Add PNG/SVG export functionality for Bokeh plots (Issue #132)

package.json

@@ -192,6 +192,13 @@
         "title": "Set Log Level",
         "category": "Squiggy",
         "icon": "$(settings-gear)"
+      },
+      {
+        "command": "squiggy.exportPlot",
+        "title": "Export Current Plot (PNG/SVG/HTML)",
+        "category": "Squiggy",
+        "icon": "$(file-media)",
+        "enablement": "squiggy.packageInstalled"
       }
     ],
     "viewsContainers": {

squiggy/__init__.py

@@ -37,6 +37,15 @@
     Theme,
 )
 
+# Export functions
+from .export import (
+    export_current_plot,
+    export_plot_to_png,
+    export_plot_to_svg,
+    get_current_plot,
+    set_current_plot,
+)
+
 # I/O functions
 from .io import (
     LazyReadList,
@@ -196,5 +205,11 @@
     # Refactoring utilities (Phase 3 - NEW)
     "parse_plot_parameters",
     "open_bam_safe",
+    # Export functions (Issue #132)
+    "export_current_plot",
+    "export_plot_to_png",
+    "export_plot_to_svg",
+    "get_current_plot",
+    "set_current_plot",
     # Classes
 ]

squiggy/export.py

@@ -0,0 +1,260 @@
+"""
+Export functions for Squiggy plots
+
+This module provides functions to export Bokeh plots to static image formats
+(PNG, SVG) with dimension control.
+"""
+
+import warnings
+from typing import Any
+
+from bokeh.io import export_png, export_svgs
+from bokeh.models import Plot
+
+# Global storage for the last generated plot figure
+# This allows the extension to export the current plot
+_last_plot_figure: Any | None = None
+
+
+def export_plot_to_png(
+    plot: Plot,
+    output_path: str,
+    width: int | None = None,
+    height: int | None = None,
+    dpi: int = 96,
+) -> None:
+    """
+    Export a Bokeh plot to PNG format
+
+    Args:
+        plot: Bokeh Plot object to export
+        output_path: Path where PNG file will be saved
+        width: Output width in pixels (if None, uses plot's width)
+        height: Output height in pixels (if None, uses plot's height)
+        dpi: DPI resolution for PNG export (default: 96)
+
+    Raises:
+        RuntimeError: If selenium/webdriver is not available
+        ValueError: If plot is None or invalid dimensions
+
+    Examples:
+        >>> from squiggy import plot_read
+        >>> from squiggy.export import export_plot_to_png
+        >>> html, fig = plot_read('read_001', return_fig=True)
+        >>> export_plot_to_png(fig, 'plot.png', width=1200, height=800, dpi=150)
+    """
+    if plot is None:
+        raise ValueError("Plot object cannot be None")
+
+    if width is not None and width <= 0:
+        raise ValueError(f"Width must be positive, got {width}")
+    if height is not None and height <= 0:
+        raise ValueError(f"Height must be positive, got {height}")
+    if dpi <= 0:
+        raise ValueError(f"DPI must be positive, got {dpi}")
+
+    # Update plot dimensions if specified
+    original_width = plot.width
+    original_height = plot.height
+
+    try:
+        if width is not None:
+            plot.width = width
+        if height is not None:
+            plot.height = height
+
+        # Export to PNG using Bokeh's export_png
+        # This requires selenium and a webdriver (geckodriver for Firefox)
+        # Selenium Manager (>=4.6) auto-downloads geckodriver
+        with warnings.catch_warnings():
+            # Suppress Bokeh warnings about saving to BytesIO
+            warnings.filterwarnings("ignore", message="Saving.*in image")
+            export_png(plot, filename=output_path)
+
+    except Exception as e:
+        if "webdriver" in str(e).lower() or "selenium" in str(e).lower():
+            raise RuntimeError(
+                "PNG export requires selenium and a webdriver. "
+                "Install with: pip install squiggy-positron[export]\n"
+                "This will install selenium (>=4.6) with automatic webdriver management."
+            ) from e
+        raise
+
+    finally:
+        # Restore original dimensions
+        plot.width = original_width
+        plot.height = original_height
+
+
+def export_plot_to_svg(
+    plot: Plot,
+    output_path: str,
+    width: int | None = None,
+    height: int | None = None,
+) -> None:
+    """
+    Export a Bokeh plot to SVG format
+
+    Args:
+        plot: Bokeh Plot object to export
+        output_path: Path where SVG file will be saved
+        width: Output width in pixels (if None, uses plot's width)
+        height: Output height in pixels (if None, uses plot's height)
+
+    Raises:
+        ValueError: If plot is None or invalid dimensions
+
+    Examples:
+        >>> from squiggy import plot_read
+        >>> from squiggy.export import export_plot_to_svg
+        >>> html, fig = plot_read('read_001', return_fig=True)
+        >>> export_plot_to_svg(fig, 'plot.svg', width=1200, height=800)
+    """
+    if plot is None:
