Rename modules

alphastats/__init__.py

@@ -43,8 +43,8 @@
 import alphastats.gui  # noqa: F401
 
 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
+from .loader.alphapept_loader import *  # noqa: F403
+from .loader.diann_loader import *  # noqa: F403
+from .loader.fragpipe_loader import *  # noqa: F403
+from .loader.maxquant_loader import *  # noqa: F403
+from .loader.spectronaut_loader import *  # noqa: F403

alphastats/DataSet.py → alphastats/dataset/dataset.py

@@ -4,20 +4,24 @@
 import plotly
 import scipy
 
-from alphastats.dataset_factory import DataSetFactory
-from alphastats.dataset_harmonizer import DataHarmonizer
-from alphastats.DataSet_Plot import Plot
-from alphastats.DataSet_Preprocess import Preprocess
-from alphastats.DataSet_Statistics import Statistics
-from alphastats.keys import Cols
-from alphastats.loader.BaseLoader import BaseLoader
-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.dataset.harmonizer import DataHarmonizer
+from alphastats.dataset.keys import Cols
+from alphastats.dataset.plotting import Plot
+from alphastats.dataset.preprocessing import Preprocess
+from alphastats.dataset.statistics import Statistics
+from alphastats.dataset.utils import (
+    LoaderError,
+    check_for_missing_values,
+    ignore_warning,
+)
+from alphastats.loader.base_loader import BaseLoader
+from alphastats.plots.clustermap import ClusterMap
+from alphastats.plots.dimensionality_reduction import DimensionalityReduction
+from alphastats.plots.intensity_plot import IntensityPlot
+from alphastats.plots.sample_histogram import SampleHistogram
+from alphastats.plots.volcano_plot import VolcanoPlot
 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_factory.py → alphastats/dataset/factory.py

@@ -5,8 +5,8 @@
 import numpy as np
 import pandas as pd
 
-from alphastats.dataset_harmonizer import DataHarmonizer
-from alphastats.keys import Cols
+from alphastats.dataset.harmonizer import DataHarmonizer
+from alphastats.dataset.keys import Cols
 
 
 class DataSetFactory:

alphastats/dataset_harmonizer.py → alphastats/dataset/harmonizer.py

@@ -4,8 +4,8 @@
 
 import pandas as pd
 
-from alphastats.keys import Cols
-from alphastats.loader.BaseLoader import BaseLoader
+from alphastats.dataset.keys import Cols
+from alphastats.loader.base_loader import BaseLoader
 
 
 class DataHarmonizer:

alphastats/DataSet_Pathway.py → alphastats/dataset/pathway.py

@@ -7,8 +7,8 @@
 import plotly.express as px
 import requests
 
-from alphastats import AlphaPeptLoader
-from alphastats.utils import check_if_df_empty, check_internetconnection
+from alphastats.dataset.utils import check_if_df_empty, check_internetconnection
+from alphastats.loader.alphapept_loader import AlphaPeptLoader
 
 
 class enrichment_df(pd.DataFrame):

alphastats/DataSet_Plot.py → alphastats/dataset/plotting.py

@@ -7,9 +7,9 @@
 import scipy
 import seaborn as sns
 
-from alphastats.keys import Cols
-from alphastats.plots.PlotUtils import PlotUtils
-from alphastats.utils import check_for_missing_values
+from alphastats.dataset.keys import Cols
+from alphastats.dataset.utils import check_for_missing_values
+from alphastats.plots.plot_utils import PlotUtils
 
 
 class plotly_object(plotly.graph_objs._figure.Figure):

alphastats/DataSet_Preprocess.py → alphastats/dataset/preprocessing.py

@@ -9,8 +9,8 @@
 import streamlit as st
 from sklearn.experimental import enable_iterative_imputer  # noqa
 
-from alphastats.keys import Cols, ConstantsClass
-from alphastats.utils import ignore_warning
+from alphastats.dataset.keys import Cols, ConstantsClass
+from alphastats.dataset.utils import ignore_warning
 
 
 class PreprocessingStateKeys(metaclass=ConstantsClass):

alphastats/DataSet_Statistics.py → alphastats/dataset/statistics.py

@@ -4,13 +4,13 @@
 import pandas as pd
 import pingouin
 
-from alphastats.keys import Cols
-from alphastats.statistics.Anova import Anova
-from alphastats.statistics.DifferentialExpressionAnalysis import (
+from alphastats.dataset.keys import Cols
+from alphastats.dataset.utils import ignore_warning
+from alphastats.statistics.anova import Anova
+from alphastats.statistics.differential_expression_analysis import (
     DifferentialExpressionAnalysis,
 )
-from alphastats.statistics.MultiCovaAnalysis import MultiCovaAnalysis
-from alphastats.utils import ignore_warning
+from alphastats.statistics.multicova_analysis import MultiCovaAnalysis
 
 
 class Statistics:

alphastats/gui/pages/02_Import Data.py

@@ -1,6 +1,6 @@
 import streamlit as st
 
-from alphastats.DataSet import DataSet
+from alphastats.dataset.dataset import DataSet
 from alphastats.gui.utils.import_helper import (
     load_example_data,
     load_proteomics_data,

alphastats/gui/pages/03_Preprocessing.py → alphastats/gui/pages/04_Preprocessing.py

