[main] adding logging

oephys2nix/main.py

@@ -1,5 +1,6 @@
 import logging
 from pathlib import Path
+from typing import Annotated
 
 import nixio
 import typer
@@ -12,7 +13,6 @@ from oephys2nix.tonix import RawToNix
 
 app = typer.Typer()
 log = logging.getLogger(__name__)
-setup_logging(log, level="DEBUG")
 console = Console()
 
 
@@ -30,8 +30,11 @@ def main(
     ttl: bool = typer.Option(default=True, help="For recordings that did not have a ttl pulse"),
     overwrite: bool = typer.Option(default=True, help="Overwrites nix file"),
     debug: bool = typer.Option(default=True, help="Shows more information and plots the results"),
+    verbose: Annotated[int, typer.Option("--verbose", "-v", count=True)] = 0,
 ) -> None:
     """Combines open ephys data with relacs data from data_path to a new nix file."""
+
+    setup_logging(logging.getLogger("oephys2nix"), verbosity=verbose)
     log.info(f"Selected data_path is {data_path}")
     open_ephys_data_paths = list(Path(data_path).rglob("*open-ephys"))
     relacs_data_paths = list(Path(data_path).rglob("*relacs/*.nix"))
@@ -88,10 +91,10 @@ def main(
         stim = StimulusToNix(open_ephys, str(relacs), str(nix_path))
         stim.create_repros_automatically()
         stim.print_table()
-        stim.checks()
+        # stim.checks()
 
-        if debug:
-            stim.plot_stimulus()
+        # if debug:
+        #     stim.plot_stimulus()
 
 
 if __name__ == "__main__":