change(aliby): Replace prints -> self._log

src/agora/io/signal.py

@@ -240,7 +240,7 @@ class Signal(BridgeH5):
                 f.visititems(self.store_signal_url)
 
         except Exception as e:
-            print("Error visiting h5: {}".format(e))
+            self._log("Exception when visiting h5: {}".format(e), "exception")
 
         return self._available
 
@@ -289,7 +289,7 @@ class Signal(BridgeH5):
             return df
 
         except Exception as e:
-            print(f"Could not fetch dataset {dataset}")
+            self._log(f"Could not fetch dataset {dataset}", "error")
             raise e
 
     def get_merges(self):

src/aliby/tile/tiler.py

@@ -493,9 +493,8 @@ class Tiler(StepABC):
         return None
 
     def get_traps_timepoint(self, *args, **kwargs):
-        #
-        print(
-            DeprecationWarning("Deprecated:Use get_tiles_timepoint instead.")
+        self._log(
+            "get_trap_timepoints is deprecated; get_tiles_timepoint instead."
         )
 
         return self.get_tiles_timepoint(*args, **kwargs)

src/logfile_parser/swainlab_parser.py

@@ -32,6 +32,7 @@ New grammar
 - Tables are assumed to end with an empty line.
 """
 
+import logging
 import typing as t
 from pathlib import PosixPath
 
@@ -229,7 +230,9 @@ def parse_from_grammar(filepath: str, grammar: t.Dict):
                     subkey = "_".join((key, subkey))
                     d[subkey] = parse_x(header, **subvalues)
         except Exception as e:
-            print(f"Parsing failed for key {key}")
+            logging.getLogger("aliby").critical(
+                f"Parsing failed for key {key}"
+            )
             raise (e)
     return d