From 145a393b0bee53a2ee5a85074a3ebf163a67982d Mon Sep 17 00:00:00 2001
From: Robert Tomek <robt_0@hotmail.com>
Date: Fri, 30 May 2025 17:53:06 -0500
Subject: [PATCH 1/7] Add copyable_data property to GrabbableChartView

---
 .../gui/pyside6/grabbablewidget.py            | 23 +++++++++++++++++++
 src/midrc_react/gui/pyside6/jsdview.py        |  2 +-
 2 files changed, 24 insertions(+), 1 deletion(-)

diff --git a/src/midrc_react/gui/pyside6/grabbablewidget.py b/src/midrc_react/gui/pyside6/grabbablewidget.py
index 99a82d1..da93022 100644
--- a/src/midrc_react/gui/pyside6/grabbablewidget.py
+++ b/src/midrc_react/gui/pyside6/grabbablewidget.py
@@ -381,3 +381,26 @@ def save_chart_to_disk(self):
         """
         self.grabbable_mixin.save_to_disk()
 
+    @property
+    def copyable_data(self) -> str:
+        """
+        Get the copyable data for the chart view.
+
+        Returns:
+            str: The data to be copied to the clipboard when requested.
+        """
+        return self.grabbable_mixin.copyable_data
+
+    @copyable_data.setter
+    def copyable_data(self, data: str):
+        """
+        Set the copyable data for the chart view.
+
+        Args:
+            data (str): The data to be copied to the clipboard when requested.
+
+        Returns:
+            None
+        """
+        self.grabbable_mixin.copyable_data = data
+
diff --git a/src/midrc_react/gui/pyside6/jsdview.py b/src/midrc_react/gui/pyside6/jsdview.py
index cf4d36b..7349707 100644
--- a/src/midrc_react/gui/pyside6/jsdview.py
+++ b/src/midrc_react/gui/pyside6/jsdview.py
@@ -418,7 +418,7 @@ def _set_spider_chart_copyable_data(self, spider_plot_values_dict: Dict[Any, Dic
                 file2 = self._dataselectiongroupbox.file_comboboxes[series_key[1]].currentText()
                 values = "\t".join(str(series[label]) for label in headers)
                 formatted_text += f"{file1}\t{file2}\t{values}\n"
-            self.spider_chart_view.grabbable_mixin.copyable_data = formatted_text
+            self.spider_chart_view.copyable_data = formatted_text
 
     def update_spider_chart(self, spider_plot_values_dict: Dict[Any, Dict[str, float]]) -> bool:
         """

From 830cac821cf8e100e9c4fbaf9219567ba9849688 Mon Sep 17 00:00:00 2001
From: Robert Tomek <robt_0@hotmail.com>
Date: Thu, 9 Oct 2025 14:15:36 -0500
Subject: [PATCH 2/7] Make sure datasets are ordered consistently in output

---
 src/midrc_react/core/aggregate_jsd_calc.py | 2 +-
 src/midrc_react/core/numeric_distances.py  | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/midrc_react/core/aggregate_jsd_calc.py b/src/midrc_react/core/aggregate_jsd_calc.py
index e8c1a9c..1b0a0f2 100644
--- a/src/midrc_react/core/aggregate_jsd_calc.py
+++ b/src/midrc_react/core/aggregate_jsd_calc.py
@@ -70,7 +70,7 @@ def calc_jsd_by_features_combined(combined_df: pd.DataFrame, cols_to_use: list[s
     # Convert dataset columns to string in case they are integers
     pivot_table.columns = pivot_table.columns.astype(str)
 
-    labels = combined_df[dataset_column].unique().astype(str)
+    labels = sorted(combined_df[dataset_column].unique().astype(str))
 
     # Create a dictionary to hold counts for each dataset
     counts_dict = {dataset: pivot_table[dataset].values if dataset in pivot_table else np.zeros(len(pivot_table)) for
diff --git a/src/midrc_react/core/numeric_distances.py b/src/midrc_react/core/numeric_distances.py
index 2edaf04..83194ab 100644
--- a/src/midrc_react/core/numeric_distances.py
+++ b/src/midrc_react/core/numeric_distances.py
@@ -55,7 +55,7 @@ def calc_numerical_metric_by_feature(df, feature: str, dataset_column: str, metr
     Returns:
         dict: A dictionary containing metric results for each dataset combination.
     """
-    dataset_names = df[dataset_column].unique()
+    dataset_names = sorted(df[dataset_column].unique())
     metric_dict = {}
 
     # Compare each dataset combination
@@ -330,10 +330,10 @@ def calc_distances_via_df(famd_df: pd.DataFrame, feature_column: str, dataset_co
     # Mapping of distance metrics to their respective functions
     distance_metric_functions = {
         'jsd': {'func': lambda scaling=None: calc_jsd_from_counts_dict(
-                                 build_histogram_dict(famd_df, dataset_column, famd_df[dataset_column].unique(),
+                                 build_histogram_dict(famd_df, dataset_column, sorted(famd_df[dataset_column].unique()),
                                                       feature_column, bin_width=jsd_scaled_bin_width,
                                                       scaling_method=scaling),
-                                 famd_df[dataset_column].unique()),
+                                 sorted(famd_df[dataset_column].unique())),
                 'scaling': True},
         'wass': {'func': lambda scaling=None: calc_wasserstein_by_feature(famd_df, feature_column, dataset_column,
                                                                           scaling=scaling),

From 6547d224fab41c06300d6a0fbb8cfbb1058f9b73 Mon Sep 17 00:00:00 2001
From: Robert Tomek <robt_0@hotmail.com>
Date: Fri, 14 Nov 2025 22:01:18 -0600
Subject: [PATCH 3/7] Make FileInfo and CategoryInfo use pydantic BaseModel
 instead of dataclass

---
 src/midrc_react/core/jsdcontroller.py         |  28 ++---
 src/midrc_react/gui/common/jsdview_base.py    | 109 +++++++++---------
 src/midrc_react/gui/common/utils.py           |  18 +--
 .../gui/dash/dataselectiongroupbox.py         |   2 +-
 .../gui/ipython/dataselectiongroupbox.py      |   2 +-
 .../gui/ipython/jsdview_ipython.py            |   8 +-
 .../gui/pyside6/dataselectiongroupbox.py      |  32 ++---
 src/react_demo.ipynb                          |   2 +-
 8 files changed, 99 insertions(+), 102 deletions(-)

diff --git a/src/midrc_react/core/jsdcontroller.py b/src/midrc_react/core/jsdcontroller.py
index 84c0998..4e0ead4 100644
--- a/src/midrc_react/core/jsdcontroller.py
+++ b/src/midrc_react/core/jsdcontroller.py
@@ -179,14 +179,14 @@ def file_changed(self, _, new_category_index=None):
             return
 
         category_info = dataselectiongroupbox.get_category_info()
-        category_index = category_info['current_index']
+        category_index = category_info.current_index
         if new_category_index is not None:
             category_index = new_category_index
 
         # Compute the intersection of category keys across all file_infos.
         category_set = None
         for cbox in file_infos:
-            ds = self.jsd_model.data_sources[cbox['source_id']]
+            ds = self.jsd_model.data_sources[cbox.source_id]
             if category_set is None:
                 category_set = set(ds.sheets.keys())
             else:
@@ -196,7 +196,7 @@ def file_changed(self, _, new_category_index=None):
 
         # Compute has_raw_data using all() with a generator expression.
         has_raw_data = all(
-            self.jsd_model.data_sources[cbox['source_id']].raw_data is not None
+            self.jsd_model.data_sources[cbox.source_id].raw_data is not None
             for cbox in file_infos
         )
 
@@ -206,7 +206,7 @@ def file_changed(self, _, new_category_index=None):
             category_list.append('Aggregate')
             category_list.append('FAMD')
             for category in category_list:
-                if category in self.jsd_model.data_sources[file_infos[0]['source_id']].numeric_cols:
+                if category in self.jsd_model.data_sources[file_infos[0].source_id].numeric_cols:
                     category_list.append(f'{category} (ks2)')
 
         dataselectiongroupbox.update_category_list(category_list, category_index)
@@ -224,7 +224,7 @@ def get_file_sheets_from_index(self, index=0):
             dict: A dictionary containing the sheets from the selected file.
         """
         try:
-            current_data = self.jsd_view.dataselectiongroupbox.get_file_infos()[index]['source_id']
+            current_data = self.jsd_view.dataselectiongroupbox.get_file_infos()[index].source_id
         except IndexError as exc:
             raise IndexError("Index out of range") from exc
 
@@ -252,7 +252,7 @@ def category_changed(self):
         """
         dataselectiongroupbox = self.jsd_view.dataselectiongroupbox
         file_infos = dataselectiongroupbox.get_file_infos()
-        category = dataselectiongroupbox.get_category_info()['current_text']
+        category = dataselectiongroupbox.get_category_info().current_text
 
         # Try to avoid a race condition where the category is changed before the file is changed
         if not category:
@@ -267,8 +267,8 @@ def build_date_list(df1, df2):
         column_infos = []
 
         for (i, cbox1), (j, cbox2) in itertools.combinations(enumerate(file_infos), 2):
-            file1 = cbox1['source_id']
-            file2 = cbox2['source_id']
+            file1 = cbox1.source_id
+            file2 = cbox2.source_id
             data_source_1 = self.jsd_model.data_sources[file1]
             data_source_2 = self.jsd_model.data_sources[file2]
 
