bokeh: update from 2.4.3 to 3.3.2

.github/workflows/test.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false  # don't cancel if a job from the matrix fails
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"] # 3.12: pyfftw not yet supported
 
     steps:
       - uses: actions/checkout@v2

app/Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:focal
+FROM ubuntu:jammy
 
 COPY requirements.txt requirements.txt
 

app/plot_app/configured_plots.py

@@ -1,5 +1,6 @@
 """ This contains the list of all drawn plots on the log plotting page """
 
+import re
 from html import escape
 
 from bokeh.layouts import column
@@ -92,7 +93,8 @@ def generate_plots(ulog, px4_ulog, db_data, vehicle_data, link_to_3d_page,
         if np.amax(cur_dataset.data['is_vtol']) == 1:
             is_vtol = True
             # check if is tailsitter
-            is_vtol_tailsitter = np.amax(cur_dataset.data['is_vtol_tailsitter']) == 1
+            is_vtol_tailsitter = ('is_vtol_tailsitter' in cur_dataset.data and
+                                  np.amax(cur_dataset.data['is_vtol_tailsitter']) == 1)
             # find mode after transitions (states: 1=transition, 2=FW, 3=MC)
             if 'vehicle_type' in cur_dataset.data:
                 vehicle_type_field = 'vehicle_type'
@@ -1008,6 +1010,12 @@ def param_changes_button_clicked():
     param_changes_button.on_click(param_changes_button_clicked)
 
 
+    user_agent = curdoc().session_context.request.headers.get("User-Agent", "")
+    is_mobile = re.search(r'Mobile|iP(hone|od|ad)|Android|BlackBerry|'
+            r'IEMobile|Kindle|NetFront|Silk-Accelerated|(hpw|web)OS|Fennec|'
+            r'Minimo|Opera M(obi|ini)|Blazer|Dolfin|'
+            r'Dolphin|Skyfire|Zune', user_agent)
+
     jinja_plot_data = []
     for i in range(len(plots)):
         if plots[i] is None:
@@ -1026,6 +1034,9 @@ def param_changes_button_clicked():
                 'fragment': fragment,
                 'title': plot_title
                 })
+        if is_mobile is not None and hasattr(plots[i], 'toolbar'):
+            # Disable panning on mobile by default
+            plots[i].toolbar.active_drag = None
 
 
     # changed parameters

app/plot_app/downsampling.py

@@ -48,7 +48,7 @@ def __init__(self, bokeh_plot, data, x_key):
             self.cur_data[k] = data[k]
 
         # first downsampling
-        self.downsample(self.cur_data, self.bokeh_plot.plot_width *
+        self.downsample(self.cur_data, self.bokeh_plot.width *
                         self.startup_density)
         self.data_source = ColumnDataSource(data=self.cur_data)
 
@@ -64,7 +64,7 @@ def x_range_change_cb(self, attr, old, new):
         new_range = [self.bokeh_plot.x_range.start, self.bokeh_plot.x_range.end]
         if None in new_range:
             return
-        plot_width = self.bokeh_plot.plot_width
+        plot_width = self.bokeh_plot.width
         init_x = self.init_data[self.x_key]
         cur_x = self.cur_data[self.x_key]
         cur_range = [cur_x[0], cur_x[-1]]

app/plot_app/plotting.py

@@ -5,7 +5,7 @@
 #pylint: disable=line-too-long, arguments-differ, unused-import
 from bokeh.models import (
     ColumnDataSource, Range1d, DataRange1d, DatetimeAxis,
-    TickFormatter, DatetimeTickFormatter, FuncTickFormatter,
+    TickFormatter, DatetimeTickFormatter, CustomJSTickFormatter,
     Grid, Legend, Plot, BoxAnnotation, Span, CustomJS, Rect, Circle, Line,
     HoverTool, BoxZoomTool, PanTool, WheelZoomTool, ResetTool, SaveTool,
     WMTSTileSource, GMapPlot, GMapOptions,
@@ -20,6 +20,7 @@
 import scipy.signal
 import pyfftw
 
