docs: add verbose arg to QueryCollection class

deeprankcore/query.py

@@ -142,13 +142,17 @@ def __init__(self):
         self.cpu_count = None
         self.ids_count = {}
 
-    def add(self, query: Query):
+    def add(self, query: Query, verbose: bool = False):
         """ Adds new query to the collection of all generated queries.
             Args:
                 query (Query): must be a Query object, either ProteinProteinInterfaceResidueQuery or SingleResidueVariantAtomicQuery.
+                verbose: bool for logging query ids added, defaults to False.
         """
         query_id = query.get_query_id()
 
+        if verbose:
+            _log.info(f'Adding query with ID {query_id}.')
+
         if query_id not in self.ids_count:
             self.ids_count[query_id] = 1
         else:
@@ -181,8 +185,12 @@ def _process_one_query(
         self,
         prefix: str,
         feature_names: List[str],
+        verbose: bool,
         query: Query):
 
+        if verbose:
+            _log.info(f'\nProcess query with process ID {os.getpid()}.')
+
         # because only one process may access an hdf5 file at the time:
         output_path = f"{prefix}-{os.getpid()}.hdf5"
 
@@ -196,12 +204,13 @@ def _process_one_query(
             _log.error(e)
             _log.warning(f'Query {query.get_query_id()}\'s graph was not saved in the hdf5 file; check the query\'s files')
 
-    def process(
+    def process( # pylint: disable=too-many-arguments
         self, 
         prefix: Optional[str] = None,
         feature_modules: List[ModuleType] = None,
         cpu_count: Optional[int] = None,
         combine_output: bool = True,
+        verbose: bool = False
         ) -> List[str]:
 
         """
@@ -220,6 +229,8 @@ def process(
 
             combine_output: boolean for combining the hdf5 files generated by the processes.
                 By default, the hdf5 files generated are combined into one, and then deleted.
+
+            verbose: bool for logging query ids processed, defaults to False.
         """
 
         if cpu_count is None:
@@ -245,7 +256,7 @@ def process(
 
         _log.info('Creating pool function to process the queries...')
         pool_function = partial(self._process_one_query, prefix,
-                                feature_names)
+                                feature_names, verbose)
 
         with Pool(self.cpu_count) as pool:
             _log.info('Starting pooling...\n')