@@ -394,7 +394,7 @@ def update_file_based_charts(self):
         sheet_dict = {}
         file_infos = self.jsd_view.dataselectiongroupbox.get_file_infos()
         for i, file_info in enumerate(file_infos):
-            if file_info['checked']:
+            if file_info.checked:
                 sheet_dict[i] = self.get_file_sheets_from_index(i)
 
         spider_plot_values = self.get_spider_plot_values(spider_plot_date)
@@ -422,7 +422,7 @@ def update_category_plots(self):
         sheet_dict = {}
         file_infos = self.jsd_view.dataselectiongroupbox.get_file_infos()
         for i, file_info in enumerate(file_infos):
-            if file_info['checked']:
+            if file_info.checked:
                 sheet_dict[i] = self.get_file_sheets_from_index(i)
 
         try:
@@ -469,11 +469,11 @@ def get_spider_plot_values(self, calc_date=None):
             calc_date = np.datetime64('today')
 
         dataselectiongroupbox = self.jsd_view.dataselectiongroupbox
-        categories = dataselectiongroupbox.get_category_info()['category_list']
+        categories = dataselectiongroupbox.get_category_info().category_list
 
         # Determine indexes to use based on checked boxes or default to all
         file_infos = dataselectiongroupbox.get_file_infos()
-        indexes_to_use = [i for i, file_info in enumerate(file_infos) if file_info['checked']]
+        indexes_to_use = [i for i, file_info in enumerate(file_infos) if file_info.checked]
         if not indexes_to_use:
             indexes_to_use = list(range(len(file_infos)))
         if len(indexes_to_use) == 1:
@@ -490,8 +490,8 @@ def get_spider_plot_values(self, calc_date=None):
                 index2_candidates = [index2]
 
             for idx2 in index2_candidates:
-                source_id1 = file_infos[index1]['source_id']
-                source_id2 = file_infos[idx2]['source_id']
+                source_id1 = file_infos[index1].source_id
+                source_id2 = file_infos[idx2].source_id
 
                 data_source_1 = self.jsd_model.data_sources[source_id1]
                 data_source_2 = self.jsd_model.data_sources[source_id2]
diff --git a/src/midrc_react/gui/common/jsdview_base.py b/src/midrc_react/gui/common/jsdview_base.py
index 79dcc3d..585a6e5 100644
--- a/src/midrc_react/gui/common/jsdview_base.py
+++ b/src/midrc_react/gui/common/jsdview_base.py
@@ -17,32 +17,38 @@
 This module contains the JsdViewBase class, which serves as a base class for JSD views.
 """
 
-from dataclasses import dataclass
+from typing import List, Optional, Union
 
+from pydantic import BaseModel, Field
 from PySide6.QtCore import QObject, Signal
 from PySide6.QtWidgets import QMainWindow
 
 
-@dataclass
-class GroupBoxData:
+class FileInfo(BaseModel):
+    description: Optional[str] = None
+    source_id: Optional[str] = None
+    index: Optional[int] = None
+    checked: bool = True
+
+class CategoryInfo(BaseModel):
+    current_text: Optional[str] = None
+    current_index: Optional[int] = None
+    category_list: List[str] = Field(default_factory=list)
+
+class GroupBoxData(BaseModel):
     """
     This class represents a group box widget for data selection. It provides functionality for creating labels and
     combo boxes for data files and a category combo box. The class has methods for setting up the layout,
     updating the category combo box, and initializing the widget.
 
     Attributes:
-        _file_infos (list): A list of file information dictionaries.
-        _category_info (dict): A dictionary containing information about the selected category.
+        file_infos (list): A list of file information dictionaries.
+        category_info (dict): A dictionary containing information about the selected category.
     """
-    _file_infos = []
-    _category_info = {
-        'current_text': None,
-        'current_index': None,
-        'category_list': [],
-    }
+    file_infos: List[FileInfo] = Field(default_factory=list)
+    category_info: CategoryInfo = Field(default_factory=CategoryInfo)
 
-    @property
-    def file_infos(self):
+    def get_file_infos(self) -> List[FileInfo]:
         """
         Get the file information dictionaries.
 
@@ -51,46 +57,32 @@ def file_infos(self):
         """
         return self._file_infos
 
-    def get_file_infos(self):
-        """
-        Get the file information dictionaries.
-
-        Returns:
-            list: A list of file information dictionaries.
-        """
-        return self._file_infos
-
-    def append_file_info(self, file_info: dict):
+    def append_file_info(self, file_info: Union[dict, FileInfo]):
         """
         Appends a file information dictionary to the list of file information dictionaries.
 
         Args:
             file_info (dict): file information dictionary to append to the list
         """
-        file_info['checked'] = file_info.get('checked', True)
-        self._file_infos.append(file_info)
+        if isinstance(file_info, dict):
+            file_info.setdefault('checked', True)
+            file_info = FileInfo(**file_info)
+        elif isinstance(file_info, FileInfo):
+            # ensure checked is set
+            file_info.checked = bool(file_info.checked)
+        self.file_infos.append(file_info)
         # TODO: Update the category list too?
 
-    @property
-    def category_info(self):
-        """
-        Get the category information dictionary.
-
-        Returns:
-            dict: A dictionary containing information about the selected category.
-        """
-        return self._category_info
-
-    def get_category_info(self):
+    def get_category_info(self) -> CategoryInfo:
         """
         Get the category information dictionary.
 
         Returns:
             dict: A dictionary containing information about the selected category.
         """
-        return self._category_info
+        return self.category_info
 
-    def update_category_list(self, categorylist, categoryindex):
+    def update_category_list(self, categorylist: List[str], categoryindex: int):
         """
         Updates the category information dictionary with the given category list and index.
 
@@ -101,13 +93,14 @@ def update_category_list(self, categorylist, categoryindex):
         Returns:
             None
         """
-        self._category_info = {
-            'current_text': categorylist[categoryindex],
-            'current_index': categoryindex,
-            'category_list': categorylist,
-        }
+        print("Updating category list to:", categorylist, "with index:", categoryindex)
+        self.category_info = CategoryInfo(
+            current_text = categorylist[categoryindex],
+            current_index = categoryindex,
+            category_list = categorylist,
+        )
 
-    def update_category_index(self, categoryindex):
+    def update_category_index(self, categoryindex: int):
         """
         Updates the category information dictionary with the given category index.
 
@@ -117,10 +110,13 @@ def update_category_index(self, categoryindex):
         Returns:
             None
         """
-        self._category_info['current_index'] = categoryindex
-        self._category_info['current_text'] = self._category_info['category_list'][categoryindex]
+        self.category_info.current_index = categoryindex
+        if 0 <= categoryindex < len(self.category_info.category_list):
+            self.category_info.current_text = self.category_info.category_list[categoryindex]
+        else:
+            self.category_info.current_text = None
 
-    def update_category_text(self, categorytext):
+    def update_category_text(self, categorytext: str):
         """
         Updates the category information dictionary with the given category text.
 
@@ -130,10 +126,9 @@ def update_category_text(self, categorytext):
         Returns:
             None
         """
-        category_list = self._category_info['category_list']
-        if categorytext in category_list:
-            self._category_info['current_text'] = categorytext
-            self._category_info['current_index'] = category_list.index(categorytext)
+        if categorytext in self.category_info.category_list:
+            self.category_info.current_text = categorytext
+            self.category_info.current_index = self.category_info.category_list.index(categorytext)
 
 
 class JsdViewBase(QObject):
@@ -178,12 +173,12 @@ def open_excel_file(self, data_source_dict):
         Args:
             data_source_dict (dict): The data source dictionary.
         """
-        self._dataselectiongroupbox.append_file_info({
-            'description': data_source_dict['description'],
-            'source_id': data_source_dict['name'],
-            'index': len(self._dataselectiongroupbox.file_infos),
-            'checked': True,
-        })
+        self._dataselectiongroupbox.append_file_info(FileInfo(
+            description = data_source_dict['description'],
+            source_id = data_source_dict['name'],
+            index = len(self._dataselectiongroupbox.file_infos),
+            checked = True,
+        ))
 
     def update_pie_chart_dock(self, sheet_dict):
         """
diff --git a/src/midrc_react/gui/common/utils.py b/src/midrc_react/gui/common/utils.py
index 1227af0..91755be 100644
--- a/src/midrc_react/gui/common/utils.py
+++ b/src/midrc_react/gui/common/utils.py
@@ -17,6 +17,8 @@
 This module contains utility functions for file handling and data processing.
 """
 
+from jsdview_base import FileInfo
+
 
 def create_file_info(data_source, index):
     """
@@ -29,12 +31,12 @@ def create_file_info(data_source, index):
     Returns:
         dict: A dictionary with description, source_id, index and checked flag.
     """
-    return {
-        'description': data_source.get('description'),
-        'source_id': data_source.get('name'),
-        'index': index,
-        'checked': True,
-    }
+    return FileInfo(
+        description = data_source.get('description'),
+        source_id = data_source.get('name'),
+        index = index,
+        checked = True,
+    )
 
 
 def get_common_categories(file_infos, jsd_model):
@@ -53,11 +55,11 @@ def get_common_categories(file_infos, jsd_model):
 
     # Get the initial set of categories from the first file info.
     cbox0 = file_infos[0]
-    common_categories = list(jsd_model.data_sources[cbox0['source_id']].sheets.keys())
+    common_categories = list(jsd_model.data_sources[cbox0.source_id].sheets.keys())
 
