jonbrenas
commented
6 months ago We will need to modify the API at some point to remove these warnings the right way (the plan is to do it before the 4th edition of the workshops) but in the meantime the easiest solution is to tell the notebook to ignore the warnings. @ahernank did it for W2M3, this way:
import warnings
warnings.simplefilter(action='ignore', category=UserWarning)This will not remove the Bokeh and Pandas warnings, though, so I would advise to silence all warnings:
import warnings
warnings.simplefilter(action='ignore', category=Warning)
Pandas and Bokeh warnings are given on plotting heterozygosity.
BokehDeprecationWarning: 'circle() method with size value' was deprecated in Bokeh 3.4.0 and will be removed, use 'scatter(size=...) instead' instead. /home/conda/developer/2835ffd46e5535e81e9672d0828c143d4f1444491ac44f0aeddd90156919e446-20240426-081151-481742-64-training-nb-maintenance-mgen-9.0.0/lib/python3.10/site-packages/malariagen_data/anoph/genome_features.py:366: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '' has dtype incompatible with float64, please explicitly cast to a compatible dtype first. data.fillna("", inplace=True) /home/conda/developer/2835ffd46e5535e81e9672d0828c143d4f1444491ac44f0aeddd90156919e446-20240426-081151-481742-64-training-nb-maintenance-mgen-9.0.0/lib/python3.10/site-packages/malariagen_data/anopheles.py:490: UserWarning: found multiple competing values for 'toolbar.active_drag' property; using the latest value fig_all = bokeh.layouts.gridplot( /home/conda/developer/2835ffd46e5535e81e9672d0828c143d4f1444491ac44f0aeddd90156919e446-20240426-081151-481742-64-training-nb-maintenance-mgen-9.0.0/lib/python3.10/site-packages/malariagen_data/anopheles.py:490: UserWarning: found multiple competing values for 'toolbar.active_scroll' property; using the latest value fig_all = bokeh.layouts.gridplot(