+from config import debug_verbose_output
 from downsampling import DynamicDownsample
 from helper import (
     map_projection, WGS84_to_mercator, flight_modes_table, vtol_modes_table, get_lat_lon_alt_deg
@@ -91,7 +92,8 @@ def add_virtual_fifo_topic_data(ulog, topic_name, instance=0):
         return True
     except (KeyError, IndexError, ValueError) as error:
         # log does not contain the value we are looking for
-        print(type(error), "(fifo data):", error)
+        if debug_verbose_output():
+            print(type(error), "(fifo data):", error)
         return False
 
 
@@ -118,7 +120,7 @@ def plot_parameter_changes(p, plots_height, changed_parameters):
         # plot as text with a fixed screen-space y offset
         labels = LabelSet(x='x', y='y', text='names',
                           y_units='screen', level='glyph', #text_alpha=0.9, text_color='black',
-                          source=source, render_mode='canvas', text_font_size='8pt')
+                          source=source, text_font_size='8pt')
         p.add_layout(labels)
         return labels
     return None
@@ -168,7 +170,7 @@ def plot_flight_modes_background(data_plot, flight_mode_changes, vtol_states=Non
                                         'y': labels_y_pos, 'textcolor': labels_color})
         labels = LabelSet(x='x', y='y', text='text',
                           y_units='screen', level='underlay',
-                          source=source, render_mode='canvas',
+                          source=source,
                           text_font_size='10pt',
                           text_color='textcolor', text_alpha=0.85,
                           background_fill_color='white',
@@ -223,7 +225,7 @@ def plot_set_equal_aspect_ratio(p, x, y, zoom_out_factor=1.3, min_range=5):
     y_center = (y_range[0]+y_range[1])/2
 
     # keep same aspect ratio as the plot
-    aspect = p.plot_width / p.plot_height
+    aspect = p.width / p.height
     if aspect > x_diff / y_diff:
         x_diff = y_diff * aspect
     else:
@@ -281,7 +283,7 @@ def plot_map(ulog, config, map_type='plain', api_key=None, setpoints=False,
 
             p = GMapPlot(
                 x_range=Range1d(), y_range=Range1d(), map_options=map_options,
-                api_key=api_key, plot_width=plots_width, plot_height=plots_height
+                api_key=api_key, width=plots_width, height=plots_height
             )
 
             pan = PanTool()
@@ -301,8 +303,8 @@ def plot_map(ulog, config, map_type='plain', api_key=None, setpoints=False,
             data_source = ColumnDataSource(data={'lat': lat, 'lon': lon})
 
             p = figure(tools=TOOLS, active_scroll=ACTIVE_SCROLL_TOOLS)
-            p.plot_width = plots_width
-            p.plot_height = plots_height
+            p.width = plots_width
+            p.height = plots_height
 
             plot_set_equal_aspect_ratio(p, lon, lat)
 
@@ -363,8 +365,8 @@ def plot_map(ulog, config, map_type='plain', api_key=None, setpoints=False,
             if bokeh_plot is None:
                 p = figure(tools=TOOLS, active_scroll=ACTIVE_SCROLL_TOOLS,
                            x_axis_label='[m]', y_axis_label='[m]')
-                p.plot_width = plots_width
-                p.plot_height = plots_height
+                p.width = plots_width
+                p.height = plots_height
 
                 plot_set_equal_aspect_ratio(p, lon, lat)
             else:
@@ -399,7 +401,8 @@ def plot_map(ulog, config, map_type='plain', api_key=None, setpoints=False,
 
     except (KeyError, IndexError, ValueError) as error:
         # log does not contain the value we are looking for
-        print(type(error), "(vehicle_gps_position):", error)
+        if debug_verbose_output():
+            print(type(error), "(vehicle_gps_position):", error)
         return None
     p.toolbar.logo = None
     # make it possible to hide graphs by clicking on the label
@@ -453,7 +456,8 @@ def __init__(self, data, config, data_name, x_axis_label=None,
                                y=y_start, size=0, alpha=0)
 
         except (KeyError, IndexError, ValueError) as error:
-            print(type(error), "("+self._data_name+"):", error)
+            if debug_verbose_output():
+                print(type(error), "("+self._data_name+"):", error)
             self._had_error = True
 
