Update docstring and render

DeToX/Calibration.py

@@ -392,13 +392,6 @@ def _fade_sound(self, sound, fade_duration=0.5, steps=10):
         -----
         The sound is automatically stopped after the fade completes, and volume
         is reset to 1.0 (maximum) so it's ready for the next playback at full volume.
-
-        Examples
-        --------
-        >>> # Fade out calibration audio when point is collected
-        >>> self._fade_sound(self.audio, fade_duration=0.5)
-        >>> # Next play() will start at full volume
-        >>> self.audio.play()
         """
         # --- Fade-out Loop ---
         # Gradually decrease volume from current level to 0

Documentation/Vignettes/Calibration.qmd

@@ -128,7 +128,13 @@ Let's break down what's happening here:
 
 **`shuffle=True`**: Randomizes which image appears at each calibration point. This prevents habituation and keeps participants engaged throughout the procedure.
 
+<<<<<<< HEAD
+**`audio=True`**: Plays an attention-getting sound along with the visual stimulus to help capture and maintain the participant's focus.
+
+**`anim_type='zoom'`**: Makes the stimuli gently pulse in size to attract attention. You can also use `'trill'` for a rotating animation.
+=======
 **`audio=True`**: Plays an attention-getting sound along with the visual stimulus to help capture and maintain the participant's focus. **`anim_type='zoom'`**: Makes the stimuli gently pulse in size to attract attention. You can also use `'trill'` for a rotating animation.
+>>>>>>> origin/main
 
 **`visualization_style='circles'`**: Displays the calibration results using dots at each point. You can also choose `'lines'` to show lines connecting the target to where the gaze landed.
 

Documentation/Vignettes/Installation.qmd

@@ -9,14 +9,6 @@ So you're interested in using DeToX? Awesome! Let's get you set up quickly.
 
 DeToX is designed as a lightweight wrapper around **PsychoPy** and **tobii_research**. Here's the good news: `tobii_research` usually comes bundled with PsychoPy, which means the only real hurdle is installing PsychoPy itself. And yes, PsychoPy *can* be a bit tricky to install due to its many dependencies—but don't worry, we'll walk you through it. Once PsychoPy is up and running, adding DeToX is a breeze.
 
-::: callout-note
-## Eye Tracker Drivers Required ![](https://connect.tobii.com/file-asset/eye_tracker_manager?v=2){fig-align="right" width="49" height="33"}
-
-Before DeToX can communicate with your Tobii eye tracker, you need to ensure the correct drivers are installed on your computer. The easiest way to do this is by downloading and installing the [Tobii Pro Eye Tracker Manager](https://www.tobii.com/products/software/applications-and-developer-kits/tobii-pro-eye-tracker-manager)—a free software provided by Tobii that allows you to installs the necessary drivers for your device.
-
-As a bonus, the Eye Tracker Manager also includes a built-in calibration tool (designed for adult self-paced calibration), which can be useful for testing that your hardware is working properly before running DeToX.
-:::
-
 ## Installing PsychoPy
 
 Since PsychoPy is the main challenge, let's tackle that first. You have **two main options**:

Documentation/_quarto.yml

@@ -86,7 +86,7 @@ website:
 format:
   html:
     theme:
-      - pulse
+      - sandstone
       - styles.scss  # your custom SCSS file
     toc: true
     toc-expand: 4   
@@ -123,15 +123,22 @@ filters:
 
 
 quartodoc:
-  style: pkgdown
   title: Reference
   package: DeToX
+
+  style: pkgdown
+  parser: numpy
+  renderer:
+    style: markdown
+    table_style: table
+  render_interlinks: true
+
   dir: api
   sidebar: api/_sidebar.yml
 
   sections:
     - title: Main Eye-tracker Class
-      desc: >
+      desc: |
         The central class of the DeToX package, responsible for connecting to 
         and managing the Tobii eye tracker. This class must be instantiated 
         before any other functionality can be used. It provides access to 
@@ -141,7 +148,7 @@ quartodoc:
         - ETracker
 
     - subtitle: Control the Recording
-      desc: >
+      desc: |
         Functions for starting, stopping, and managing the capture of eye-tracking 
         data. These methods allow you to initiate and terminate recordings, 
         mark events of interest, and save collected data to disk.
@@ -152,7 +159,7 @@ quartodoc:
         - ETracker.save_data
 
