conda dependencies

[shenwei356]

Hi Fernando,

I installed cami-opal with conda and got some error caused by bokeh.

log

``` 2021-04-06 10:48:04,833 INFO Loading profiles... 2021-04-06 10:48:04,835 INFO done 2021-04-06 10:48:04,835 INFO Computing metrics... 2021-04-06 10:48:04,909 INFO done 2021-04-06 10:48:04,909 INFO Saving computed metrics... 2021-04-06 10:48:05,002 INFO done 2021-04-06 10:48:05,003 INFO Creating beta diversity plots... 2021-04-06 10:48:05,003 INFO done 2021-04-06 10:48:05,003 INFO Creating rarefaction curves... 2021-04-06 10:48:05,577 INFO done 2021-04-06 10:48:05,577 INFO Creating spider plots... /home/shenwei/Public/app/miniconda3/envs/kmcp/lib/python3.9/site-packages/src/plots.py:340: UserWarning: FixedFormatter should only be used together with FixedLocator axs.set_xticklabels([''] + c.ALL_RANKS) /home/shenwei/Public/app/miniconda3/envs/kmcp/lib/python3.9/site-packages/src/plots.py:340: UserWarning: FixedFormatter should only be used together with FixedLocator axs.set_xticklabels([''] + c.ALL_RANKS) 2021-04-06 10:48:05,926 INFO done 2021-04-06 10:48:05,926 INFO Computing rankings... 2021-04-06 10:48:05,981 INFO done 2021-04-06 10:48:05,981 INFO Creating HTML page... Traceback (most recent call last): File "/home/shenwei/Public/app/miniconda3/envs/kmcp/bin/opal.py", line 377, in main() File "/home/shenwei/Public/app/miniconda3/envs/kmcp/bin/opal.py", line 370, in main html.create_html(pd_rankings, ranks_scored, pd_metrics, labels, sample_ids_list, plots_list, output_dir, args.desc) File "/home/shenwei/Public/app/miniconda3/envs/kmcp/lib/python3.9/site-packages/src/html_opal.py", line 487, in create_html col_rankings = create_rankings_html(pd_rankings, ranks_scored) File "/home/shenwei/Public/app/miniconda3/envs/kmcp/lib/python3.9/site-packages/src/html_opal.py", line 187, in create_rankings_html weight_recall = Slider(start=0, end=10, value=1, step=.1, title=c.RECALL + " weight", callback=callback) File "/home/shenwei/Public/app/miniconda3/envs/kmcp/lib/python3.9/site-packages/bokeh/models/widgets/sliders.py", line 76, in __init__ super().__init__(**kwargs) File "/home/shenwei/Public/app/miniconda3/envs/kmcp/lib/python3.9/site-packages/bokeh/model.py", line 236, in __init__ super().__init__(**kwargs) File "/home/shenwei/Public/app/miniconda3/envs/kmcp/lib/python3.9/site-packages/bokeh/core/has_props.py", line 268, in __init__ setattr(self, name, value) File "/home/shenwei/Public/app/miniconda3/envs/kmcp/lib/python3.9/site-packages/bokeh/core/has_props.py", line 304, in __setattr__ raise AttributeError("unexpected attribute '%s' to %s, %s attributes are %s" % AttributeError: unexpected attribute 'callback' to Slider, similar attributes are js_event_callbacks ```

The version of installed bokeh is v2.3.0, though the recipe of cami-opal requiresbokeh ==0.13.0, which is only available for python 3.7.

$ mamba install bokeh=0.13.0
Problem: package bokeh-0.13.0-py37_0 requires python >=3.7,<3.8.0a0, but none of the providers can be installed

So, can you adapt opal to new bokeh, or simply requires python=3.7 in the conda recipe.

Thank you! Wei

[fernandomeyer]

Dear Wei,

thank you for reporting this. The conda recipe was now updated with python==3.7.

The issue, however, seemed to only occur if cami-opal was installed in an existing environment with python >3.7. If installed in a new environment, installation of the appropriate python version was triggered. Anyway, I hope that the change will avoid the version conflict.

Best, Fernando

[shenwei356]

The issue, however, seemed to only occur if cami-opal was installed in an existing environment with python >3.7.

Right.

Thank you for this rapid reply.