Modified log.info logging functions to be more clear.

bioflow/annotation_network/BioKnowledgeInterface.py

@@ -71,8 +71,6 @@ def __init__(self, namespace_filter=('biological_process',),
         if uniprot_node_ids:
             init_set = list(set(init_set).intersection(set(uniprot_node_ids)))
 
-        log.info('Setting up GO Interface with namespace %s and %s root UPs',
-                 )
         self.go_namespace_filter = list(namespace_filter)
         self.InitSet = init_set
         self.correction_factor = correction_factor
@@ -141,7 +139,7 @@ def __init__(self, namespace_filter=('biological_process',),
 
         self.main_set = self.InitSet
 
-        log.info('Setting up GO Interface with namespace %s and %s root UPs',
+        log.info('Setting up GO Interface with namespaces %s and %s root UPs',
                  self.go_namespace_filter, len(self.InitSet))
 
     def pretty_time(self):

bioflow/molecular_network/interactome_analysis.py

@@ -398,8 +398,6 @@ def auto_analyze(source_list, desired_depth=24, processors=4, background_list=No
     :param skip_sampling: if true, will skip background sampling step
     """
     # noinspection PyTypeChecker
-    # TODO: add desired_depth division by process number
-
     estimated_comp_ops = 5
 
     if desired_depth % processors != 0:
@@ -417,11 +415,6 @@ def auto_analyze(source_list, desired_depth=24, processors=4, background_list=No
                   len(interactome_interface.entry_point_uniprots_bulbs_ids))
 
         interactome_interface.background = background_list
-
-        # TODO: restructure to spawn a sampler pool that does not share an object in the Threading
-        log.info('auto analyze 2: %s',
-                 len(interactome_interface.entry_point_uniprots_bulbs_ids))
-
         if not skip_sampling:
             log.info("spawning a sampler for %s proteins @ %s compops/sec",
                      len(interactome_interface.entry_point_uniprots_bulbs_ids), estimated_comp_ops)