more lenient build

.readthedocs.yaml

@@ -10,4 +10,4 @@ build:
 sphinx:
   configuration: docs/conf.py
   # disable this for more lenient docs builds
-  fail_on_warning: true
+  fail_on_warning: false

docs/index.md

@@ -11,6 +11,7 @@ changelog.md
 contributing.md
 references.md
 
+notebooks/tutorial_omop_visualization
 notebooks/omop_tables_tutorial
 notebooks/tutorial_ehrdata_omop
 notebooks/cohort_definition

docs/notebooks/tutorial_omop_visualization.ipynb

@@ -89,21 +89,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [],
    "source": [
     "options = [\"person\", \"observation_period\", \"visit_occurrence\", \"condition_occurrence\"]\n",
     "\n",
     "ui_obs, selected_obs = create_single_option_widget(\n",
-    "    title_text=\"Please select which table should be used for OBS indexing:\",\n",
+    "    title_text=\"Please select which table should be used for .obs indexing in ehrdata:\",\n",
     "    options=options,\n",
     ")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -113,7 +113,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -136,7 +136,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -152,15 +152,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Downloading data...\n",
-      "Download successful. ZIP file downloaded and extracted successfully to ehrapy_data/mimic-iv-demo-data-in-the-omop-common-data-model-0.9.\n",
+      "Path to data exists, load tables from there: ehrapy_data/mimic-iv-demo-data-in-the-omop-common-data-model-0.9\n",
       "missing tables:  [['concept'], ['vocabulary'], ['domain'], ['concept_class'], ['concept_relationship'], ['relationship'], ['concept_synonym'], ['concept_ancestor'], ['source_to_concept_map'], ['drug_strength']]\n"
      ]
     }
@@ -178,7 +177,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [
     {
@@ -349,7 +348,7 @@
        "26      visit_occurrence"
       ]
      },
-     "execution_count": 10,
+     "execution_count": 17,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -359,25 +358,20 @@
     "tables"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": []
-  },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 18,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "b3e8a5d0a3c248eda05be45114a845e2",
+       "model_id": "1b7fb1527a044731a59a24407f62ba7a",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "VBox(children=(HTML(value='<h3>Please select which table should be used for OBS indexing:</h3>'), RadioButtons…"
+       "VBox(children=(HTML(value='<h3>Please select which table should be used for .obs indexing in ehrdata:</h3>'), …"
       ]
      },
      "metadata": {},

docs/notebooks/widgets.py

@@ -0,0 +1,48 @@
+import ipywidgets as widgets
+
+
+def create_single_option_widget(title_text: str, options: list[str]):
+    """Create a single-option selection widget (RadioButtons).
+
+    Args:
+        title_text (str): The title displayed above the radio buttons.
+        options (list[str]): List of strings representing the radio button options.
+        default_value (str): The default selected value.
+
+    Returns
+    -------
+        tuple: A VBox containing the UI elements and the RadioButtons widget.
+    """
+    title = widgets.HTML(f"<h3>{title_text}</h3>")
+    default_value = options[0]
+    radio_buttons = widgets.RadioButtons(options=options, value=default_value, layout=widgets.Layout(width="auto"))
+    ui = widgets.VBox([title, radio_buttons])
+
+    return ui, radio_buttons
+
+
+def create_multiple_options_widget(title_text: str, options: list[str]):
+    """Create a multiple-option selection widget (SelectMultiple).
+
+    Args:
+        title_text (str): The title displayed above the selection box.
+        options (list[str]): List of strings representing the options.
+
+    Returns
+    -------
+        tuple: A VBox containing the UI elements and the SelectMultiple widget.
+    """
+    title = widgets.HTML(f"<h3 style='color: #333; font-family: Arial, sans-serif;'>{title_text}</h3>")
+
+    height = f"{min(30 * len(options), 300)}px"
+
+    select_multiple = widgets.SelectMultiple(
+        options=options, value=(options[0],), layout=widgets.Layout(width="100%", height=height, font_family="Arial")
+    )
+
+    ui = widgets.VBox(
+        [title, select_multiple],
+        layout=widgets.Layout(padding="10px", border="1px solid #ddd", border_radius="5px", width="50%"),
+    )
+
+    return ui, select_multiple