     # Intersect with the categories from subsequent file infos.
     for cbox in file_infos[1:]:
-        categorylist = jsd_model.data_sources[cbox['source_id']].sheets.keys()
+        categorylist = jsd_model.data_sources[cbox.source_id].sheets.keys()
         common_categories = [value for value in common_categories if value in categorylist]
 
     return common_categories
diff --git a/src/midrc_react/gui/dash/dataselectiongroupbox.py b/src/midrc_react/gui/dash/dataselectiongroupbox.py
index e81769d..9ceff7f 100644
--- a/src/midrc_react/gui/dash/dataselectiongroupbox.py
+++ b/src/midrc_react/gui/dash/dataselectiongroupbox.py
@@ -277,7 +277,7 @@ def update_category_combobox(self):
         """
         Update the category combobox based on the selected data sources.
         """
-        previous_value = self.get_category_info()['current_text']
+        previous_value = self.get_category_info().current_text
 
         file_infos = self.get_file_infos()
 
diff --git a/src/midrc_react/gui/ipython/dataselectiongroupbox.py b/src/midrc_react/gui/ipython/dataselectiongroupbox.py
index 3b52163..25f3cc6 100644
--- a/src/midrc_react/gui/ipython/dataselectiongroupbox.py
+++ b/src/midrc_react/gui/ipython/dataselectiongroupbox.py
@@ -191,7 +191,7 @@ def update_category_combobox(self):
         """
         Update the category combobox based on the selected data sources.
         """
-        previous_value = self.get_category_info()['current_text']
+        previous_value = self.get_category_info().current_text
 
         file_infos = self.get_file_infos()
 
diff --git a/src/midrc_react/gui/ipython/jsdview_ipython.py b/src/midrc_react/gui/ipython/jsdview_ipython.py
index f1827ad..eb0bcb9 100644
--- a/src/midrc_react/gui/ipython/jsdview_ipython.py
+++ b/src/midrc_react/gui/ipython/jsdview_ipython.py
@@ -297,7 +297,7 @@ def update_area_chart(self, category):
         if self.plot_method == 'interactive_plotly':
             return self.update_area_chart_interactive_plotly()
 
-        category = self.dataselectiongroupbox.get_category_info()['current_text']
+        category = self.dataselectiongroupbox.get_category_info().current_text
 
         # Set up the figure with multiple subplots
         _fig, axes = plt.subplots(len(category), 1, figsize=(10, 6 * len(category)), sharex=True)
@@ -335,7 +335,7 @@ def update_area_chart(self, category):
             # Final plot settings for each subplot
             ax.set_xlabel('Date')
             ax.set_ylabel(f'{category} Distribution Over Time')
-            source_id = self.dataselectiongroupbox.file_infos[index]['source_id']
+            source_id = self.dataselectiongroupbox.file_infos[index].source_id
             ax.set_title(f"{source_id} {category} Distribution Over Time")
             ax.grid(True)
             ax.legend()
@@ -352,7 +352,7 @@ def update_area_chart_interactive_plotly(self):
         """
         Update the area chart using interactive plotting with Plotly.
         """
-        category = self.dataselectiongroupbox.get_category_info()['current_text']
+        category = self.dataselectiongroupbox.get_category_info().current_text
 
         # Find the global minimum and maximum date
         global_min_date = min(sheets[category].df['date'].min() for sheets in category.values())
@@ -376,7 +376,7 @@ def update_area_chart_interactive_plotly(self):
 
             # Update the layout for each individual figure
             fig.update_layout(
-                title=f"{self.dataselectiongroupbox.file_infos[index]['source_id']} {category} Distribution Over Time",
+                title=f"{self.dataselectiongroupbox.file_infos[index].source_id} {category} Distribution Over Time",
                 xaxis_title="Date",
                 yaxis_title="Percentage (%)",
                 height=400,
diff --git a/src/midrc_react/gui/pyside6/dataselectiongroupbox.py b/src/midrc_react/gui/pyside6/dataselectiongroupbox.py
index 69f494b..961365c 100644
--- a/src/midrc_react/gui/pyside6/dataselectiongroupbox.py
+++ b/src/midrc_react/gui/pyside6/dataselectiongroupbox.py
@@ -21,10 +21,10 @@
 from PySide6.QtCore import QSignalBlocker, Signal
 from PySide6.QtWidgets import QCheckBox, QComboBox, QFormLayout, QGroupBox, QHBoxLayout, QLabel
 
-from midrc_react.gui.common.jsdview_base import GroupBoxData
+from midrc_react.gui.common.jsdview_base import GroupBoxData, FileInfo
 
 
-class JsdDataSelectionGroupBox(QGroupBox, GroupBoxData):
+class JsdDataSelectionGroupBox(QGroupBox):
     """
     This class represents a group box widget for data selection. It provides functionality for creating labels and
     combo boxes for data files and a category combo box. The class has methods for setting up the layout,
@@ -53,6 +53,8 @@ def __init__(self, data_sources):
         """
         super().__init__()
 
+        self.data = GroupBoxData()
+
         self.setTitle('Data Selection')
 
         self.form_layout = QFormLayout()
@@ -101,15 +103,15 @@ def get_file_infos(self):
         Returns:
             List[dict]: A list of dictionaries containing information about each file.
         """
-        self._file_infos = []
+        self.data.file_infos = []
         for i, cbox in enumerate(self.file_comboboxes):
-            self._file_infos.append({
-                'description': cbox.currentText(),
-                'source_id': cbox.currentData(),
-                'index': i,
-                'checked': self.file_checkboxes[i].isChecked(),
-            })
-        return self._file_infos
+            self.data.append_file_info(FileInfo(
+                description = cbox.currentText(),
+                source_id = cbox.currentData(),
+                index = i,
+                checked = self.file_checkboxes[i].isChecked(),
+            ))
+        return self.data.file_infos
 
     def get_category_info(self):
         """
@@ -118,12 +120,9 @@ def get_category_info(self):
         Returns:
             dict: A dictionary containing the category information.
         """
-        self._category_info = {
-            'current_text': self.category_combobox.currentText(),
-            'current_index': self.category_combobox.currentIndex(),
-            'category_list': [self.category_combobox.itemText(i) for i in range(self.category_combobox.count())],
-        }
-        return self._category_info
+        category_list = [self.category_combobox.itemText(i) for i in range(self.category_combobox.count())]
+        category_index = self.category_combobox.currentIndex()
+        return self.data.category_info
 
     def add_file_combobox_to_layout(self, auto_populate: bool = True):
         """
@@ -233,3 +232,4 @@ def update_category_list(self, categorylist, categoryindex):
             self.category_combobox.clear()
             self.category_combobox.addItems(categorylist)
             self.category_combobox.setCurrentIndex(categoryindex)
+        self.data.update_category_list(categorylist, categoryindex)
diff --git a/src/react_demo.ipynb b/src/react_demo.ipynb
index bd0727d..a29f01f 100644
--- a/src/react_demo.ipynb
+++ b/src/react_demo.ipynb
@@ -210,7 +210,7 @@
    "source": [
     "#display(jsd_view_base.dataselectiongroupbox.get_file_infos())\n",
     "#display(jsd_view_base.dataselectiongroupbox.get_category_info())\n",
-    "#display(jsd_view_base.dataselectiongroupbox.get_category_info()['current_text'])\n",
+    "#display(jsd_view_base.dataselectiongroupbox.get_category_info().current_text)\n",
     "#display(jsd_view_base.dataselectiongroupbox.category_combobox.value)\n",
     "display(jsd_table_model.data_sources['MIDRC'].data_source)\n",
     "\n",

From 90e730ee36288bb72ec309554de46ed2888f0798 Mon Sep 17 00:00:00 2001
From: Robert Tomek <robt_0@hotmail.com>
Date: Wed, 19 Nov 2025 10:43:30 -0600
Subject: [PATCH 4/7] Moving config data to pydantic.BaseModel

---
 src/midrc_react/core/data_preprocessing.py    |  3 +
 src/midrc_react/core/excel_layout.py          | 46 ++++++------
 src/midrc_react/core/jsdconfig.py             | 71 ++++++++++++++++---
 src/midrc_react/core/jsdcontroller.py         | 11 +--
 src/midrc_react/core/jsdmodel.py              | 14 ++--
 src/midrc_react/gui/common/file_upload.py     |  4 +-
 src/midrc_react/gui/common/jsdview_base.py    | 12 ++--
 src/midrc_react/gui/common/utils.py           | 21 +++---
 src/midrc_react/gui/dash/jsdview_dash.py      |  6 +-
 .../gui/ipython/jsdview_ipython.py            |  2 +-
 .../gui/pyside6/dataselectiongroupbox.py      | 11 +--
 src/midrc_react/gui/pyside6/jsdview.py        |  5 +-
 src/midrc_react/gui/pyside6/launch_react.py   |  6 +-
 src/react_demo.ipynb                          |  6 +-
 14 files changed, 146 insertions(+), 72 deletions(-)

diff --git a/src/midrc_react/core/data_preprocessing.py b/src/midrc_react/core/data_preprocessing.py
index a5b61a3..3e63a35 100644
--- a/src/midrc_react/core/data_preprocessing.py
+++ b/src/midrc_react/core/data_preprocessing.py
@@ -95,6 +95,7 @@ def bin_dataframe_column(df_to_bin: pd.DataFrame, column_name: str, cut_column_n
     Returns:
         pd.DataFrame: pandas DataFrame with the binned column and the labels
     """
+    print(f"Binning column '{column_name}' into '{cut_column_name}' with bins: {bins} and labels: {labels}")
     if column_name not in df_to_bin.columns:
         return df_to_bin
 
