Only warn about empty entities

Warn about any entities that have no
sequence, but don't raise an exception about
duplicates if there are multiple empty
entities. Closes #128.

ihm/dumper.py

@@ -5,6 +5,7 @@
 import collections
 import operator
 import itertools
+import warnings
 import ihm.format
 import ihm.format_bcif
 import ihm.model
@@ -261,13 +262,20 @@ def dump(self, system, writer):
 
 class _EntityDumper(Dumper):
     def finalize(self, system):
-        # Assign IDs and check for duplicates
+        # Assign IDs and check for duplicates or empty entities
         seen = {}
+        empty = []
         for num, entity in enumerate(system.entities):
-            if entity in seen:
+            if entity in seen and len(entity.sequence) > 0:
                 raise ValueError("Duplicate entity %s found" % entity)
+            if len(entity.sequence) == 0:
+                empty.append(entity)
             entity._id = num + 1
             seen[entity] = None
+        if empty:
+            warnings.warn(
+                "At least one empty Entity (with no sequence) was found: %s"
+                % empty)
 
     def dump(self, system, writer):
         # Count all molecules (if any) for each entity

test/test_dumper.py

@@ -1,6 +1,7 @@
 import utils
 import os
 import unittest
+import warnings
 import sys
 if sys.version_info[0] >= 3:
     from io import StringIO
@@ -445,6 +446,32 @@ def test_entity_duplicate_branched(self):
 #
 """)
 
+    def test_entity_empty(self):
+        """Test EntityDumper with empty entity"""
+        system = ihm.System()
+        system.entities.append(ihm.Entity(''))
+        dumper = ihm.dumper._EntityDumper()
+
+        with warnings.catch_warnings(record=True) as w:
+            warnings.simplefilter("always")
+            dumper.finalize(system)  # Assign IDs
+            _ = _get_dumper_output(dumper, system)
+            self.assertEqual(len(w), 1)
+            self.assertIn('At least one empty Entity', str(w[0].message))
+
+    def test_entity_duplicate_empty(self):
+        """Test EntityDumper with duplicate empty entities"""
+        system = ihm.System()
+        system.entities.append(ihm.Entity(''))
+        system.entities.append(ihm.Entity(''))
+        dumper = ihm.dumper._EntityDumper()
+
+        with warnings.catch_warnings(record=True) as w:
+            warnings.simplefilter("always")
+            dumper.finalize(system)  # Assign IDs
+            _ = _get_dumper_output(dumper, system)
+            self.assertIn('At least one empty Entity', str(w[0].message))
+
     def test_entity_src_nat_dumper(self):
         """Test EntitySrcNatDumper"""
         system = ihm.System()