Main

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

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"

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))