@@ -113,6 +114,8 @@ def bin_dataframe_column(df_to_bin: pd.DataFrame, column_name: str, cut_column_n
         ).astype("string"),
     })
 
+    print(f"Completed binning column '{column_name}' into '{cut_column_name}'.")
+
     if df_out[cut_column_name].isna().any():
         df_out = _adjust_outliers(df_out, cut_column_name, column_name, bins)
 
diff --git a/src/midrc_react/core/excel_layout.py b/src/midrc_react/core/excel_layout.py
index 69ac805..000e691 100644
--- a/src/midrc_react/core/excel_layout.py
+++ b/src/midrc_react/core/excel_layout.py
@@ -41,20 +41,20 @@ def __init__(self, data_source, custom_age_ranges=None):
             data_source (dict): The data source configuration.
             custom_age_ranges (dict, optional): A dictionary of custom age ranges.
         """
-        self.name = data_source['name']
+        self.name = data_source.name
         self.sheets = {}
-        self.datatype = data_source['data type']
-        self.filename = data_source['filename']
+        self.datatype = data_source.data_type
+        self.filename = data_source.filename
         self.data_source = data_source
         self.custom_age_ranges = custom_age_ranges
-        self._numeric_cols = data_source.get('numeric_cols', {})  # Extract numeric columns from config
-        self._columns = data_source.get('columns', [])
+        self._numeric_cols = data_source.numeric_cols  # Extract numeric columns from config
+        self._columns = data_source.columns
         self.raw_data = None
 
         # Load preprocessing plugin if specified
         self.preprocessor = None
-        if 'plugin' in data_source and data_source['plugin']:
-            plugin_name = data_source['plugin']
+        if data_source.plugin:
+            plugin_name = data_source.plugin
             plugin_path = os.path.join("plugins", f"{plugin_name}.py")
             self.preprocessor = DataSource.load_plugin(plugin_path)
 
@@ -64,8 +64,8 @@ def __init__(self, data_source, custom_age_ranges=None):
                 self.build_data_frames_from_csv(self.filename)
             else:
                 self.build_data_frames_from_file(self.filename)
-        if self.datatype == 'content' and 'content' in data_source:
-            self.build_data_frames_from_content(data_source['content'])
+        if self.datatype == 'content' and hasattr(data_source, 'content') and data_source.content is not None:
+            self.build_data_frames_from_content(data_source.content)
 
     def raw_columns_to_use(self):
         """
@@ -126,9 +126,10 @@ def apply_numeric_column_adjustments(self, df: pd.DataFrame):
             pd.DataFrame: The DataFrame with numeric column adjustments.
         """
         for str_col, col_dict in self._numeric_cols.items():
-            num_col = col_dict['raw column'] if 'raw column' in col_dict else str_col
-            bins = col_dict['bins'] if 'bins' in col_dict else None
-            labels = col_dict['labels'] if 'labels' in col_dict else None
+            print(f"Applying numeric adjustments for column: {str_col} with settings: {col_dict}")
+            num_col = col_dict.raw_column if hasattr(col_dict, 'raw_column') else str_col
+            bins = col_dict.bins if hasattr(col_dict, 'bins') else None
+            labels = col_dict.labels if hasattr(col_dict, 'labels') else None
 
             if num_col in df.columns:
                 df = bin_dataframe_column(df, num_col, str_col, bins=bins, labels=labels)
@@ -139,7 +140,7 @@ def apply_numeric_column_adjustments(self, df: pd.DataFrame):
                 # else:
                 #     # Default "N-N" format conversion
                 #     df[str_col] = df[num_col].apply(lambda x: f'{int(x)}-{int(x)}' if pd.notna(x) else x)
-
+        print(f"Data after numeric column adjustments has columns: {df.columns.tolist()}")
         return df
 
     def build_data_frames_from_csv(self, filename: str):
@@ -155,9 +156,11 @@ def build_data_frames_from_csv(self, filename: str):
         delimiter = ',' if filename.endswith('.csv') else '\t'
         df = pd.read_csv(filename, delimiter=delimiter, low_memory=False)
 
+        print(f"Loaded data from {filename} with columns: {df.columns.tolist()}")
         # Apply preprocessing if a plugin is available
         if self.preprocessor:
             df = self.preprocessor(df)
+        print(f"Data after preprocessing has columns: {df.columns.tolist()}")
 
         # Apply numeric column adjustments
         df = self.apply_numeric_column_adjustments(df)
@@ -226,7 +229,7 @@ def create_sheets_from_df(self, df: pd.DataFrame):
             if col in df.columns:
                 df_cumsum = self.calculate_cumulative_sums(df, col)
                 if col in self._numeric_cols:
-                    labels = self._numeric_cols[col].get('labels', None)
+                    labels = self._numeric_cols[col].labels if hasattr(self._numeric_cols[col], 'labels') else None
                     if labels:
                         # The first column (e.g., date) remains at index 0.
                         date_column = df_cumsum.columns[0]
@@ -333,25 +336,28 @@ def _process_date_column(self, data_source: dict):
         """
 
         # This assumes that the first column is either the date column or does not have useful data
-        if data_source.get('date'):
+        date_value = getattr(data_source, 'date', None)
+        if date_value:
             self._df.drop(self._df.columns[0], axis=1, inplace=True)
-            self._df.insert(0, 'date', data_source['date'], False)
+            self._df.insert(0, 'date', date_value, False)
 
         self._df['date'] = pd.to_datetime(self._df['date'], errors='coerce')
 
         self._columns['date'] = self._df.columns[0]
 
-    def _process_columns(self, data_source: dict):
+    def _process_columns(self, data_source):
         """
         Process and rename columns according to the data source settings.
 
         Args:
-            data_source (dict): The data source object.
+            data_source (DataSource): The data source object.
         """
         for col in self._df.columns[1:]:
             col_name = col
-            if 'remove column name text' in data_source:
-                for txt in data_source['remove column name text']:
+            # Access remove_column_name_text from pydantic model
+            remove_text = getattr(data_source, 'remove_column_name_text', None)
+            if remove_text:
+                for txt in remove_text:
                     col_name = col.split(txt)[0]
             col_name = col_name.rstrip()
             self._columns[col_name] = col
diff --git a/src/midrc_react/core/jsdconfig.py b/src/midrc_react/core/jsdconfig.py
index a28fe49..9ea607f 100644
--- a/src/midrc_react/core/jsdconfig.py
+++ b/src/midrc_react/core/jsdconfig.py
@@ -17,9 +17,11 @@
 This module contains the JSDConfig class, which loads and stores data from a YAML file.
 """
 
-from dataclasses import dataclass, field
 import os
+from typing import List, Optional, Dict, Union, Any
 
+from pydantic import BaseModel, Field, ValidationError
+from pydantic.dataclasses import dataclass
 from yaml import load
 try:
     from yaml import CLoader as Loader
@@ -27,7 +29,52 @@
     from yaml import Loader
 
 
-@dataclass
+class NumericColumnConfig(BaseModel):
+    """
+    NumericColumnConfig model to represent numeric column configurations in the YAML configuration.
+    """
+    raw_column: str = Field(..., alias='raw column')
+    bins: List[float]
+    labels: Optional[List[str]] = None
+    adjust_outliers: bool = Field(False, alias='adjust outliers')
+
+class DataSource(BaseModel):
+    """
+    DataSource model to represent individual data sources in the YAML configuration.
+    """
+    name: str
+    description: Optional[str] = None
+    data_type: str = Field(..., alias='data type')
+    filename: str
+    columns: Optional[List[str]] = None
+    numeric_cols: Optional[Dict[str, NumericColumnConfig]] = None
+    plugin: Optional[str] = None
+    date: Optional[str] = None
+    remove_column_name_text: Optional[List[str]] = Field(None, alias='remove column name text')
+
+    content: Optional[Any] = None  # Placeholder for loaded content
+    content_type: Optional[str] = None  # Placeholder for content type after loading
+
+    class Config:
+        validate_by_name = True
+        extra = 'allow'
+
+DataSourceList = List[DataSource]
+
+class ConfigData(BaseModel):
+    """
+    ConfigData model to represent the structure of the YAML configuration data.
+    """
+    # Define fields based on expected YAML structure
+    data_sources: DataSourceList = Field(..., alias='data sources')
+    custom_age_ranges: Optional[Dict[str, List[Union[int, float]]]] = Field(None, alias='custom_age_range')
+
+    class Config:
+        validate_by_name = True
+        # accept extra fields in the YAML
+        extra = 'allow'
+
+
 class JSDConfig:
     """
     The JSDConfig class loads and stores data from a YAML file.
@@ -38,13 +85,16 @@ class JSDConfig:
 
     Methods:
         __init__(self, filename='jsdconfig.yaml'): Initializes a new instance of JSDConfig.
-        __post_init__(self): Loads the YAML data from the current filename.
+        _load_data(self): Loads the YAML data from the current filename.
+        set_filename(self, new_filename): Sets a new filename and reloads the data.
     """
-    filename: str = 'jsdconfig.yaml'
-    data: dict = field(init=False)
+    filename: str
+    data: Optional[ConfigData]
 
