diff --git a/environment-dev.yaml b/environment-dev.yaml index 5f056b3..3f43939 100644 --- a/environment-dev.yaml +++ b/environment-dev.yaml @@ -1,4 +1,4 @@ -name: rplibs +name: rr_cache channels: - conda-forge - nodefaults diff --git a/rr_cache/Args.py b/rr_cache/Args.py index ff8418b..324407f 100644 --- a/rr_cache/Args.py +++ b/rr_cache/Args.py @@ -1,9 +1,6 @@ from argparse import ArgumentParser -from typing import Callable from os import path as os_path -from brs_utils import add_logger_args - HERE = os_path.dirname(os_path.abspath(__file__)) CONFIG_PATH = os_path.join(HERE, "config") # Default values for the arguments @@ -17,28 +14,7 @@ } -def build_args_parser( - prog: str, - description: str = "", - epilog: str = "", - m_add_args: Callable = None, -) -> ArgumentParser: - - parser = ArgumentParser(prog=prog, description=description, epilog=epilog) - - # Build Parser with rptools common arguments - parser = add_arguments(parser) - - # Add module specific arguments - if m_add_args is not None: - parser = m_add_args(parser) - - return parser - - def add_arguments(parser: ArgumentParser) -> ArgumentParser: - # Add arguments related to the logger - parser = add_logger_args(parser) parser.add_argument( "--chemical-space", diff --git a/rr_cache/__init__.py b/rr_cache/__init__.py index 519c1d9..201728a 100644 --- a/rr_cache/__init__.py +++ b/rr_cache/__init__.py @@ -1,4 +1,4 @@ -from rr_cache.rr_cache import rrCache +from .rr_cache import rrCache # from rr_cache._version import __version__ diff --git a/rr_cache/__main__.py b/rr_cache/__main__.py index 263af05..fd2d7cf 100644 --- a/rr_cache/__main__.py +++ b/rr_cache/__main__.py @@ -1,41 +1,16 @@ from rr_cache.rr_cache import ( rrCache, ) -from rr_cache.Args import build_args_parser +from rr_cache.Args import add_arguments +from brs_utils import init as init_logger, build_args_parser from logging import Logger, getLogger from colored import fg, attr -from argparse import ArgumentParser, Namespace from json import dumps from typing import ( List, ) from .Args import CONFIG_PATH - - -def init(parser: "ArgumentParser", args: "Namespace") -> Logger: - from brs_utils import create_logger - from rr_cache._version import __version__ - - if args.log.lower() in ["silent", "quiet"] or args.silent: - args.log = "CRITICAL" - - if args.log.lower() in ["silent", "quiet", "def_info"] or args.silent: - disable_rdkit_logging() - # # Disable RDKIT logging - # from rdkit import RDLogger - # RDLogger.DisableLog('rdApp.*') - - # Create logger - logger = create_logger(parser.prog, args.log, "rr_cache.log") - - logger.info( - "{color}{typo}rr_cache {version}{rst}{color}{rst}\n".format( - version=__version__, color=fg("white"), typo=attr("bold"), rst=attr("reset") - ) - ) - logger.debug(args) - - return logger +from ._version import __version__ def disable_rdkit_logging(): @@ -51,10 +26,17 @@ def disable_rdkit_logging(): def entry_point(): - parser = build_args_parser(prog="rr_cache", description="RetroRules Cache") + parser = build_args_parser( + prog="rr_cache", + version=__version__, + description="RetroRules Cache", + m_add_args=add_arguments, + ) args = parser.parse_args() + if args.log.lower() in ["silent", "quiet", "def_info"] or args.silent: + disable_rdkit_logging() - logger = init(parser, args) + logger = init_logger(parser, args, __version__) if args.list_chemical_spaces: # list config_*.json files in CONFIG_PATH