@@ -1,6 +1,6 @@
 import streamlit as st
 
-from alphastats.DataSet_Preprocess import PreprocessingStateKeys
+from alphastats.dataset.preprocessing import PreprocessingStateKeys
 from alphastats.gui.utils.preprocessing_helper import (
     configure_preprocessing,
     display_preprocessing_info,

alphastats/gui/utils/analysis.py

@@ -7,10 +7,10 @@
 import pandas as pd
 import streamlit as st
 
-from alphastats.DataSet import DataSet
-from alphastats.keys import Cols, ConstantsClass
-from alphastats.plots.PlotUtils import PlotlyObject
-from alphastats.plots.VolcanoPlot import VolcanoPlot
+from alphastats.dataset.dataset import DataSet
+from alphastats.dataset.keys import Cols, ConstantsClass
+from alphastats.plots.plot_utils import PlotlyObject
+from alphastats.plots.volcano_plot import VolcanoPlot
 
 
 class PlottingOptions(metaclass=ConstantsClass):

alphastats/gui/utils/analysis_helper.py

@@ -13,7 +13,7 @@
     StateKeys,
     show_button_download_df,
 )
-from alphastats.plots.PlotUtils import PlotlyObject
+from alphastats.plots.plot_utils import PlotlyObject
 
 
 @st.fragment

alphastats/gui/utils/import_helper.py

@@ -7,9 +7,10 @@
 import streamlit as st
 from streamlit.runtime.uploaded_file_manager import UploadedFile
 
-from alphastats.DataSet import DataSet
+from alphastats.dataset.dataset import DataSet
 from alphastats.gui.utils.options import SOFTWARE_OPTIONS
-from alphastats.loader.MaxQuantLoader import BaseLoader, MaxQuantLoader
+from alphastats.loader.base_loader import BaseLoader
+from alphastats.loader.maxquant_loader import MaxQuantLoader
 
 
 def load_proteomics_data(uploaded_file, intensity_column, index_column, software):

alphastats/gui/utils/options.py

@@ -1,10 +1,10 @@
-from alphastats import SpectronautLoader
-from alphastats.loader.AlphaPeptLoader import AlphaPeptLoader
-from alphastats.loader.DIANNLoader import DIANNLoader
-from alphastats.loader.FragPipeLoader import FragPipeLoader
-from alphastats.loader.GenericLoader import GenericLoader
-from alphastats.loader.MaxQuantLoader import MaxQuantLoader
-from alphastats.loader.mzTabLoader import mzTabLoader
+from alphastats.loader.alphapept_loader import AlphaPeptLoader
+from alphastats.loader.diann_loader import DIANNLoader
+from alphastats.loader.fragpipe_loader import FragPipeLoader
+from alphastats.loader.generic_loader import GenericLoader
+from alphastats.loader.maxquant_loader import MaxQuantLoader
+from alphastats.loader.mztab_loader import mzTabLoader
+from alphastats.loader.spectronaut_loader import SpectronautLoader
 
 SOFTWARE_OPTIONS = {
     "MaxQuant": {

alphastats/gui/utils/overview_helper.py

@@ -1,7 +1,7 @@
 import pandas as pd
 import streamlit as st
 
-from alphastats.DataSet import DataSet
+from alphastats.dataset.dataset import DataSet
 from alphastats.gui.utils.ui_helper import StateKeys, show_button_download_df
 
 

alphastats/gui/utils/preprocessing_helper.py

@@ -4,8 +4,8 @@
 import streamlit as st
 from st_cytoscape import cytoscape
 
-from alphastats.DataSet import DataSet
-from alphastats.keys import Cols
+from alphastats.dataset.dataset import DataSet
+from alphastats.dataset.keys import Cols
 
 CYTOSCAPE_STYLESHEET = [
     {

alphastats/gui/utils/ui_helper.py

@@ -5,8 +5,8 @@
 import streamlit as st
 
 from alphastats import __version__
+from alphastats.dataset.keys import ConstantsClass
 from alphastats.gui.utils.preprocessing_helper import PREPROCESSING_STEPS
-from alphastats.keys import ConstantsClass
 
 # TODO add logo above the options when issue is closed
 # https://github.com/streamlit/streamlit/issues/4984

alphastats/llm/llm_functions.py

@@ -4,7 +4,7 @@
 
 import pandas as pd
 
-from alphastats.DataSet import DataSet
+from alphastats.dataset.dataset import DataSet
 from alphastats.llm.enrichment_analysis import get_enrichment_data
 from alphastats.llm.uniprot_utils import get_gene_function
 

alphastats/llm/llm_integration.py

@@ -10,7 +10,7 @@
 from openai import OpenAI
 from openai.types.chat import ChatCompletion, ChatCompletionMessageToolCall
 
