bokeh visualisation error

[ardy20]

Hello

I installed WGD for whole genome duplication analysis. I run the bokeh and the viz command as following but I get error when I run on your example data . Could you please guide how to solve this?

bokeh serve &

wgd viz -i -ks ath.ks.tsv

Traceback (most recent call last): File "/home/usr/miniconda3/bin/wgd", line 8, in sys.exit(cli()) File "/home/usr/miniconda3/lib/python3.9/site-packages/click/core.py", line 1130, in call return self.main(args, kwargs) File "/home/usr/miniconda3/lib/python3.9/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/home/usr/miniconda3/lib/python3.9/site-packages/click/core.py", line 1657, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/usr/miniconda3/lib/python3.9/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/usr/miniconda3/lib/python3.9/site-packages/click/core.py", line 760, in invoke return __callback(args, **kwargs) File "/home/usr/miniconda3/lib/python3.9/site-packages/wgdcli.py", line 1289, in viz viz( File "/home/usr/miniconda3/lib/python3.9/site-packages/wgdcli.py", line 1355, in viz histogram_bokeh(dists_files, labels) File "/home/usr/miniconda3/lib/python3.9/site-packages/wgd/viz.py", line 389, in histogram_bokeh from bokeh.io import curdoc File "/home/usr/miniconda3/lib/python3.9/site-packages/bokeh/io/init.py", line 51, in from .export import export_png File "/home/usr/miniconda3/lib/python3.9/site-packages/bokeh/io/export.py", line 34, in from ..embed import file_html File "/home/usr/miniconda3/lib/python3.9/site-packages/bokeh/embed/init.py", line 54, in from .server import server_document File "/home/usr/miniconda3/lib/python3.9/site-packages/bokeh/embed/server.py", line 29, in from ..core.templates import AUTOLOAD_TAG, FILE File "/home/usr/miniconda3/lib/python3.9/site-packages/bokeh/core/templates.py", line 43, in from jinja2 import Environment, Markup, FileSystemLoader ImportError: cannot import name 'Markup' from 'jinja2' (/home/usr/miniconda3/lib/python3.9/site-packages/jinja2/init.py)

[Wyinghao]

Hello, I also encountered the same problem, I would like to ask you if you solve it

[heche-psb]

Hi, in the next version we're working on, we don't maintain the bokeh related function in wgd viz any more, but more focused on the implementation of mixture modeling (ELMM for instance). The problem you encounter might be due to the higher version of bokeh in python3.9 you used. It might help if you try with lower version instead.