Fix archive cleanup and bump version to 0.0.4

Improves archive management in ProgramDatabase by removing stale program references before evaluating archive capacity and replacement logic. Also updates the project version to 0.0.4 in both pyproject.toml and setup.py.

Author: codelion

openevolve/database.py

@@ -662,13 +662,38 @@ def _update_archive(self, program: Program) -> None:
             self.archive.add(program.id)
             return
 
-        # Otherwise, find worst program in archive
-        archive_programs = [self.programs[pid] for pid in self.archive]
-        worst_program = min(archive_programs, key=lambda p: safe_numeric_average(p.metrics))
+        # Clean up stale references and get valid archive programs
+        valid_archive_programs = []
+        stale_ids = []
 
-        # Replace if new program is better
-        if self._is_better(program, worst_program):
-            self.archive.remove(worst_program.id)
+        for pid in self.archive:
+            if pid in self.programs:
+                valid_archive_programs.append(self.programs[pid])
+            else:
+                stale_ids.append(pid)
+
+        # Remove stale references from archive
+        for stale_id in stale_ids:
+            self.archive.discard(stale_id)
+            logger.debug(f"Removing stale program {stale_id} from archive")
+
+        # If archive is now not full after cleanup, just add the new program
+        if len(self.archive) < self.config.archive_size:
+            self.archive.add(program.id)
+            return
+
+        # Find worst program among valid programs
+        if valid_archive_programs:
+            worst_program = min(
+                valid_archive_programs, key=lambda p: safe_numeric_average(p.metrics)
+            )
+
+            # Replace if new program is better
+            if self._is_better(program, worst_program):
+                self.archive.remove(worst_program.id)
+                self.archive.add(program.id)
+        else:
+            # No valid programs in archive, just add the new one
             self.archive.add(program.id)
 
     def _update_best_program(self, program: Program) -> None:

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "openevolve"
-version = "0.0.3"
+version = "0.0.4"
 description = "Open-source implementation of AlphaEvolve"
 readme = "README.md"
 requires-python = ">=3.9"

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name="openevolve",
-    version="0.0.3",
+    version="0.0.4",
     packages=find_packages(),
     include_package_data=True,
 )