-from io import BytesIO
+from alphastats.load_data import load_data
 
 # TODO: Turn the helpers into fixtures