Merge pull request #63 from bigbio/copilot/sub-pr-59-another-one

Implement lazy initialization for UnimodDatabase

Author: ypriverol

quantmsutils/diann/dianncfg.py

@@ -13,7 +13,27 @@
 
 logging.basicConfig(format="%(asctime)s [%(funcName)s] - %(message)s", level=logging.DEBUG)
 logger = logging.getLogger(__name__)
-unimod_database = UnimodDatabase()
+
+# Lazy initialization of UnimodDatabase for improved testability.
+# The database is created on first access rather than at module import time,
+# which allows tests to mock or replace it more easily.
+_unimod_database = None
+
+
+def get_unimod_database():
+    """
+    Get the UnimodDatabase instance, creating it lazily on first access.
+
+    This pattern improves testability by avoiding database initialization at module
+    import time. For testing purposes, the internal _unimod_database variable can be
+    set to None to force re-initialization on the next call.
+
+    :return: The UnimodDatabase instance.
+    """
+    global _unimod_database
+    if _unimod_database is None:
+        _unimod_database = UnimodDatabase()
+    return _unimod_database
 
 # Met-loss modification constant (UniMod:765) with mass shift and site specification
 MET_LOSS_MODIFICATION = "UniMod:765,-131.040485,*nM"
@@ -68,7 +88,7 @@ def get_mod(mod, mod_type):
     modification_found = 0
     diann_mod_accession = None
     diann_mod_name = None
-    for modification in unimod_database.modifications:
+    for modification in get_unimod_database().modifications:
         if modification.get_name() == mod.split(" ")[0]:
             diann_mod_accession = modification.get_accession().replace("UNIMOD:", "UniMod:") + "," + str(modification._delta_mono_mass)
             diann_mod_name = modification.get_name()