     - subtitle: Calibration
-      desc: >
+      desc: |
         Methods for running and managing eye tracker calibration. These include 
         displaying calibration status, initiating calibration routines, and 
         saving or loading calibration settings to ensure accurate gaze data.
@@ -163,7 +170,7 @@ quartodoc:
         - ETracker.load_calibration
 
     - subtitle: Gaze Contingent
-      desc: >
+      desc: |
         Tools for running gaze-contingent experiments, where visual presentation 
         adapts dynamically to a participants gaze position. Includes functionality 
         for live gaze-contingent control and methods to compute average gaze 
@@ -173,7 +180,7 @@ quartodoc:
         - ETracker.get_gaze_position
 
     - title: Internal Calibration 
-      desc: >
+      desc: |
         Classes for running eye-tracker calibration. These get called internally by the ETracker class, and are reported here only for completeness.
         They are comprise of a base calibration class that set the common interface, and the specific implementations for Tobii and Mouse calibration.
       contents:
@@ -182,7 +189,7 @@ quartodoc:
         - MouseCalibrationSession
 
     - title: Coordinate Conversion
-      desc: >
+      desc: |
         A collection of utility functions designed to help the conversion of the data from different formats.
         These are called internally by the ETracker class, but can be used independently if needed.
       contents:
@@ -195,15 +202,15 @@ quartodoc:
         - get_psychopy_pos_from_trackbox
 
     - title: Utilities
-      desc: >
+      desc: |
         A set of utility classes and functions for presenting stimuli
         and formatted text. These are called internally by the ETracker class.
       contents:
         - NicePrint
         - InfantStimuli
 
     - title: Configuration Settings
-      desc: >
+      desc: |
         Configuration classes and module-level instances for customizing the 
         behavior and appearance of the DeToX eye-tracking system. These settings 
         control animation parameters, colors, UI element sizes, and data formats.