     @property
@@ -501,7 +505,8 @@ def change_dataset(self, data_name, topic_instance=0):
             self._cur_dataset = [elem for elem in self._data
                                  if elem.name == data_name and elem.multi_id == topic_instance][0]
         except (KeyError, IndexError, ValueError) as error:
-            print(type(error), "("+self._data_name+"):", error)
+            if debug_verbose_output():
+                print(type(error), "("+self._data_name+"):", error)
             self._had_error = True
             self._cur_dataset = None
 
@@ -550,7 +555,7 @@ def add_graph(self, field_names, colors, legends, use_downsample=True,
                     # plot as text with a fixed screen-space y offset
                     labels = LabelSet(x='x', y='y', text='names',
                                       y_units='screen', level='glyph', text_color=nan_color,
-                                      source=source, render_mode='canvas')
+                                      source=source)
                     p.add_layout(labels)
 
 
@@ -573,7 +578,8 @@ def add_graph(self, field_names, colors, legends, use_downsample=True,
                            legend_label=legend, line_width=2, line_color=color)
 
         except (KeyError, IndexError, ValueError) as error:
-            print(type(error), "("+self._data_name+"):", error)
+            if debug_verbose_output():
+                print(type(error), "("+self._data_name+"):", error)
             self._had_error = True
 
     def add_circle(self, field_names, colors, legends):
@@ -595,7 +601,8 @@ def add_circle(self, field_names, colors, legends):
                          fill_color=None)
 
         except (KeyError, IndexError, ValueError) as error:
-            print(type(error), "("+self._data_name+"):", error)
+            if debug_verbose_output():
+                print(type(error), "("+self._data_name+"):", error)
             self._had_error = True
 
 
@@ -630,7 +637,8 @@ def add_span(self, field_name, accumulator_func=np.mean,
                 self._p.add_layout(data_span)
 
         except (KeyError, IndexError, ValueError) as error:
-            print(type(error), "("+self._data_name+"):", error)
+            if debug_verbose_output():
+                print(type(error), "("+self._data_name+"):", error)
             self._had_error = True
 
     def add_horizontal_background_boxes(self, colors, limits):
@@ -668,8 +676,8 @@ def _setup_plot(self):
         plots_height = self.plot_height
         p = self._p
 
-        p.plot_width = plots_width
-        p.plot_height = plots_height
+        p.width = plots_width
+        p.height = plots_height
 
         # -> other attributes are set via theme.yaml
 
@@ -688,7 +696,7 @@ def _setup_plot(self):
 
         # axis labels: format time
         if self._use_time_formatter:
-            p.xaxis[0].formatter = FuncTickFormatter(code='''
+            p.xaxis[0].formatter = CustomJSTickFormatter(code='''
                     //func arguments: ticks, x_range
                     // assume us ticks
                     var ms = Math.round(tick / 1000);
@@ -717,7 +725,8 @@ def _setup_plot(self):
                 ''', args={'x_range': p.x_range})
 
         # make it possible to hide graphs by clicking on the label
-        p.legend.click_policy = "hide"
+        if len(p.legend) > 0:
+            p.legend.click_policy = "hide"
 
 
 class DataPlot2D(DataPlot):
@@ -739,8 +748,8 @@ def __init__(self, data, config, data_name, x_axis_label=None,
         self._equal_aspect = equal_aspect
         self._is_first_graph = True
 
-        self._p.plot_width = self._config['plot_width']
-        self._p.plot_height = self._config['plot_height'][self._plot_height_name]
+        self._p.width = self._config['plot_width']
+        self._p.height = self._config['plot_height'][self._plot_height_name]
 
 
     def add_graph(self, dataset_x, dataset_y, color, legend, check_if_all_zero=False):
@@ -774,7 +783,8 @@ def add_graph(self, dataset_x, dataset_y, color, legend, check_if_all_zero=False
                     plot_set_equal_aspect_ratio(p, x, y)
 
         except (KeyError, IndexError, ValueError) as error:
-            print(type(error), "("+self._data_name+"):", error)
+            if debug_verbose_output():
+                print(type(error), "("+self._data_name+"):", error)
             self._had_error = True
 
