Python 3.11 install fails

[gbouras13]

I'm trying to install spae in a conda env with Python 3.11 installed.

Seems like Snakemake has an issue with Python 3.11 and ratelimiter.

https://stackoverflow.com/questions/74343982/module-asyncio-has-no-attribute-coroutine-on-snakemake

phage_genome_assembly install database --snake-default="--conda-frontend conda"

Config file /hpcfs/users/a1667917/spae/phage_genome_assembly/workflow/../config/config.yaml is extended by additional config specified via the command line.
Config file /hpcfs/users/a1667917/spae/phage_genome_assembly/workflow/../config/databases.yaml is extended by additional config specified via the command line.
Databases are being saved in, databases

Building DAG of jobs...
Traceback (most recent call last):
File "/hpcfs/users/a1667917/myconda/envs/spae/lib/python3.11/site-packages/snakemake/init.py", line 730, in snakemake
success = workflow.execute(
^^^^^^^^^^^^^^^^^
File "/hpcfs/users/a1667917/myconda/envs/spae/lib/python3.11/site-packages/snakemake/workflow.py", line 943, in execute
self.scheduler = JobScheduler(
^^^^^^^^^^^^^
File "/hpcfs/users/a1667917/myconda/envs/spae/lib/python3.11/site-packages/snakemake/scheduler.py", line 105, in init
from ratelimiter import RateLimiter
File "/hpcfs/users/a1667917/myconda/envs/spae/lib/python3.11/site-packages/ratelimiter.py", line 36, in
class RateLimiter(object):
File "/hpcfs/users/a1667917/myconda/envs/spae/lib/python3.11/site-packages/ratelimiter.py", line 127, in RateLimiter
aexit = asyncio.coroutine(exit)
^^^^^^^^^^^^^^^^^
AttributeError: module 'asyncio' has no attribute 'coroutine'

Installation in a python 3.10 env works fine.

Separately, I ran into this issue with snakemake snakemake/snakemake#1899

with Snakemake 7.14.0. I changed setup.py to be snakemake>=7.14.0 and it works fine for me now with snakemake 7.19.1.

This will be in the pull request when I am done adding the Medaka module.

George

[npbhavya]

Should be resolved now.