Expose --cpu option in CLI and pass through to spa_analyze

Author: mdbarnesUCSD

SigProfilerAssignment/controllers/cli_controller.py

@@ -85,6 +85,12 @@ def parse_arguments_common(args: List[str], description: str) -> argparse.Namesp
         default=False,
         help="Verbose output (default: False).",
     )
+    parser.add_argument(
+        "--cpu",
+        type=int,
+        default=-1,
+        help="Number of processor cores to use during assignment (default: -1 = all cores).",
+    )
     parser.add_argument(
         "--new_signature_thresh_hold",
         type=float,
@@ -148,6 +154,7 @@ def parse_arguments_common(args: List[str], description: str) -> argparse.Namesp
             "'png' (PNG only, PDF removed)."
         ),
     )
+    
 
     return parser.parse_args(args)
 
@@ -170,6 +177,7 @@ def dispatch_decompose_fit(self, user_args: List[str]) -> None:
             make_plots=parsed_args.make_plots,
             collapse_to_SBS96=parsed_args.collapse_to_SBS96,
             connected_sigs=parsed_args.connected_sigs,
+            cpu=parsed_args.cpu,
             verbose=parsed_args.verbose,
             decompose_fit_option=True,
             denovo_refit_option=False,
@@ -202,6 +210,7 @@ def dispatch_denovo_fit(self, user_args: List[str]) -> None:
             collapse_to_SBS96=parsed_args.collapse_to_SBS96,
             connected_sigs=parsed_args.connected_sigs,
             verbose=parsed_args.verbose,
+            cpu=parsed_args.cpu,
             decompose_fit_option=False,
             denovo_refit_option=True,
             cosmic_fit_option=False,
@@ -230,6 +239,7 @@ def dispatch_cosmic_fit(self, user_args: List[str]) -> None:
             collapse_to_SBS96=parsed_args.collapse_to_SBS96,
             connected_sigs=parsed_args.connected_sigs,
             verbose=parsed_args.verbose,
+            cpu=parsed_args.cpu,
             decompose_fit_option=False,
             denovo_refit_option=False,
             cosmic_fit_option=True,