 
@@ -896,7 +906,8 @@ def add_graph(self, field_names, legends, window='hann', window_length=256, nove
             self._p.toolbar.active_scroll = wheel_zoom
 
         except (KeyError, IndexError, ValueError, ZeroDivisionError) as error:
-            print(type(error), "(" + self._data_name + "):", error)
+            if debug_verbose_output():
+                print(type(error), "(" + self._data_name + "):", error)
             self._had_error = True
 
 class DataPlotFFT(DataPlot):
@@ -984,7 +995,8 @@ def add_graph(self, field_names, colors, legends):
                              line_color=color, line_width=2, legend_label=legend)
 
         except (KeyError, IndexError, ValueError, ZeroDivisionError) as error:
-            print(type(error), "(" + self._data_name + "):", error)
+            if debug_verbose_output():
+                print(type(error), "(" + self._data_name + "):", error)
             self._had_error = True
 
     def mark_frequency(self, frequency, label, y_screen_offset=0):
@@ -1002,7 +1014,6 @@ def mark_frequency(self, frequency, label, y_screen_offset=0):
         # plot as text with a fixed screen-space y offset
         label = Label(x=frequency, y=self.plot_height/2-10-y_screen_offset,
                       text=label, y_units='screen', level='glyph',
-                      text_font_size='8pt', text_color=mark_color,
-                      render_mode='canvas')
+                      text_font_size='8pt', text_color=mark_color)
         p.add_layout(label)
 

app/plot_app/static/css/main.css

@@ -36,19 +36,8 @@ h1 .name {
 	font-weight: 400;
 }
 
-/* navigation anchor links for plots */
-a.fragment {
-	position: absolute;
-	top: -14px;
-	left: -16px;
-	z-index: 100;
-}
-a.fragment:not(:hover) {
-	color: #a8a8a8;
-}
-
+/* upload page */
 table.spaced {
-	/* upload page */
 	margin: 16px 0;
 	width: 680px;
 }
@@ -95,20 +84,6 @@ pre {
 }
 
 
-/* bokeh plots */
-.bk-plot-layout {
-	/* spacing between plots */
-	margin-top: 12px;
-}
-.bk-grid-column {
-	/* adjust to changed spacing */
-	height: 100% !important;
-}
-/* bootstrap interferences */
-.bk-slick-header-column {
-	box-sizing: content-box;
-}
-
 /* override the bokeh font with the one used in the boostrap theme
  * (there's no option for that in theme.yaml)
  */

app/plot_app/statistics_plots.py

@@ -9,7 +9,7 @@
 from bokeh.plotting import figure
 from bokeh.palettes import viridis # alternatives: magma, inferno
 from bokeh.models import (
-    DatetimeTickFormatter, FixedTicker, FuncTickFormatter,
+    DatetimeTickFormatter, FixedTicker, CustomJSTickFormatter,
     HoverTool, ColumnDataSource, LabelSet #, CustomJS
     )
 
@@ -549,7 +549,7 @@ def _plot_public_data_statistics(self, all_data, version_attr_name,
         if area.legend:
             area.legend[0].items.reverse()
 
-        area.xaxis.formatter = FuncTickFormatter(code="""
+        area.xaxis.formatter = CustomJSTickFormatter(code="""
             var versions = """ + str(versions_spaced) + """;
             return versions[Math.floor(tick)]
         """)
@@ -569,8 +569,8 @@ def _setup_plot(self, p, plot_height='normal'):
 
         plots_width = self._config['plot_width']
         plots_height = self._config['plot_height'][plot_height]
-        p.plot_width = plots_width
-        p.plot_height = plots_height
+        p.width = plots_width
+        p.height = plots_height
 
         p.xgrid.grid_line_color = 'navy'
         p.xgrid.grid_line_alpha = 0.13

app/plot_app/templates/header.html

@@ -11,7 +11,8 @@
     <link href="plot_app/static/css/font-awesome.min.css" rel="stylesheet">
     <link href="plot_app/static/css/animate.min.css" rel="stylesheet">
     <link href="plot_app/static/css/main.css" rel="stylesheet">
-
+    <link rel="icon" type="image/x-icon" href="plot_app/static/images/favicon-32x32.png">
+
     <link rel="stylesheet" href="https://unpkg.com/[email protected]/dist/leaflet.css"
     integrity="sha512-puBpdR0798OZvTTbP4A8Ix/l+A4dHDD0DGqYW6RQ+9jxkRFclaxxQb/SJAWZfWAkuyeQUytO7+7N4QKrDh+drA=="
     crossorigin=""/>