-    def __post_init__(self):
+    def __init__(self, filename: str = 'jsdconfig.yaml'):
         """Load the YAML data from the current filename."""
+        self.filename = filename
+        self.data = None
         # os.chdir(os.path.join(os.path.dirname(os.path.abspath(__file__)), '..'))
         self._load_data()
 
@@ -53,11 +103,16 @@ def _load_data(self):
         if not os.path.exists(self.filename):
             print(f"File {self.filename} does not exist. Skipping load.")
             print(f"Current working directory: {os.getcwd()}")
-            self.data = {}
+            self.data = None
             return
 
         with open(self.filename, 'r', encoding='utf-8') as stream:
-            self.data = load(stream, Loader=Loader)
+            raw = load(stream, Loader=Loader)
+        try:
+            self.data = ConfigData(**raw)
+        except ValidationError as e:
+            self.data = None
+            raise
         # print(dump(self.data))
 
     def set_filename(self, new_filename: str):
diff --git a/src/midrc_react/core/jsdcontroller.py b/src/midrc_react/core/jsdcontroller.py
index 4e0ead4..e9850c6 100644
--- a/src/midrc_react/core/jsdcontroller.py
+++ b/src/midrc_react/core/jsdcontroller.py
@@ -187,6 +187,7 @@ def file_changed(self, _, new_category_index=None):
         category_set = None
         for cbox in file_infos:
             ds = self.jsd_model.data_sources[cbox.source_id]
+            print(f"Data source '{ds.name}' has categories: {list(ds.sheets.keys())}")
             if category_set is None:
                 category_set = set(ds.sheets.keys())
             else:
@@ -305,7 +306,7 @@ def build_date_list(df1, df2):
                 numeric_cols = []
                 for str_col, col_info in data_source_1.numeric_cols.items():
                     cols_to_use.remove(str_col)
-                    num_col = col_info['raw column']
+                    num_col = col_info.raw_column
                     cols_to_use.append(num_col)
                     numeric_cols.append(num_col)
                 input_data = calc_famd_ks2_at_dates(
@@ -321,7 +322,7 @@ def build_date_list(df1, df2):
                 combined_df = combine_datasets_from_list([raw_df1, raw_df2])
                 date_list = build_date_list(raw_df1, raw_df2)
                 str_col = category[:-6]
-                num_col = data_source_1.numeric_cols[str_col]['raw column']
+                num_col = data_source_1.numeric_cols[str_col].raw_column
 
                 input_data = [calc_ks2_samp_by_feature(combined_df[combined_df['date'] <= date],
                                                              num_col)['Dataset 0 vs Dataset 1'] for date in date_list]
@@ -448,7 +449,7 @@ def get_cols_to_use_for_jsd_calc(self, source_id, category):
         """
         cols_to_use = self.jsd_model.data_sources[source_id].sheets[category].data_columns
 
-        custom_age_ranges = self._config.data.get('custom age ranges', None)
+        custom_age_ranges = self._config.data.custom_age_ranges
         if custom_age_ranges and category in custom_age_ranges:
             cols_to_use = [f'{age_range[0]}-{age_range[1]} Custom' for
                            age_range in custom_age_ranges[category]] + [JSDController.NOT_REPORTED_COLUMN_NAME]
@@ -525,7 +526,7 @@ def get_spider_plot_values(self, calc_date=None):
                         numeric_cols = []
                         for str_col, col_info in data_source_1.numeric_cols.items():
                             cols_to_use.remove(str_col)
-                            num_col = col_info['raw column']
+                            num_col = col_info.raw_column
                             cols_to_use.append(num_col)
                             numeric_cols.append(num_col)
                         jsd_dict[(index1, idx2)][category] = calc_famd_ks2_at_date(
@@ -540,7 +541,7 @@ def get_spider_plot_values(self, calc_date=None):
                         raw_df2 = data_source_2.raw_data
                         combined_df = combine_datasets_from_list([raw_df1, raw_df2])
                         str_col = category[:-6]
-                        num_col = data_source_1.numeric_cols[str_col]['raw column']
+                        num_col = data_source_1.numeric_cols[str_col].raw_column
                         jsd_dict[(index1, idx2)][category] = calc_ks2_samp_by_feature(
                             combined_df[combined_df['date'] <= calc_date],
                             num_col,
diff --git a/src/midrc_react/core/jsdmodel.py b/src/midrc_react/core/jsdmodel.py
index 6a046a5..180688c 100644
--- a/src/midrc_react/core/jsdmodel.py
+++ b/src/midrc_react/core/jsdmodel.py
@@ -24,6 +24,7 @@
 from PySide6.QtGui import QColor
 
 from midrc_react.core.excel_layout import DataSource
+from midrc_react.core.jsdconfig import DataSourceList
 
 
 def convert_to_builtin(val):
@@ -51,18 +52,18 @@ class JSDTableModel(QAbstractTableModel):
     ]
     data_source_added = Signal()
 
-    def __init__(self, data_source_list=None, custom_age_ranges=None):
+    def __init__(self, data_source_list: DataSourceList=None, custom_age_ranges=None):
         """
         Initialize the JSDTableModel.
 
         This method initializes the JSDTableModel by setting up the input data, mapping, and raw data sources.
 
         Args:
-            data_source_list (List[dict], optional): A list of data sources. Each data source is a dictionary with the\
-                                                     following keys:
+            data_source_list (List[DataSource], optional): A list of data sources. Each data source has the following
+                                                                attributes (plus others):
 
                 - 'name' (str): The name of the data source.
-                - 'data type' (str): The type of the data source.
+                - 'data_type' (str): The type of the data source.
                 - 'filename' (str): The filename of the data source.
 
             custom_age_ranges (Any, optional): Custom age ranges for the data sources.
@@ -79,9 +80,12 @@ def __init__(self, data_source_list=None, custom_age_ranges=None):
         self.max_row_count = 0
 
         self.data_sources = {}
+
         if data_source_list is not None:
             for data_source_dict in data_source_list:
                 self.add_data_source(data_source_dict)
+        else:
+            print("No data sources provided to JSDTableModel")
 
     def add_data_source(self, data_source_dict):
         """
@@ -104,7 +108,7 @@ def add_data_source(self, data_source_dict):
         Returns:
             None
         """
-        self.data_sources[data_source_dict['name']] = DataSource(data_source_dict, self.custom_age_ranges)
+        self.data_sources[data_source_dict.name] = DataSource(data_source_dict, self.custom_age_ranges)
         self.data_source_added.emit()
 
     def rowCount(self, parent: QModelIndex = None) -> int:
diff --git a/src/midrc_react/gui/common/file_upload.py b/src/midrc_react/gui/common/file_upload.py
index c69b671..af7126e 100644
--- a/src/midrc_react/gui/common/file_upload.py
+++ b/src/midrc_react/gui/common/file_upload.py
@@ -26,9 +26,9 @@ def process_file_upload(view, data_source_dict):
     Args:
         view: An instance that implements open_excel_file and holds a
               data_selection_group_box attribute.
-        data_source_dict (dict): Contains the uploaded file information.
+        data_source_dict (DataSource): Contains the uploaded file information.
     """
-    print(f"handle_excel_file_uploaded() triggered with file: {data_source_dict['name']}")
+    print(f"handle_excel_file_uploaded() triggered with file: {data_source_dict.name}")
     view.open_excel_file(data_source_dict)
     print("Excel file loaded, try to update layout")
     if hasattr(view, 'data_selection_group_box'):
diff --git a/src/midrc_react/gui/common/jsdview_base.py b/src/midrc_react/gui/common/jsdview_base.py
index 585a6e5..483a983 100644
--- a/src/midrc_react/gui/common/jsdview_base.py
+++ b/src/midrc_react/gui/common/jsdview_base.py
@@ -30,6 +30,8 @@ class FileInfo(BaseModel):
     index: Optional[int] = None
     checked: bool = True
 
+FileInfoList = List[FileInfo]
+
 class CategoryInfo(BaseModel):
     current_text: Optional[str] = None
     current_index: Optional[int] = None
@@ -45,10 +47,10 @@ class GroupBoxData(BaseModel):
         file_infos (list): A list of file information dictionaries.
         category_info (dict): A dictionary containing information about the selected category.
     """
-    file_infos: List[FileInfo] = Field(default_factory=list)
+    file_infos: FileInfoList = Field(default_factory=list)
     category_info: CategoryInfo = Field(default_factory=CategoryInfo)
 
-    def get_file_infos(self) -> List[FileInfo]:
+    def get_file_infos(self) -> FileInfoList:
         """
         Get the file information dictionaries.
 
@@ -171,11 +173,11 @@ def open_excel_file(self, data_source_dict):
         Opens an Excel file and adds it to the data selection group box.
 
         Args:
-            data_source_dict (dict): The data source dictionary.
+            data_source_dict (DataSource): The data source dictionary.
         """
         self._dataselectiongroupbox.append_file_info(FileInfo(
-            description = data_source_dict['description'],
-            source_id = data_source_dict['name'],
+            description = data_source_dict.description,
+            source_id = data_source_dict.name,
             index = len(self._dataselectiongroupbox.file_infos),
             checked = True,
         ))
diff --git a/src/midrc_react/gui/common/utils.py b/src/midrc_react/gui/common/utils.py
index 91755be..529c2b5 100644
--- a/src/midrc_react/gui/common/utils.py
+++ b/src/midrc_react/gui/common/utils.py
@@ -18,6 +18,7 @@
 """
 
 from jsdview_base import FileInfo
+from midrc_react.core.jsdconfig import DataSource
 
 
 def create_file_info(data_source, index):
@@ -25,15 +26,15 @@ def create_file_info(data_source, index):
     Create a file info dictionary from a data source.
 
