Updated core.py, adding a wrapper function that takes args, while the…

… underlying functions takes specific arguments (so they can be called from jupyter notebooks etc).
Hjorthmedh · Sep 21, 2023 · 8a59e37 · 8a59e37
1 parent 3b97119
commit 8a59e37
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Showing 3 changed files with 213 additions and 138 deletions.
diff --git a/snudda/cli.py b/snudda/cli.py
@@ -44,7 +44,7 @@ def snudda_cli():
                              help="Path to neurons_dir, default is $DATA/neurons (DEPRECATED, use --snudda_data instead")
     init_parser.add_argument("-overwrite", "--overwrite", help="Allow overwriting of old directory",
                              action="store_true")
-    init_parser.add_argument("-connectionFile", "--connectionFile", default=None,
+    init_parser.add_argument("-connectionFile", "--connectionFile", default=None, dest="connection_file",
                              help="Use connectivity from user specified JSON file")
     init_parser.add_argument("-randomseed", "--randomseed", "--seed", default=None, help="Random seed", type=int)
     init_parser.add_argument("--profile", help="Run python cProfile", action="store_true")
@@ -74,7 +74,6 @@ def snudda_cli():
     detect_parser.add_argument("-parallel", "--parallel", action="store_true", default=False)
     detect_parser.add_argument("-ipython_profile", "--ipython_profile", default=None)
 
-
     prune_parser = sub_parsers.add_parser("prune")
     prune_parser.add_argument("path", help="Location of network")
     prune_parser.add_argument("-randomseed", "--randomseed", "--seed", default=None, help="Random seed", type=int)
@@ -90,7 +89,6 @@ def snudda_cli():
     prune_parser.add_argument("-parallel", "--parallel", action="store_true", default=False)
     prune_parser.add_argument("-ipython_profile", "--ipython_profile", default=None)
 
-
     input_parser = sub_parsers.add_parser("input")
     input_parser.add_argument("path", help="Location of network")
     input_parser.add_argument("--input", help="Input json config file (for input setup)", default=None)
@@ -154,15 +152,15 @@ def snudda_cli():
 
     snudda = Snudda(args.path)
 
-    actions = {"init": snudda.init_config,
-               "place": snudda.place_neurons,
-               "detect": snudda.touch_detection,
-               "prune": snudda.prune_synapses,
-               "input": snudda.setup_input,
-               "export": snudda.export_to_SONATA,
-               "convert": snudda.export_to_SONATA,
+    actions = {"init": snudda.init_config_wrapper,
+               "place": snudda.place_neurons_wrapper,
+               "detect": snudda.touch_detection_wrapper,
+               "prune": snudda.prune_synapses_wrapper,
+               "input": snudda.setup_input_wrapper,
+               "export": snudda.export_to_SONATA_wrapper,
+               "convert": snudda.export_to_SONATA_wrapper,
                "analyse": snudda.analyse,
-               "simulate": snudda.simulate,
+               "simulate": snudda.simulate_wrapper,
                "help": snudda.help_info}
 
     if not hasattr(args, 'ipython_profile'):