snakemake >8.0.0 does not respect custom logging config #3044
Description
With Snakemake 7.32.4, I could have a SnakeFile like this where I reconfigured the log format of snakemake to be consistent with the log format used by the rest of my python code :
import logging.config
log_dict_config = {
"version": 1,
"disable_existing_loggers": False,
'formatters': {
'standard': {
'format': '%(asctime)s [%(levelname)s] %(name)s: %(message)s'
},
},
"handlers": {
"console": {
'level': 'INFO',
'formatter': 'standard',
'class': 'logging.StreamHandler',
'stream': 'ext://sys.stdout', # Default is stderr
},
},
"loggers": {
"snakemake": {
"level": "DEBUG",
"handlers": ["console"],
"propagate": False,
},
},
}
logging.config.dictConfig(log_dict_config)This worked as expected:
$ snakemake --cores 1
2024-08-23 19:43:38,047 [WARNING] snakemake.logging: Building DAG of jobs...
2024-08-23 19:43:38,049 [WARNING] snakemake.logging: Nothing to be done (all requested files are present and up to date).
2024-08-23 19:43:38,049 [WARNING] snakemake.logging: Complete log: .snakemake/log/2024-08-23T194337.961575.snakemake.log
With Snakemake 8.0.0 and higher, the custom formatted logs still print, but snakemake itself seems to be printing its own lines in yellow as well, so every log message is repeated:
$ snakemake --cores 1
Building DAG of jobs...
2024-08-23 19:47:35,891 [WARNING] snakemake.logging: Building DAG of jobs...
Retrieving input from storage.
2024-08-23 19:47:35,893 [WARNING] snakemake.logging: Retrieving input from storage.
Nothing to be done (all requested files are present and up to date).
2024-08-23 19:47:35,893 [WARNING] snakemake.logging: Nothing to be done (all requested files are present and up to date).
How do I get the previous behavior back?