     Args:
-        data_source (dict): Dictionary containing file info.
+        data_source (DataSource): Dictionary containing file info.
         index (int): The index to assign.
 
     Returns:
         dict: A dictionary with description, source_id, index and checked flag.
     """
     return FileInfo(
-        description = data_source.get('description'),
-        source_id = data_source.get('name'),
+        description = data_source.description,
+        source_id = data_source.name,
         index = index,
         checked = True,
     )
@@ -78,10 +79,10 @@ def create_data_source_dict(filename, file_content, data_type='content', content
     Returns:
         dict: A dictionary with file details.
     """
-    return {
-        'description': filename,
-        'name': filename,
-        'content': file_content,
-        'data type': data_type,
-        'content type': content_type,
-    }
+    return DataSource(
+        description = filename,
+        name = filename,
+        content = file_content,
+        data_type = data_type,
+        content_type = content_type,
+    )
diff --git a/src/midrc_react/gui/dash/jsdview_dash.py b/src/midrc_react/gui/dash/jsdview_dash.py
index 1b1be0d..50470b5 100644
--- a/src/midrc_react/gui/dash/jsdview_dash.py
+++ b/src/midrc_react/gui/dash/jsdview_dash.py
@@ -206,13 +206,13 @@ def run(self):
 if __name__ == '__main__':
     # Example usage:
     my_config = JSDConfig()
-    my_data_source_list = my_config.data['data sources']
-    my_jsd_model = JSDTableModel(my_data_source_list, my_config.data.get('custom age ranges', None))
+    my_data_source_list = my_config.data.data_sources
+    my_jsd_model = JSDTableModel(my_data_source_list, my_config.data.custom_age_ranges)
     dash_view = JSDViewDash(my_jsd_model, my_config)
 
     # Load data sources
     for my_data_source in my_data_source_list:
-        print(f"Loading: {my_data_source['description']}...")
+        print(f"Loading: {my_data_source.description}...")
         dash_view.open_excel_file(my_data_source)
 
     print("Done Loading Files")
diff --git a/src/midrc_react/gui/ipython/jsdview_ipython.py b/src/midrc_react/gui/ipython/jsdview_ipython.py
index eb0bcb9..2538d3e 100644
--- a/src/midrc_react/gui/ipython/jsdview_ipython.py
+++ b/src/midrc_react/gui/ipython/jsdview_ipython.py
@@ -67,7 +67,7 @@ def open_excel_file(self, data_source_dict):
         Open an Excel file and add it as a data source.
 
         Args:
-            data_source_dict (dict): The data source information used for loading the data.
+            data_source_dict (DataSource): The data source information used for loading the data.
         """
         super().open_excel_file(data_source_dict)
         self.add_data_source.emit(data_source_dict)
diff --git a/src/midrc_react/gui/pyside6/dataselectiongroupbox.py b/src/midrc_react/gui/pyside6/dataselectiongroupbox.py
index 961365c..14b86cd 100644
--- a/src/midrc_react/gui/pyside6/dataselectiongroupbox.py
+++ b/src/midrc_react/gui/pyside6/dataselectiongroupbox.py
@@ -22,6 +22,7 @@
 from PySide6.QtWidgets import QCheckBox, QComboBox, QFormLayout, QGroupBox, QHBoxLayout, QLabel
 
 from midrc_react.gui.common.jsdview_base import GroupBoxData, FileInfo
+from midrc_react.core.jsdconfig import DataSourceList
 
 
 class JsdDataSelectionGroupBox(QGroupBox):
@@ -49,7 +50,7 @@ def __init__(self, data_sources):
         category combo box.
 
         Parameters:
-            data_sources (list): A list of data sources.
+            data_sources (DataSourceList): A list of data sources.
         """
         super().__init__()
 
@@ -64,7 +65,7 @@ def __init__(self, data_sources):
         self.category_combobox = QComboBox()
         self.set_layout(data_sources)
 
-    def set_layout(self, data_sources):
+    def set_layout(self, data_sources: DataSourceList):
         """
         Set the layout for the given data sources.
 
@@ -87,7 +88,7 @@ def set_layout(self, data_sources):
         self.add_file_combobox_to_layout(auto_populate=False)
 
         # Add the file comboboxes and labels to the form layout
-        items = [(d['description'], d['name']) for d in data_sources]
+        items = [(d.description, d.name) for d in data_sources]
         for combobox_item in items:
             self.add_file_to_comboboxes(combobox_item[0], combobox_item[1])
         self.file_comboboxes[0].setCurrentIndex(0)
@@ -101,9 +102,9 @@ def get_file_infos(self):
         Get the file information for all files.
 
         Returns:
-            List[dict]: A list of dictionaries containing information about each file.
+            FileInfoList: A list of dictionaries containing information about each file.
         """
-        self.data.file_infos = []
+        self.data.file_infos: FileInfoList = []
         for i, cbox in enumerate(self.file_comboboxes):
             self.data.append_file_info(FileInfo(
                 description = cbox.currentText(),
diff --git a/src/midrc_react/gui/pyside6/jsdview.py b/src/midrc_react/gui/pyside6/jsdview.py
index 7349707..eb9f470 100644
--- a/src/midrc_react/gui/pyside6/jsdview.py
+++ b/src/midrc_react/gui/pyside6/jsdview.py
@@ -37,6 +37,7 @@
 )
 
 from midrc_react.core.datetimetools import convert_date_to_milliseconds, numpy_datetime64_to_qdate
+from midrc_react.core.jsdconfig import DataSourceList
 from midrc_react.gui.common.jsdview_base import JsdViewBase
 from midrc_react.gui.pyside6.copyabletableview import CopyableTableView
 from midrc_react.gui.pyside6.dataselectiongroupbox import JsdDataSelectionGroupBox
@@ -69,12 +70,12 @@ class JsdWindow(QMainWindow, JsdViewBase):
                                 "#fb9a99", "#e31a1c", "#fdbf6f", "#ff7f00",
                                 "#cab2d6", "#6a3d9a"]
 
-    def __init__(self, data_sources: Any) -> None:
+    def __init__(self, data_sources: DataSourceList) -> None:
         """
         Initialize the JsdWindow with provided data sources and set up the GUI.
 
         Args:
-            data_sources (Any): Data sources used to initialize the data selection group box.
+            data_sources (DataSourceList): Data sources used to initialize the data selection group box.
         """
         super().__init__()
         # Set up the data selection group box
diff --git a/src/midrc_react/gui/pyside6/launch_react.py b/src/midrc_react/gui/pyside6/launch_react.py
index af965f6..7ddd82a 100644
--- a/src/midrc_react/gui/pyside6/launch_react.py
+++ b/src/midrc_react/gui/pyside6/launch_react.py
@@ -108,13 +108,13 @@ def launch_react():
     q_app.processEvents()
 
     config = JSDConfig()
-    if 'data sources' not in config.data:
+    if config.data is None or config.data.data_sources is None or len(config.data.data_sources) == 0:
         raise ValueError(f"No data sources found in the configuration file. \n"
                          f"            Check that the file < {config.filename} > exists and is in the correct format.")
-    data_source_list = config.data['data sources']
+    data_source_list = config.data.data_sources
     w = JsdWindow(data_source_list)  # Note: We should have the controller populate this once the tablemodel is loaded
     w.jsd_controller = JSDController(w,
-                                     JSDTableModel(data_source_list, config.data.get('custom age ranges', None)),
+                                     JSDTableModel(data_source_list, config.data.custom_age_ranges),
                                      config)
 
     # Set the default widget sizes, show the window, then reset the minimum sizes
diff --git a/src/react_demo.ipynb b/src/react_demo.ipynb
index a29f01f..353a8b1 100644
--- a/src/react_demo.ipynb
+++ b/src/react_demo.ipynb
@@ -37,11 +37,11 @@
     "from midrc_react.gui.ipython.jsdview_ipython import JsdViewIPython\n",
     "\n",
     "config = JSDConfig()\n",
-    "jsd_model = JSDTableModel(None, config.data.get('custom age ranges', None))\n",
+    "jsd_model = JSDTableModel(None, config.data.custom_age_range)\n",
     "jsd_view = JsdViewIPython(jsd_model)\n",
     "jsd_controller = JSDController(jsd_view, jsd_model, config)\n",
-    "for data_source in config.data['data sources']:\n",
-    "    print(f\"Loading: {data_source['description']}...\")\n",
+    "for data_source in config.data.data_sources:\n",
+    "    print(f\"Loading: {data_source.description}...\")\n",
     "    jsd_view.open_excel_file(data_source)\n",
     "\n",
     "print(\"Done Loading Files\")\n",

From c528dce4c134f9dee015fa427db1288aa8db2096 Mon Sep 17 00:00:00 2001
From: Robert Tomek <robt_0@hotmail.com>
Date: Wed, 19 Nov 2025 10:49:26 -0600
Subject: [PATCH 5/7] Refactor DataSourceConfig to differentiate between config
 metadata and actual data