Documentation/api/BaseCalibrationSession.qmd

@@ -7,6 +7,7 @@ BaseCalibrationSession(
     audio=None,
     anim_type='zoom',
     visualization_style='lines',
+    visualization_style='lines',
 )
 ```
 
@@ -43,15 +44,15 @@ simulation modes support 2-9 calibration points.
 
 #### Parameters {.doc-section .doc-section-parameters}
 
-| Name               | Type   | Description                                        | Default    |
-|--------------------|--------|----------------------------------------------------|------------|
-| calibration_points | list   | List of calibration point coordinates to validate. | _required_ |
+| Name               | Type           | Description                                        | Default    |
+|--------------------|----------------|----------------------------------------------------|------------|
+| calibration_points | [list](`list`) | List of calibration point coordinates to validate. | _required_ |
 
 #### Raises {.doc-section .doc-section-raises}
 
-| Name   | Type       | Description                                           |
-|--------|------------|-------------------------------------------------------|
-|        | ValueError | If number of points is less than 2 or greater than 9. |
+| Name   | Type                       | Description                                           |
+|--------|----------------------------|-------------------------------------------------------|
+|        | [ValueError](`ValueError`) | If number of points is less than 2 or greater than 9. |
 
 ### show_message_and_wait { #DeToX.BaseCalibrationSession.show_message_and_wait }
 
@@ -67,8 +68,14 @@ then pauses execution until any key is pressed.
 
 #### Parameters {.doc-section .doc-section-parameters}
 
-| Name   | Type   | Description                                                       | Default      |
-|--------|--------|-------------------------------------------------------------------|--------------|
-| body   | str    | The main message text to display.                                 | _required_   |
-| title  | str    | Title for the message box. Default empty string.                  | `''`         |
-| pos    | tuple  | Position of the message box center on screen. Default (0, -0.15). | `(0, -0.15)` |
+| Name   | Type   | Description                                                                                                            | Default      |
+|--------|--------|------------------------------------------------------------------------------------------------------------------------|--------------|
+| body   | str    | The main message text to display. Will be formatted with box-drawing characters via NicePrint.                         | _required_   |
+| title  | str    | Title for the message box. Appears at the top of the formatted box. Default empty string.                              | `''`         |
+| pos    | tuple  | Position of the message box center on screen in window units. Default (0, -0.15) places message slightly below center. | `(0, -0.15)` |
+
+#### Returns {.doc-section .doc-section-returns}
+
+| Name   | Type   | Description   |
+|--------|--------|---------------|
+|        | None   |               |

Documentation/api/ETSettings.AnimationSettings.qmd

@@ -22,17 +22,17 @@ in height units (percentage of screen height).
 
 ## Attributes {.doc-section .doc-section-attributes}
 
-| Name                  | Type   | Description                                                                                                                                |
-|-----------------------|--------|--------------------------------------------------------------------------------------------------------------------------------------------|
-| focus_time            | float  | Wait time in seconds before collecting calibration data at each point. Allows participant to fixate on the target. Default is 0.5 seconds. |
-| zoom_speed            | float  | Speed multiplier for the zoom animation. Higher values make the size oscillation faster. Default is 6.0.                                   |
-| max_zoom_size         | float  | Maximum size for zoom animation as percentage of screen height. Default is 0.11 (11% of screen height).                                    |
-| min_zoom_size         | float  | Minimum size for zoom animation as percentage of screen height. Default is 0.05 (5% of screen height).                                     |
-| trill_size            | float  | Fixed size for trill animation as percentage of screen height. Default is 0.075 (7.5% of screen height).                                   |
-| trill_rotation_range  | float  | Maximum rotation angle in degrees for trill animation. Default is 20 degrees.                                                              |
-| trill_cycle_duration  | float  | Total cycle time for trill animation in seconds (active + pause). Default is 1.5 seconds.                                                  |
-| trill_active_duration | float  | Duration of active trill rotation in seconds, within each cycle. Default is 1.1 seconds (leaves 0.4s pause).                               |
-| trill_frequency       | float  | Number of back-and-forth rotation oscillations per second during active trill phase. Default is 3.0 oscillations/second.                   |
+| Name                  | Type             | Description                                                                                                                                |
+|-----------------------|------------------|--------------------------------------------------------------------------------------------------------------------------------------------|
+| focus_time            | [float](`float`) | Wait time in seconds before collecting calibration data at each point. Allows participant to fixate on the target. Default is 0.5 seconds. |
+| zoom_speed            | [float](`float`) | Speed multiplier for the zoom animation. Higher values make the size oscillation faster. Default is 6.0.                                   |
+| max_zoom_size         | [float](`float`) | Maximum size for zoom animation as percentage of screen height. Default is 0.11 (11% of screen height).                                    |
+| min_zoom_size         | [float](`float`) | Minimum size for zoom animation as percentage of screen height. Default is 0.05 (5% of screen height).                                     |
+| trill_size            | [float](`float`) | Fixed size for trill animation as percentage of screen height. Default is 0.075 (7.5% of screen height).                                   |