-from alphastats.DataSet import DataSet
+from alphastats.dataset.dataset import DataSet
 from alphastats.llm.llm_functions import (
     GENERAL_FUNCTION_MAPPING,
     get_assistant_functions,

alphastats/llm/prompts.py

@@ -5,7 +5,7 @@
 
 from openai.types.chat import ChatCompletionMessageToolCall
 
-from alphastats.DataSet import DataSet
+from alphastats.dataset.dataset import DataSet
 from alphastats.llm.llm_utils import get_subgroups_for_each_group
 
 

alphastats/loader/AlphaPeptLoader.py → alphastats/loader/alphapept_loader.py

@@ -3,7 +3,7 @@
 import numpy as np
 import pandas as pd
 
-from alphastats.loader.BaseLoader import BaseLoader
+from alphastats.loader.base_loader import BaseLoader
 
 
 class AlphaPeptLoader(BaseLoader):

alphastats/loader/BaseLoader.py → alphastats/loader/base_loader.py

@@ -5,7 +5,7 @@
 import numpy as np
 import pandas as pd
 
-from alphastats.utils import find_duplicates_in_list
+from alphastats.dataset.utils import find_duplicates_in_list
 
 if sys.version_info >= (3, 9):
     import importlib.resources as importlib_resources

alphastats/loader/DIANNLoader.py → alphastats/loader/diann_loader.py

@@ -1,4 +1,4 @@
-from alphastats.loader.BaseLoader import BaseLoader
+from alphastats.loader.base_loader import BaseLoader
 
 
 class DIANNLoader(BaseLoader):

alphastats/loader/FragPipeLoader.py → alphastats/loader/fragpipe_loader.py

@@ -2,7 +2,7 @@
 
 import pandas as pd
 
-from alphastats.loader.BaseLoader import BaseLoader
+from alphastats.loader.base_loader import BaseLoader
 
 
 # Philosopher

alphastats/loader/GenericLoader.py → alphastats/loader/generic_loader.py

@@ -2,7 +2,7 @@
 
 import pandas as pd
 
-from alphastats.loader.BaseLoader import BaseLoader
+from alphastats.loader.base_loader import BaseLoader
 
 
 class GenericLoader(BaseLoader):

alphastats/loader/MaxQuantLoader.py → alphastats/loader/maxquant_loader.py

@@ -3,7 +3,7 @@
 import numpy as np
 import pandas as pd
 
-from alphastats.loader.BaseLoader import BaseLoader
+from alphastats.loader.base_loader import BaseLoader
 
 
 class MaxQuantLoader(BaseLoader):

alphastats/loader/mzTabLoader.py → alphastats/loader/mztab_loader.py

@@ -1,6 +1,6 @@
 from pyteomics import mztab
 
-from alphastats.loader.BaseLoader import BaseLoader
+from alphastats.loader.base_loader import BaseLoader
 
 
 class mzTabLoader(BaseLoader):

alphastats/loader/SpectronautLoader.py → alphastats/loader/spectronaut_loader.py

@@ -5,7 +5,7 @@
 import numpy as np
 import pandas as pd
 
-from alphastats.loader.BaseLoader import BaseLoader
+from alphastats.loader.base_loader import BaseLoader
 
 SPECTRONAUT_COLUMN_DELIM = "."
 

alphastats/multicova/multicova.py

@@ -15,7 +15,7 @@
 from sklearn.preprocessing import StandardScaler
 from statsmodels.stats.multitest import multipletests
 
-from alphastats.keys import Cols
+from alphastats.dataset.keys import Cols
 
 # code taken from Isabel Bludau - multicova
 

alphastats/plots/ClusterMap.py → alphastats/plots/clustermap.py

@@ -4,9 +4,9 @@
 import pandas as pd
 import seaborn as sns
 
-from alphastats.DataSet_Statistics import Statistics
-from alphastats.keys import Cols
-from alphastats.plots.PlotUtils import PlotUtils
+from alphastats.dataset.keys import Cols
+from alphastats.dataset.statistics import Statistics
+from alphastats.plots.plot_utils import PlotUtils
 
 
 class ClusterMap(PlotUtils):

alphastats/plots/DimensionalityReduction.py → alphastats/plots/dimensionality_reduction.py

@@ -6,9 +6,9 @@
 import plotly.graph_objects as go
 import sklearn
 
-from alphastats.DataSet_Preprocess import Preprocess
-from alphastats.keys import Cols
-from alphastats.plots.PlotUtils import PlotlyObject, PlotUtils
+from alphastats.dataset.keys import Cols
+from alphastats.dataset.preprocessing import Preprocess
+from alphastats.plots.plot_utils import PlotlyObject, PlotUtils
 
 # make own alphastats theme
 plotly.io.templates["alphastats_colors"] = plotly.graph_objects.layout.Template(

alphastats/plots/IntensityPlot.py → alphastats/plots/intensity_plot.py

@@ -8,8 +8,8 @@
 import plotly.graph_objects as go
 import scipy
 
-from alphastats.keys import Cols
-from alphastats.plots.PlotUtils import PlotlyObject, PlotUtils
+from alphastats.dataset.keys import Cols
+from alphastats.plots.plot_utils import PlotlyObject, PlotUtils
 
 plotly.io.templates["alphastats_colors"] = plotly.graph_objects.layout.Template(
     layout=plotly.graph_objects.Layout(