---
 src/Untitled.ipynb                                   | 12 ++++++------
 src/midrc_react/core/data_preprocessing.py           |  3 ---
 src/midrc_react/core/excel_layout.py                 |  4 ----
 src/midrc_react/core/jsdconfig.py                    |  6 +++---
 src/midrc_react/core/jsdmodel.py                     |  4 ++--
 src/midrc_react/gui/common/utils.py                  |  6 +++---
 src/midrc_react/gui/pyside6/dataselectiongroupbox.py |  4 ++--
 src/midrc_react/gui/pyside6/jsdview.py               |  4 ++--
 8 files changed, 18 insertions(+), 25 deletions(-)

diff --git a/src/Untitled.ipynb b/src/Untitled.ipynb
index 7bf834d..3b02cf9 100644
--- a/src/Untitled.ipynb
+++ b/src/Untitled.ipynb
@@ -1561,7 +1561,7 @@
     "import importlib\n",
     "importlib.reload(ExcelLayout)\n",
     "\n",
-    "midrc_data = ExcelLayout.DataSource('MIDRC')\n",
+    "midrc_data = ExcelLayout.DataSourceConfig('MIDRC')\n",
     "print( midrc_data.sheets['Race'].columns.values() )\n",
     "print( midrc_data.sheets['Race'].df.columns )\n",
     "cols_to_use = midrc_data.sheets['Race'].df.columns.intersection(midrc_data.sheets['Race'].columns.values())\n",
@@ -1571,7 +1571,7 @@
     "midrc_race_data = np.asarray(midrc_data.sheets['Race'].df[cols_to_use].iloc[-1].values,dtype=float)\n",
     "print(midrc_race_data)\n",
     "\n",
-    "cdc_data = ExcelLayout.DataSource('CDC')\n",
+    "cdc_data = ExcelLayout.DataSourceConfig('CDC')\n",
     "#print( cdc_data.sheets['Race'].columns )\n",
     "cols_to_use = cdc_data.sheets['Race'].df.columns.intersection(cdc_data.sheets['Race'].columns.values())\n",
     "#Remove date column\n",
@@ -1579,7 +1579,7 @@
     "cdc_race_data = np.asarray(cdc_data.sheets['Race'].df[cols_to_use].iloc[-1].values,dtype=float)\n",
     "print(cdc_race_data)\n",
     "\n",
-    "census_data = ExcelLayout.DataSource('Census')\n",
+    "census_data = ExcelLayout.DataSourceConfig('Census')\n",
     "#print( census_data.sheets['Race'].columns.values() )\n",
     "#print( census_data.sheets['Race'].df.columns )\n",
     "cols_to_use = census_data.sheets['Race'].df.columns.intersection(census_data.sheets['Race'].columns.values())\n",
@@ -1607,17 +1607,17 @@
     "\n",
     "sheet_name = 'Race'\n",
     "\n",
-    "midrc_data = ExcelLayout.DataSource('MIDRC')\n",
+    "midrc_data = ExcelLayout.DataSourceConfig('MIDRC')\n",
     "cols_to_use = midrc_data.sheets[sheet_name].df.columns.intersection(midrc_data.sheets[sheet_name].columns.values())\n",
     "cols_to_use = cols_to_use[1:]\n",
     "midrc_sheet_data = np.asarray(midrc_data.sheets[sheet_name].df[cols_to_use].iloc[-1].values,dtype=float)\n",
     "\n",
-    "cdc_data = ExcelLayout.DataSource('CDC')\n",
+    "cdc_data = ExcelLayout.DataSourceConfig('CDC')\n",
     "cols_to_use = cdc_data.sheets[sheet_name].df.columns.intersection(cdc_data.sheets[sheet_name].columns.values())\n",
     "cols_to_use = cols_to_use[1:]\n",
     "cdc_sheet_data = np.asarray(cdc_data.sheets[sheet_name].df[cols_to_use].iloc[-1].values,dtype=float)\n",
     "\n",
-    "census_data = ExcelLayout.DataSource('Census')\n",
+    "census_data = ExcelLayout.DataSourceConfig('Census')\n",
     "cols_to_use = census_data.sheets[sheet_name].df.columns.intersection(census_data.sheets[sheet_name].columns.values())\n",
     "cols_to_use = cols_to_use[1:]\n",
     "census_sheet_data = np.asarray(census_data.sheets[sheet_name].df[cols_to_use].iloc[-1].values,dtype=float)\n",
diff --git a/src/midrc_react/core/data_preprocessing.py b/src/midrc_react/core/data_preprocessing.py
index 3e63a35..a5b61a3 100644
--- a/src/midrc_react/core/data_preprocessing.py
+++ b/src/midrc_react/core/data_preprocessing.py
@@ -95,7 +95,6 @@ def bin_dataframe_column(df_to_bin: pd.DataFrame, column_name: str, cut_column_n
     Returns:
         pd.DataFrame: pandas DataFrame with the binned column and the labels
     """
-    print(f"Binning column '{column_name}' into '{cut_column_name}' with bins: {bins} and labels: {labels}")
     if column_name not in df_to_bin.columns:
         return df_to_bin
 
@@ -114,8 +113,6 @@ def bin_dataframe_column(df_to_bin: pd.DataFrame, column_name: str, cut_column_n
         ).astype("string"),
     })
 
-    print(f"Completed binning column '{column_name}' into '{cut_column_name}'.")
-
     if df_out[cut_column_name].isna().any():
         df_out = _adjust_outliers(df_out, cut_column_name, column_name, bins)
 
diff --git a/src/midrc_react/core/excel_layout.py b/src/midrc_react/core/excel_layout.py
index 000e691..c5446f3 100644
--- a/src/midrc_react/core/excel_layout.py
+++ b/src/midrc_react/core/excel_layout.py
@@ -126,7 +126,6 @@ def apply_numeric_column_adjustments(self, df: pd.DataFrame):
             pd.DataFrame: The DataFrame with numeric column adjustments.
         """
         for str_col, col_dict in self._numeric_cols.items():
-            print(f"Applying numeric adjustments for column: {str_col} with settings: {col_dict}")
             num_col = col_dict.raw_column if hasattr(col_dict, 'raw_column') else str_col
             bins = col_dict.bins if hasattr(col_dict, 'bins') else None
             labels = col_dict.labels if hasattr(col_dict, 'labels') else None
@@ -140,7 +139,6 @@ def apply_numeric_column_adjustments(self, df: pd.DataFrame):
                 # else:
                 #     # Default "N-N" format conversion
                 #     df[str_col] = df[num_col].apply(lambda x: f'{int(x)}-{int(x)}' if pd.notna(x) else x)
-        print(f"Data after numeric column adjustments has columns: {df.columns.tolist()}")
         return df
 
     def build_data_frames_from_csv(self, filename: str):
@@ -156,11 +154,9 @@ def build_data_frames_from_csv(self, filename: str):
         delimiter = ',' if filename.endswith('.csv') else '\t'
         df = pd.read_csv(filename, delimiter=delimiter, low_memory=False)
 
-        print(f"Loaded data from {filename} with columns: {df.columns.tolist()}")
         # Apply preprocessing if a plugin is available
         if self.preprocessor:
             df = self.preprocessor(df)
-        print(f"Data after preprocessing has columns: {df.columns.tolist()}")
 
         # Apply numeric column adjustments
         df = self.apply_numeric_column_adjustments(df)
diff --git a/src/midrc_react/core/jsdconfig.py b/src/midrc_react/core/jsdconfig.py
index 9ea607f..5dba159 100644
--- a/src/midrc_react/core/jsdconfig.py
+++ b/src/midrc_react/core/jsdconfig.py
@@ -38,7 +38,7 @@ class NumericColumnConfig(BaseModel):
     labels: Optional[List[str]] = None
     adjust_outliers: bool = Field(False, alias='adjust outliers')
 
-class DataSource(BaseModel):
+class DataSourceConfig(BaseModel):
     """
     DataSource model to represent individual data sources in the YAML configuration.
     """
@@ -59,14 +59,14 @@ class Config:
         validate_by_name = True
         extra = 'allow'
 
-DataSourceList = List[DataSource]
+DataSourceConfigList = List[DataSourceConfig]
 
 class ConfigData(BaseModel):
     """
     ConfigData model to represent the structure of the YAML configuration data.
     """
     # Define fields based on expected YAML structure
-    data_sources: DataSourceList = Field(..., alias='data sources')
+    data_sources: DataSourceConfigList = Field(..., alias='data sources')
     custom_age_ranges: Optional[Dict[str, List[Union[int, float]]]] = Field(None, alias='custom_age_range')
 
     class Config:
diff --git a/src/midrc_react/core/jsdmodel.py b/src/midrc_react/core/jsdmodel.py
index 180688c..3bbefc7 100644
--- a/src/midrc_react/core/jsdmodel.py
+++ b/src/midrc_react/core/jsdmodel.py
@@ -24,7 +24,7 @@
 from PySide6.QtGui import QColor
 
 from midrc_react.core.excel_layout import DataSource
-from midrc_react.core.jsdconfig import DataSourceList
+from midrc_react.core.jsdconfig import DataSourceConfigList
 
 
 def convert_to_builtin(val):
@@ -52,7 +52,7 @@ class JSDTableModel(QAbstractTableModel):
     ]
     data_source_added = Signal()
 
-    def __init__(self, data_source_list: DataSourceList=None, custom_age_ranges=None):
+    def __init__(self, data_source_list: DataSourceConfigList=None, custom_age_ranges=None):
         """
         Initialize the JSDTableModel.
 
diff --git a/src/midrc_react/gui/common/utils.py b/src/midrc_react/gui/common/utils.py
index 529c2b5..040d337 100644
--- a/src/midrc_react/gui/common/utils.py
+++ b/src/midrc_react/gui/common/utils.py
@@ -18,7 +18,7 @@
 """
 
 from jsdview_base import FileInfo
-from midrc_react.core.jsdconfig import DataSource
+from midrc_react.core.jsdconfig import DataSourceConfig
 
 
 def create_file_info(data_source, index):
@@ -26,7 +26,7 @@ def create_file_info(data_source, index):
     Create a file info dictionary from a data source.
 