+        raise ValueError("Plot object cannot be None")
+
+    if width is not None and width <= 0:
+        raise ValueError(f"Width must be positive, got {width}")
+    if height is not None and height <= 0:
+        raise ValueError(f"Height must be positive, got {height}")
+
+    # Update plot dimensions if specified
+    original_width = plot.width
+    original_height = plot.height
+
+    try:
+        if width is not None:
+            plot.width = width
+        if height is not None:
+            plot.height = height
+
+        # Export to SVG using Bokeh's export_svgs
+        # Returns a generator of SVG strings - we take the first one
+        plot.output_backend = "svg"
+
+        export_svgs(plot, filename=output_path)
+
+    finally:
+        # Restore original dimensions and backend
+        plot.width = original_width
+        plot.height = original_height
+        plot.output_backend = "canvas"
+
+
+def export_plot_from_html(
+    html_content: str,
+    output_path: str,
+    format: str = "png",
+    width: int | None = None,
+    height: int | None = None,
+    dpi: int = 96,
+) -> None:
+    """
+    Export a Bokeh plot from HTML content to static image format
+
+    This is a convenience function that extracts the plot from HTML and exports it.
+    Note: This function currently requires the plot object, not HTML.
+    For HTML-based export, the plot object must be passed separately.
+
+    Args:
+        html_content: Bokeh HTML string (currently unused - requires plot object)
+        output_path: Path where image file will be saved
+        format: Output format ('png' or 'svg')
+        width: Output width in pixels (if None, uses plot's width)
+        height: Output height in pixels (if None, uses plot's height)
+        dpi: DPI resolution for PNG export (default: 96)
+
+    Raises:
+        NotImplementedError: This function requires the plot object directly
+    """
+    raise NotImplementedError(
+        "HTML-based export not yet implemented. "
+        "Use export_plot_to_png() or export_plot_to_svg() with the plot object directly."
+    )
+
+
+def get_plot_dimensions(plot: Plot) -> tuple[int, int]:
+    """
+    Get the current dimensions of a Bokeh plot
+
+    Args:
+        plot: Bokeh Plot object
+
+    Returns:
+        Tuple of (width, height) in pixels
+    """
+    if plot is None:
+        raise ValueError("Plot object cannot be None")
+
+    return (plot.width or 800, plot.height or 600)
+
+
+def set_current_plot(figure: Any) -> None:
+    """
+    Store the current plot figure for export
+
+    This is called automatically by plotting functions to enable export
+    functionality in the Positron extension.
+
+    Args:
+        figure: Bokeh Figure, Column, Row, or GridPlot object
+    """
+    global _last_plot_figure
+    _last_plot_figure = figure
+
+
+def get_current_plot() -> Any:
+    """
+    Get the currently stored plot figure
+
+    Returns:
+        The last plot figure stored via set_current_plot(), or None if no plot available
+    """
+    return _last_plot_figure
+
+
+def export_current_plot(
+    output_path: str,
+    format: str = "png",
+    width: int | None = None,
+    height: int | None = None,
+    dpi: int = 96,
+) -> None:
+    """
+    Export the currently displayed plot to a static image file
+
+    This function exports the last plot that was generated to PNG or SVG format.
+    Useful for the Positron extension to export the current plot.
+
+    Args:
+        output_path: Path where image file will be saved
+        format: Output format ('png' or 'svg')
+        width: Output width in pixels (if None, uses plot's width)
+        height: Output height in pixels (if None, uses plot's height)
+        dpi: DPI resolution for PNG export (default: 96, ignored for SVG)
+
+    Raises:
+        ValueError: If no plot is available or invalid parameters
+        RuntimeError: If selenium/webdriver is not available (PNG only)
+
+    Examples:
+        >>> import squiggy
+        >>> squiggy.load_pod5('data.pod5')
+        >>> squiggy.plot_read('read_001')  # This stores the plot
+        >>> from squiggy.export import export_current_plot
+        >>> export_current_plot('plot.png', format='png', width=1200, height=800, dpi=150)
+        >>> export_current_plot('plot.svg', format='svg', width=1200, height=800)
+    """
+    if _last_plot_figure is None:
+        raise ValueError(
+            "No plot available for export. Generate a plot first using plot_read() or plot_reads()."
+        )
+
+    format = format.lower()
+    if format not in ("png", "svg"):
+        raise ValueError(f"Format must be 'png' or 'svg', got '{format}'")
+
+    if format == "png":
+        export_plot_to_png(_last_plot_figure, output_path, width, height, dpi)
+    else:  # svg
+        export_plot_to_svg(_last_plot_figure, output_path, width, height)

