Fix logging in worker processes

src/ms_deisotope/tools/deisotoper/process.py

@@ -182,7 +182,7 @@ def _make_scan_batch(self) -> Tuple[
             except StopIteration:
                 break
             except Exception as e:
-                self.log_handler("An error occurred in _make_scan_batch: %r" % e)
+                self.log_handler(f"An error occurred in _make_scan_batch: {e}")
                 break
             if not self.ignore_tandem_scans:
                 batch.append((scan_id, product_scan_ids, True))
@@ -198,12 +198,12 @@ def _initialize_iterator(self):
                     self.start_scan, require_ms1=self.loader.has_ms1_scans(), grouped=True)
             except IndexError as e:
                 self.log_handler(
-                    "An error occurred while locating start scan", e)
+                    f"An error occurred while locating start scan {e}", e)
                 self.loader.reset()
                 self.loader.make_iterator(grouped=True)
             except AttributeError as e:
                 self.log_handler(
-                    "The reader does not support random access, start time will be ignored", e)
+                    f"The reader does not support random access, start time will be ignored {e}")
                 self.loader.reset()
                 self.loader.make_iterator(grouped=True)
         else:
@@ -254,12 +254,12 @@ def run(self):
             except StopIteration:
                 break
             except Exception as e:
-                self.log_handler("An error occurred while fetching scans: %r" % e)
+                self.log_handler(f"An error occurred while fetching scans: {e}")
                 break
 
         if self.no_more_event is not None:
             self.no_more_event.set()
-            self.log_handler("All Scan IDs have been dealt. %d scan bunches." % (count,))
+            self.log_handler(f"All Scan IDs have been dealt. {count} scan bunches.")
         else:
             self.scan_id_queue.put(DONE)
 
@@ -272,9 +272,7 @@ class _ScanTransformMixin(object):
     def log_error(self, error: Exception, scan_id: str, scan: Scan, product_scan_ids: List[str]):
         tb = traceback.format_exc()
         self.log_handler(
-            "An %r occurred for %s (index %r) in Process %r\n%s" % (
-                error, scan_id, scan.index, multiprocessing.current_process(),
-                tb))
+            f"An {error} occurred for {scan_id} (index {scan.index}) in Process {multiprocessing.current_process()}\n{tb}")
 
     def _init_batch_store(self):
         self._batch_store = deque()
@@ -290,8 +288,7 @@ def get_work(self, block: bool=True, timeout: float=30) -> Tuple[str, List[str],
             return result
 
     def log_message(self, message):
-        self.log_handler(message + ", %r" %
-                         (multiprocessing.current_process().name))
+        self.log_handler(message + f", {multiprocessing.current_process().name}")
 
     def all_work_done(self) -> bool:
         return self._work_complete.is_set()

src/ms_deisotope/tools/deisotoper/scan_generator.py

@@ -299,7 +299,7 @@ def _make_scan_id_yielder(self, start_scan: str, end_scan: str, max_scans: int)
 
     def _make_scan_packer(self):
         """
-        This method initializes a helper object that will be shared with workersto pre-serialize
+        Initialize a helper object that will be shared with workersto pre-serialize
         scans before they are sent over IPC to save space, and avoid needing to reconstitute whole
         objects on the other side. If the serializing type changes, then the scan packer may also
         need to change.