From 1fa218df20b9ddc310a9cda4de882083fbf49b54 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joan=20H=C3=A9risson?= Date: Wed, 8 Apr 2026 12:07:54 +0200 Subject: [PATCH 1/4] fix(environment-dev.yaml): update env name --- environment-dev.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From 4804934ac22985807ac6dca3cebc1960c48736a4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joan=20H=C3=A9risson?= Date: Wed, 8 Apr 2026 12:08:28 +0200 Subject: [PATCH 2/4] chore(rr_cache/__init__.py): change import path --- rr_cache/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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__ From 0eb2f6e817a90e82dd17c356309930163978d062 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joan=20H=C3=A9risson?= Date: Wed, 8 Apr 2026 12:08:51 +0200 Subject: [PATCH 3/4] chore: change arg parser handling --- rr_cache/Args.py | 22 ---------------------- rr_cache/__main__.py | 45 +++++++++++++++----------------------------- 2 files changed, 15 insertions(+), 52 deletions(-) diff --git a/rr_cache/Args.py b/rr_cache/Args.py index ff8418b..895ec1f 100644 --- a/rr_cache/Args.py +++ b/rr_cache/Args.py @@ -2,7 +2,6 @@ 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") @@ -17,28 +16,7 @@ } -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/__main__.py b/rr_cache/__main__.py index 263af05..cbca180 100644 --- a/rr_cache/__main__.py +++ b/rr_cache/__main__.py @@ -1,41 +1,19 @@ 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 +29,17 @@ 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 From 3769d293412380b63b0732d1dffb07783d17e3f3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joan=20H=C3=A9risson?= Date: Wed, 8 Apr 2026 12:09:56 +0200 Subject: [PATCH 4/4] style: clean up --- rr_cache/Args.py | 2 -- rr_cache/__main__.py | 9 +++------ 2 files changed, 3 insertions(+), 8 deletions(-) diff --git a/rr_cache/Args.py b/rr_cache/Args.py index 895ec1f..324407f 100644 --- a/rr_cache/Args.py +++ b/rr_cache/Args.py @@ -1,8 +1,6 @@ from argparse import ArgumentParser -from typing import Callable from os import path as os_path - HERE = os_path.dirname(os_path.abspath(__file__)) CONFIG_PATH = os_path.join(HERE, "config") # Default values for the arguments diff --git a/rr_cache/__main__.py b/rr_cache/__main__.py index cbca180..fd2d7cf 100644 --- a/rr_cache/__main__.py +++ b/rr_cache/__main__.py @@ -2,10 +2,7 @@ rrCache, ) from rr_cache.Args import add_arguments -from brs_utils import ( - init as init_logger, - build_args_parser -) +from brs_utils import init as init_logger, build_args_parser from logging import Logger, getLogger from colored import fg, attr from json import dumps @@ -31,9 +28,9 @@ def disable_rdkit_logging(): def entry_point(): parser = build_args_parser( prog="rr_cache", - version = __version__, + version=__version__, description="RetroRules Cache", - m_add_args=add_arguments + m_add_args=add_arguments, ) args = parser.parse_args() if args.log.lower() in ["silent", "quiet", "def_info"] or args.silent: