error about pyscenic grnboost

[xiexiaowei]

Hi,
When I ran "pyscenic -h", it showed that I have successfully installed this software.
But when I ran "pyscenic grnboost", I met the errors as belows:

2018-12-04 13:46:44,213 - pyscenic.cli.pyscenic - INFO - Loading expression matrix.
2018-12-04 13:46:46,673 - pyscenic.cli.pyscenic - INFO - Inferring regulatory networks.
Traceback (most recent call last):
File "/public/home/xiexiaowei/.local/bin/pyscenic", line 11, in
sys.exit(main())
File "/public/home/xiexiaowei/.local/lib/python3.6/site-packages/pyscenic/cli/pyscenic.py", line 356, in main
args.func(args)
File "/public/home/xiexiaowei/.local/lib/python3.6/site-packages/pyscenic/cli/pyscenic.py", line 119, in find_adjacencies_command
client, shutdown_callback = _prepare_client(args.client_or_address, num_workers=args.num_workers)
File "/public/home/xiexiaowei/.local/lib/python3.6/site-packages/pyscenic/prune.py", line 64, in _prepare_client
client = Client(local_cluster)
File "/public/home/bioinfo/software/anaconda3/lib/python3.6/site-packages/distributed/client.py", line 556, in init
dask.set_options(get=self.get)
File "/public/home/xiexiaowei/.local/lib/python3.6/site-packages/dask/context.py", line 18, in set_options
raise TypeError("The dask.set_options function has been deprecated.\n"
TypeError: The dask.set_options function has been deprecated.
Please use dask.config.set instead

Before: with dask.set_options(foo='bar'):
...
After: with dask.config.set(foo='bar'):

So, what happened and how to solve this problem?
Thanks very much!
xiaowei,

[bramvds]

Dear Xiaowei,

This seems to be a problem with the latest version of Dask which introduced a breaking change: http://matthewrocklin.com/blog/work/2018/06/14/dask-0.18.0 .

Because this is a bug in the arboreta package (https://github.com/tmoerman/arboreto), could you resubmit this issue there and provide the aforementioned documentation? Many thanks.

As a temporary workaround, I propose the following approach: create a virgin (miniconda) environment in the following way:

For Linux OS:

conda create -n pyscenic python=3.6
. activate pyscenic
pip install tornado==4.5
pip install dask==0.18.1
pip install pyscenic

For Windows:

conda create -n pyscenic python=3.6
activate pyscenic
pip install tornado==4.5
pip install dask==0.18.1
pip install pyscenic

Kindest regards,
Bram

[cflerin]

Closing this since the recent updates have hopefully fixed this