     Args:
-        data_source (DataSource): Dictionary containing file info.
+        data_source (DataSourceConfig): Dictionary containing file info.
         index (int): The index to assign.
 
     Returns:
@@ -79,7 +79,7 @@ def create_data_source_dict(filename, file_content, data_type='content', content
     Returns:
         dict: A dictionary with file details.
     """
-    return DataSource(
+    return DataSourceConfig(
         description = filename,
         name = filename,
         content = file_content,
diff --git a/src/midrc_react/gui/pyside6/dataselectiongroupbox.py b/src/midrc_react/gui/pyside6/dataselectiongroupbox.py
index 14b86cd..011027c 100644
--- a/src/midrc_react/gui/pyside6/dataselectiongroupbox.py
+++ b/src/midrc_react/gui/pyside6/dataselectiongroupbox.py
@@ -22,7 +22,7 @@
 from PySide6.QtWidgets import QCheckBox, QComboBox, QFormLayout, QGroupBox, QHBoxLayout, QLabel
 
 from midrc_react.gui.common.jsdview_base import GroupBoxData, FileInfo
-from midrc_react.core.jsdconfig import DataSourceList
+from midrc_react.core.jsdconfig import DataSourceConfigList
 
 
 class JsdDataSelectionGroupBox(QGroupBox):
@@ -65,7 +65,7 @@ def __init__(self, data_sources):
         self.category_combobox = QComboBox()
         self.set_layout(data_sources)
 
-    def set_layout(self, data_sources: DataSourceList):
+    def set_layout(self, data_sources: DataSourceConfigList):
         """
         Set the layout for the given data sources.
 
diff --git a/src/midrc_react/gui/pyside6/jsdview.py b/src/midrc_react/gui/pyside6/jsdview.py
index eb9f470..f59e7aa 100644
--- a/src/midrc_react/gui/pyside6/jsdview.py
+++ b/src/midrc_react/gui/pyside6/jsdview.py
@@ -37,7 +37,7 @@
 )
 
 from midrc_react.core.datetimetools import convert_date_to_milliseconds, numpy_datetime64_to_qdate
-from midrc_react.core.jsdconfig import DataSourceList
+from midrc_react.core.jsdconfig import DataSourceConfigList
 from midrc_react.gui.common.jsdview_base import JsdViewBase
 from midrc_react.gui.pyside6.copyabletableview import CopyableTableView
 from midrc_react.gui.pyside6.dataselectiongroupbox import JsdDataSelectionGroupBox
@@ -70,7 +70,7 @@ class JsdWindow(QMainWindow, JsdViewBase):
                                 "#fb9a99", "#e31a1c", "#fdbf6f", "#ff7f00",
                                 "#cab2d6", "#6a3d9a"]
 
-    def __init__(self, data_sources: DataSourceList) -> None:
+    def __init__(self, data_sources: DataSourceConfigList) -> None:
         """
         Initialize the JsdWindow with provided data sources and set up the GUI.
 

From bc0faeb10f878bcf7e0c0dafc97cd1a0c4db37d0 Mon Sep 17 00:00:00 2001
From: Robert Tomek <robt_0@hotmail.com>
Date: Wed, 19 Nov 2025 11:45:15 -0600
Subject: [PATCH 6/7] Remove tabulate from GUI requirements. It's only used for
 error printing when using command line functions

---
 requirements.txt                           | 1 -
 setup.py                                   | 1 -
 src/midrc_react/core/famd_calc.py          | 7 +++++--
 src/midrc_react/core/jsdcontroller.py      | 1 -
 src/midrc_react/gui/common/jsdview_base.py | 1 -
 5 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index c5ba0ac..7adccb6 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -13,5 +13,4 @@ seaborn>=0.13.2
 ipywidgets>=8.1.5
 ipython>=8.28.0
 python-dateutil>=2.9.0.post0
-tabulate>=0.9.0
 scikit-learn>=1.6.1
diff --git a/setup.py b/setup.py
index bf526f3..62f6aa8 100644
--- a/setup.py
+++ b/setup.py
@@ -38,7 +38,6 @@
         "ipywidgets>=8.1.5",
         "ipython>=8.28.0",
         "python-dateutil>=2.9.0.post0",
-        "tabulate>=0.9.0",
         "scikit-learn>=1.6.1",
     ],
     python_requires=">=3.10",
diff --git a/src/midrc_react/core/famd_calc.py b/src/midrc_react/core/famd_calc.py
index 5889857..153a25e 100644
--- a/src/midrc_react/core/famd_calc.py
+++ b/src/midrc_react/core/famd_calc.py
@@ -22,7 +22,6 @@
 import numpy as np
 import pandas as pd
 import prince
-from tabulate import tabulate
 
 from midrc_react.core.data_preprocessing import combine_datasets_from_list
 from midrc_react.core.numeric_distances import calc_distances_via_df, scale_feature
@@ -132,7 +131,11 @@ def calc_famd_df(raw_df, cols_to_use, numeric_cols, dataset_column='_dataset_',
         if len(outlier_df) > 0:
             outlier_df = outlier_df.sort_values(by=famd_column, ascending=False)
             print(f"Outliers in FAMD fitting: {outlier_df.shape[0]}")
-            print(tabulate(outlier_df, headers='keys', tablefmt='psql'))
+            try:
+                from tabulate import tabulate
+                print(tabulate(outlier_df, headers='keys', tablefmt='psql'))
+            except ImportError:
+                print(outlier_df)
 
     return c_df
 
diff --git a/src/midrc_react/core/jsdcontroller.py b/src/midrc_react/core/jsdcontroller.py
index e9850c6..5772cd3 100644
--- a/src/midrc_react/core/jsdcontroller.py
+++ b/src/midrc_react/core/jsdcontroller.py
@@ -187,7 +187,6 @@ def file_changed(self, _, new_category_index=None):
         category_set = None
         for cbox in file_infos:
             ds = self.jsd_model.data_sources[cbox.source_id]
-            print(f"Data source '{ds.name}' has categories: {list(ds.sheets.keys())}")
             if category_set is None:
                 category_set = set(ds.sheets.keys())
             else:
diff --git a/src/midrc_react/gui/common/jsdview_base.py b/src/midrc_react/gui/common/jsdview_base.py
index 483a983..a3154f2 100644
--- a/src/midrc_react/gui/common/jsdview_base.py
+++ b/src/midrc_react/gui/common/jsdview_base.py
@@ -95,7 +95,6 @@ def update_category_list(self, categorylist: List[str], categoryindex: int):
         Returns:
             None
         """
-        print("Updating category list to:", categorylist, "with index:", categoryindex)
         self.category_info = CategoryInfo(
             current_text = categorylist[categoryindex],
             current_index = categoryindex,

From 505d1b4d659b32b4080b1375148efe2ac6a8d52f Mon Sep 17 00:00:00 2001
From: Robert Tomek <robt_0@hotmail.com>
Date: Thu, 20 Nov 2025 12:27:48 -0600
Subject: [PATCH 7/7] Make some of the dependencies optional

---
 setup.py | 29 ++++++++++++++++++++++-------
 1 file changed, 22 insertions(+), 7 deletions(-)

diff --git a/setup.py b/setup.py
index 62f6aa8..704b279 100644
--- a/setup.py
+++ b/setup.py
@@ -28,18 +28,33 @@
         "PySide6>=6.6.0",
         "scipy>=1.12.0",
         "openpyxl>=3.1.0",
-        "pytest>=8.1.0",
         "PyYAML>=6.0.0",
         "prince>=0.15.0",
-        "dash>=2.18.2",
-        "plotly>=5.24.1",
-        "matplotlib>=3.9.0",
-        "seaborn>=0.13.2",
-        "ipywidgets>=8.1.5",
-        "ipython>=8.28.0",
+        "pydantic>=2.7.0",
         "python-dateutil>=2.9.0.post0",
         "scikit-learn>=1.6.1",
     ],
+    optional_dependencies={
+        "ipython": [
+            "ipywidgets>=8.1.5",
+            "ipython>=8.28.0",
+            "matplotlib>=3.9.0",
+            "seaborn>=0.13.2",
+            "plotly>=5.24.1",
+        ],
+        "dash": [
+            "dash>=2.18.2",
+            "dash-bootstrap-components>=1.4.1",
+            "plotly>=5.24.1",
+        ],
+        "dev": [
+            "pytest>=8.1.0",
+            "black>=24.9.1",
+            "flake8>=6.1.0",
+            "mypy>=1.3.0",
+        ],
+    },
+
     python_requires=">=3.10",
     entry_points={
         "console_scripts": [