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Fix the chrome install issue #423

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Merged
wdecoster merged 3 commits into from
Aug 19, 2025
Merged

Fix the chrome install issue #423

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416517b
fix plot.py to work with kaleido v1
microbemarsh Jul 23, 2025
dcff25d
use plotly for chrome depend
microbemarsh Aug 19, 2025
00edd05
Merge branch 'master' into kaleido_update
microbemarsh Aug 19, 2025
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25 changes: 14 additions & 11 deletions nanoplotter/plot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,13 +5,16 @@
import sys
import logging

# bring in kaleido and ensure Chrome is installed
import kaleido
# this will download a small headless Chrome build the first time you run it
kaleido.get_chrome_sync()

from kaleido import write_fig_sync

# Use Plotly's Chrome bootstrapper instead of kaleido
import plotly.io as pio
try:
# This should find or install a compatible Chrome in a user-writable location
pio.get_chrome()
except Exception as e:
logging.warning(
"Plotly could not fetch or find Chrome automatically. "
"Static exports may fail unless BROWSER_PATH is set. Details: %s", e
)

class Plot(object):
"""A Plot object is defined by a path to the output file and the title of the plot."""
Expand Down Expand Up @@ -56,7 +59,7 @@ def save(self, settings):
p = os.path.splitext(self.path)[0] + ".png"
if os.path.exists(p):
os.remove(p)
logging.warning("No static plots are saved due to some kaleido problem:")
logging.warning("No static plots are saved due to an export problem:")
logging.warning(e)

elif self.fig:
Expand Down Expand Up @@ -84,13 +87,13 @@ def show(self):

def save_static(self, figformat):
"""
Export a Plotly figure via Kaleido v1’s write_fig_sync.
Export a Plotly figure using Plotly's image writer.
"""
output_path = self.path.replace(".html", f".{figformat}")
try:
write_fig_sync(self.fig, path=output_path)
pio.write_image(self.fig, output_path, format=figformat)
logging.info(f"Saved {output_path} as {figformat}")
except Exception as e:
logging.warning("No static plots are saved due to some kaleido problem:")
logging.warning("No static plots are saved due to an export problem:")
logging.warning(e)

16 changes: 16 additions & 0 deletions scripts/agm_test.sh
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Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
#! /bin/bash

#SBATCH --time=04-00:00:00
#SBATCH --partition=defq
#SBATCH --mail-user=myemail@email.org
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH --ntasks-per-node=64
#SBATCH --mem=128GB
#SBATCH --nodes=1
#SBATCH --job-name=nplot
#SBATCH --comment=nplot

source /path/to/nanoplot_env/bin/activate

# test fresh nanoplot with update
python /path/to/NanoPlot/nanoplot/NanoPlot.py --fastq /path/to/test_file.fastq.gz --verbose --minqual 4 --color red -o scripts/agm_tests
2 changes: 2 additions & 0 deletions scripts/agm_tests/LengthvsQualityScatterPlot_dot.html
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2 changes: 2 additions & 0 deletions scripts/agm_tests/LengthvsQualityScatterPlot_kde.html
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