clarify logging and function docs

medema-group · Nov 1, 2024 · 36820d0 · 36820d0
1 parent ca764cc
commit 36820d0
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Showing 2 changed files with 12 additions and 12 deletions.
diff --git a/big_scape/run_bigscape.py b/big_scape/run_bigscape.py
@@ -134,6 +134,8 @@ def signal_handler(sig, frame):
     else:
         all_bgc_records = bs_files.get_all_bgc_records(run, gbks)
 
+    logging.info("Continuing with %s BGC records", len(all_bgc_records))
+
     # INCLUDE/EXCLUDE CATEGORIES
     if run["include_categories"] or run["exclude_categories"]:
         all_bgc_records = category_filter(run, all_bgc_records)
@@ -187,12 +189,10 @@ def signal_handler(sig, frame):
 
     # DOMAIN INCLUSION LIST FILTER
     if run["domain_includelist_all"] or run["domain_includelist_any"]:
-        logging.info("Filtering records by domain_includelist")
-
         all_bgc_records = domain_includelist_filter(run, all_bgc_records)
 
         logging.info(
-            "Continuing with %i filtered records",
+            "Continuing with %i BGC records after domain_includelist filtering",
             len(all_bgc_records),
         )
 

diff --git a/big_scape/utility/filters.py b/big_scape/utility/filters.py
@@ -44,19 +44,19 @@ def domain_includelist_filter(run: dict, all_bgc_records: list[bs_gbk.BGCRecord]
 def generic_category_class_filter(
     class_categ: set[str], include: set[str], exclude: set[str]
 ) -> bool:
-    """Generic function for both class and category based filtering of records
+    """Generic function for both class and category based filtering of a single record
 
-    exclude class/category is checked first, removing any records that contain any of
-    these classes/categories. Then, include class/category is checked, keeping only any
+    exclude class/category is checked first, failing any records that contain any of
+    these classes/categories. Then, include class/category is checked, passing only any
     records that contain any of these classes/categories.
 
     Args:
-        class_categ (set[str]): set of classes or categories
+        class_categ (set[str]): set of classes or categories present in a single record
         include (set[str]): set of classes or categories to include
         exclude (set[str]): set of classes or categories to exclude
 
     Returns:
-        bool: false if filtered out, true if kept
+        bool: True if the current record passes filters, False if it is filtered out
     """
     if exclude:
         if class_categ & exclude:
@@ -97,13 +97,13 @@ def category_filter(
 
     if len(filtered_bgc_records) == 0:
         logging.error(
-            "No GBKs remain after include/exclude categories filtering",
+            "No BGC records remain after include/exclude categories filtering",
         )
         raise RuntimeError()
 
     if orig_size != len(filtered_bgc_records):
         logging.info(
-            "%s GBKs remain after include/exclude categories filtering",
+            "Continuing with %s BGC records after include/exclude categories filtering",
             len(filtered_bgc_records),
         )
     return filtered_bgc_records
@@ -136,13 +136,13 @@ def class_filter(
 
     if len(filtered_bgc_records) == 0:
         logging.error(
-            "No GBKs remain after include/exclude classes filtering",
+            "No BGC records remain after include/exclude classes filtering",
         )
         raise RuntimeError()
 
     if orig_size != len(filtered_bgc_records):
         logging.info(
-            "%s GBKs remain after include/exclude classes filtering",
+            "Continuing with %s BGC records after include/exclude classes filtering",
             len(filtered_bgc_records),
         )
     return filtered_bgc_records