chore(args)!: change arg name with_orphan_species

brsynth · Nov 29, 2023 · b56cb0f · b56cb0f
1 parent 66895b1
commit b56cb0f
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Showing 2 changed files with 5 additions and 8 deletions.
diff --git a/rptools/rpfba/Args.py b/rptools/rpfba/Args.py
@@ -15,7 +15,7 @@
     "sim": "fraction",
     "fraction_coeff": 0.75,
     "merge": "",
-    "ignore_orphan_species": True,
+    "with_orphan_species": False,
 }
 
 def add_arguments(parser: ArgumentParser):
@@ -61,10 +61,10 @@ def add_arguments(parser: ArgumentParser):
         help="output the full merged model in addition of heterologous pathway only (default: False)",
     )
     parser.add_argument(
-        "--ignore_orphan_species",
+        "--with_orphan_species",
         action="store_true",
-        default=DEFAULT_ARGS["ignore_orphan_species"],
-        help="ignore metabolites that are only consumed or produced (default: True)",
+        default=DEFAULT_ARGS["with_orphan_species"],
+        help="Take metabolites that are only consumed (default: False)",
     )
 
     return parser
diff --git a/rptools/rpfba/rpfba.py b/rptools/rpfba/rpfba.py
@@ -65,13 +65,10 @@ def preprocess(
     # CHECKING
     # Detect orphan species among missing ones in the model,
     # i.e. that are only consumed or produced
-    if args.ignore_orphan_species:
+    if not args.with_orphan_species:
         merged_model.search_isolated_species(missing_species)
 
     if args.merge != "":
-        # merged_outfile = (
-        #     pathway.get_id() + "__MERGED_IN__" + model.getName() + ".sbml"
-        # )
         logger.info(f"Write merged rpSBML file to {args.merge}")
         merged_model.write_to_file(args.merge)