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Update to Bokeh 3.4.3 #44

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Update to Bokeh 3.4.3 #44

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b9bc825
Use embed.components instead of embed.json_item to use Bokeh 3.4.3
BenjaminCharmes Jun 16, 2025
6443ee0
Update pyproject.toml
BenjaminCharmes Jun 16, 2025
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1 change: 1 addition & 0 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ dependencies = [
"nmrglue>=0.11",
"navani>=0.1.11",
"datalab-server >= 0.5.3",
"bokeh==3.4.3",
]
[project.optional-dependencies]
local = ["datalab-api >= 0.2.10"]
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13 changes: 8 additions & 5 deletions src/datalab_app_plugin_insitu/apps/nmr/blocks.py
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Expand Up @@ -3,9 +3,9 @@
from pathlib import Path
from typing import Any, Dict, List, Optional, Tuple

import bokeh.embed
import numpy as np
import pandas as pd
from bokeh.embed import components
from bokeh.events import DoubleTap
from bokeh.layouts import gridplot
from bokeh.models import (
Expand Down Expand Up @@ -263,7 +263,8 @@ def generate_insitu_nmr_plot(
grid = [[None, nmrplot_figure], [echemplot_figure, heatmap_figure]]
gp = gridplot(grid, merge_tools=True)

self.data["bokeh_plot_data"] = bokeh.embed.json_item(gp, theme=DATALAB_BOKEH_THEME)
script, div = components(gp, theme=DATALAB_BOKEH_THEME)
self.data["bokeh_plot_data"] = {"script": script, "div": div}

return self.data.get("time_data"), ["Plot successfully generated"]

Expand Down Expand Up @@ -392,11 +393,13 @@ def _create_heatmap_figure(

color_mapper = LinearColorMapper(palette="Turbo256", low=intensity_min, high=intensity_max)

flipped_intensity_matrix = np.fliplr(intensity_matrix)

heatmap_figure.image(
image=[intensity_matrix],
x=max(ppm_values),
image=[flipped_intensity_matrix],
x=min(ppm_values),
y=time_range["start"],
dw=abs(max(ppm_values) - min(ppm_values)),
dw=max(ppm_values) - min(ppm_values),
dh=time_range["end"] - time_range["start"],
color_mapper=color_mapper,
level="image",
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