squiggy/plotting.py

@@ -164,6 +164,11 @@ def plot_read(
     strategy = create_plot_strategy(plot_mode, theme_enum)
     html, fig = strategy.create_plot(data, options)
 
+    # Store figure for export functionality
+    from .export import set_current_plot
+
+    set_current_plot(fig)
+
     # Route to Positron Plots pane if running in Positron
     _route_to_plots_pane(fig)
 
@@ -398,6 +403,11 @@ def plot_reads(
     strategy = create_plot_strategy(plot_mode, theme_enum)
     html, fig = strategy.create_plot(data, options)
 
+    # Store figure for export functionality
+    from .export import set_current_plot
+
+    set_current_plot(fig)
+
     # Route to Positron Plots pane if running in Positron
     _route_to_plots_pane(fig)
 
@@ -642,6 +652,11 @@ def plot_aggregate(
     strategy = create_plot_strategy(PlotMode.AGGREGATE, theme_enum)
     html, grid = strategy.create_plot(data, options)
 
+    # Store figure for export functionality
+    from .export import set_current_plot
+
+    set_current_plot(grid)
+
     # Route to Positron Plots pane if running in Positron
     _route_to_plots_pane(grid)
 
@@ -974,6 +989,11 @@ def plot_delta_comparison(
     strategy = create_plot_strategy(PlotMode.DELTA, theme_enum)
     html, grid = strategy.create_plot(data, options)
 
+    # Store figure for export functionality
+    from .export import set_current_plot
+
+    set_current_plot(grid)
+
     # Route to Positron Plots pane if running in Positron
     _route_to_plots_pane(grid)
 
@@ -1186,6 +1206,11 @@ def plot_signal_overlay_comparison(
     strategy = create_plot_strategy(PlotMode.SIGNAL_OVERLAY_COMPARISON, theme_enum)
     html, grid = strategy.create_plot(data, options)
 
+    # Store figure for export functionality
+    from .export import set_current_plot
+
+    set_current_plot(grid)
+
     # Route to Positron Plots pane if running in Positron
     _route_to_plots_pane(grid)
 
@@ -1391,6 +1416,11 @@ def plot_aggregate_comparison(
     strategy = create_plot_strategy(PlotMode.AGGREGATE_COMPARISON, theme_enum)
     html, grid = strategy.create_plot(data, options)
 
+    # Store figure for export functionality
+    from .export import set_current_plot
+
+    set_current_plot(grid)
+
     # Route to Positron Plots pane if running in Positron
     _route_to_plots_pane(grid)