+| trill_rotation_range  | [float](`float`) | Maximum rotation angle in degrees for trill animation. Default is 20 degrees.                                                              |
+| trill_cycle_duration  | [float](`float`) | Total cycle time for trill animation in seconds (active + pause). Default is 1.5 seconds.                                                  |
+| trill_active_duration | [float](`float`) | Duration of active trill rotation in seconds, within each cycle. Default is 1.1 seconds (leaves 0.4s pause).                               |
+| trill_frequency       | [float](`float`) | Number of back-and-forth rotation oscillations per second during active trill phase. Default is 3.0 oscillations/second.                   |
 
 ## Examples {.doc-section .doc-section-examples}
 

Documentation/api/ETSettings.CalibrationPatterns.qmd

@@ -1,37 +0,0 @@
-# ETSettings.CalibrationPatterns { #DeToX.ETSettings.CalibrationPatterns }
-
-```python
-ETSettings.CalibrationPatterns(
-    points_5=(lambda: [(0.0, 0.0), (-0.8, 0.8), (0.8, 0.8), (-0.8, -0.8), (0.8, -0.8)])(),
-    points_9=(lambda: [(-0.8, 0.8), (0.0, 0.8), (0.8, 0.8), (-0.8, 0.0), (0.0, 0.0), (0.8, 0.0), (-0.8, -0.8), (0.0, -0.8), (0.8, -0.8)])(),
-    num_samples_mouse=5,
-)
-```
-
-Standard calibration point patterns in normalized coordinates.
-
-Defines commonly used calibration patterns in normalized units where
-the screen ranges from -1 to +1 in both dimensions. These universal
-coordinates work across different screen sizes, aspect ratios, and
-PsychoPy unit systems.
-
-Convert to window-specific coordinates at runtime using the
-norm_to_window_units() function from the Coords module.
-
-## Attributes {.doc-section .doc-section-attributes}
-
-| Name              | Type          | Description                                                                                                                                                           |
-|-------------------|---------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| points_5          | list of tuple | 5-point calibration pattern (4 corners + center). Standard for quick calibrations with good coverage. Pattern: corners at �0.4 from edges to avoid screen boundaries. |
-| points_9          | list of tuple | 9-point calibration pattern (3�3 grid). Standard for comprehensive calibrations requiring high accuracy. Pattern: 3 rows � 3 columns with �0.4 positioning.           |
-| num_samples_mouse | int           | Number of mouse position samples to collect per calibration point in simulation mode. Default 5.                                                                      |
-
-## Examples {.doc-section .doc-section-examples}
-
-```python
->>> from DeToX import ETSettings as cfg
->>> from DeToX.Coords import norm_to_window_units
->>> 
->>> # Change number of mouse samples collected per point
->>> cfg.calibration.num_samples_mouse = 10
-```

Documentation/api/ETSettings.UIElementSizes.qmd

@@ -27,6 +27,23 @@ PsychoPy window configuration.
 
 ## Attributes {.doc-section .doc-section-attributes}
 
+<<<<<<< HEAD
+| Name                | Type             | Description                                                                                                         |
+|---------------------|------------------|---------------------------------------------------------------------------------------------------------------------|
+| highlight           | [float](`float`) | Radius of circles highlighting selected calibration points for retry. Default is 0.02 (2% of screen height).        |
+| line_width          | [float](`float`) | Thickness of lines drawn in calibration visualizations. Default is 0.003 (0.3% of screen height).                   |
+| marker              | [float](`float`) | Size of markers indicating data collection points. Default is 0.02 (2% of screen height).                           |
+| border              | [float](`float`) | Thickness of the red calibration mode border around the screen. Default is 0.005 (0.5% of screen height).           |
+| plot_line           | [float](`float`) | Width of lines in calibration result plots connecting targets to samples. Default is 0.002 (0.2% of screen height). |
+| text                | [float](`float`) | Base text height (deprecated - use specific text sizes below). Default is 0.025 (2.5% of screen height).            |
+| target_circle       | [float](`float`) | Radius of target circles drawn in calibration result visualizations. Default is 0.012 (1.2% of screen height).      |
+| target_circle_width | [float](`float`) | Line width for target circle outlines in result visualizations. Default is 0.003 (0.3% of screen height).           |
+| sample_marker       | [float](`float`) | Radius of sample markers in circle visualization style. Default is 0.005 (0.5% of screen height).                   |
+| instruction_text    | [float](`float`) | Text height for instruction displays during calibration. Default is 0.019 (1.9% of screen height).                  |
+| message_text        | [float](`float`) | Text height for general message displays. Default is 0.016 (1.6% of screen height).                                 |
+| title_text          | [float](`float`) | Text height for title text in message boxes. Default is 0.018 (1.8% of screen height).                              |
+| legend_text         | [float](`float`) | Text height for legend labels showing eye color coding. Default is 0.015 (1.5% of screen height).                   |
+=======
 | Name                | Type   | Description                                                                                                         |
 |---------------------|--------|---------------------------------------------------------------------------------------------------------------------|
 | highlight           | float  | Radius of circles highlighting selected calibration points for retry. Default is 0.02 (2% of screen height).        |
@@ -42,6 +59,7 @@ PsychoPy window configuration.
 | message_text        | float  | Text height for general message displays. Default is 0.016 (1.6% of screen height).                                 |
 | title_text          | float  | Text height for title text in message boxes. Default is 0.018 (1.8% of screen height).                              |
 | legend_text         | float  | Text height for legend labels showing eye color coding. Default is 0.015 (1.5% of screen height).                   |
+>>>>>>> origin/main
 
 ## Notes {.doc-section .doc-section-notes}