diff --git a/bbconf/bbagent.py b/bbconf/bbagent.py index 8ce3b7b..c41f350 100644 --- a/bbconf/bbagent.py +++ b/bbconf/bbagent.py @@ -18,6 +18,7 @@ _LOGGER = logging.getLogger(PKG_NAME) + class BedBaseAgent(object): def __init__( self, @@ -53,7 +54,7 @@ def __repr__(self) -> str: repr += f"\n{self.bed}" repr += f"\n{self.bedset}" repr += f"\n{self.objects}" - return repr + return repr def get_stats(self) -> StatsReturn: """ diff --git a/bbconf/config_parser/bedbaseconfig.py b/bbconf/config_parser/bedbaseconfig.py index cf9eaad..8bc0a49 100644 --- a/bbconf/config_parser/bedbaseconfig.py +++ b/bbconf/config_parser/bedbaseconfig.py @@ -45,6 +45,7 @@ class BedBaseConfig(object): """ Class to handle BEDbase configuration file and create objects for different modules. """ + def __init__(self, config: Union[Path, str], init_search_interfaces: bool = True): _LOGGER.info(f"Loading configuration file: {config}") self.cfg_path = get_bedbase_cfg(config) diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt index cf4f5cf..a202b34 100644 --- a/requirements/requirements-all.txt +++ b/requirements/requirements-all.txt @@ -1,6 +1,6 @@ yacman >= 0.9.1 sqlalchemy >= 2.0.0 -geniml[ml] >= 0.5.1 +geniml[ml] >= 0.5.2 psycopg >= 3.1.15 colorlogs pydantic >= 2.9.0