diff --git a/environment.yaml b/environment.yaml index 480b42a..8a3f29a 100644 --- a/environment.yaml +++ b/environment.yaml @@ -5,7 +5,7 @@ dependencies: - python=3.11 - pandas - rdkit - - rr_cache - - brs_utils - - rxn_rebuild - - rplibs + - rr_cache>=3.6.3 + - brs_utils>=1.26.0 + - rxn_rebuild>=3.1.7 + - rplibs>=6.9.3 diff --git a/rpcompletion/Args.py b/rpcompletion/Args.py index c899bd1..aad7957 100644 --- a/rpcompletion/Args.py +++ b/rpcompletion/Args.py @@ -1,17 +1,13 @@ from argparse import ArgumentParser -from brs_utils import add_logger_args - default_upper_flux_bound = 10000 default_lower_flux_bound = -default_upper_flux_bound default_maxsubpaths = 10 default_cofactors = None -default_cspace = "mnx4.4" +default_cspace = "rr2026" def add_arguments(parser: ArgumentParser) -> ArgumentParser: - # Add arguments related to the logger - parser = add_logger_args(parser) parser.add_argument( "rp2_metnet", type=str, help="Retrosynthesis network provided by RetroPath2.0" diff --git a/rpcompletion/__main__.py b/rpcompletion/__main__.py index eb14923..d7a2801 100644 --- a/rpcompletion/__main__.py +++ b/rpcompletion/__main__.py @@ -6,20 +6,25 @@ ) from colored import fg, attr from rr_cache import rrCache -from rplibs import build_args_parser -from rpcompletion import rp_completion -from brs_utils import init -from rpextractsink._version import __version__ +from brs_utils import ( + init as init_logger, + build_args_parser, +) +from .Args import add_arguments +from .completion import rp_completion +from ._version import __version__ def _cli(): parser = build_args_parser( prog="rpcompletion", + version=__version__, description="Parse RP2 pathways to generate rpSBML collection of unique and complete (cofactors) pathways", + m_add_args=add_arguments, ) args = parser.parse_args() - logger = init(parser, args, __version__) + logger = init_logger(parser, args, __version__) logger.debug("Parameters") logger.debug(" |--> rp2_metnet: " + str(args.rp2_metnet))