Fix network restore loop

brian2/conftest.py

@@ -98,6 +98,7 @@ def setup_and_teardown(request):
 
     yield  # run test
 
+    brian2.prefs._restore()
     # Reset defaultclock.dt to be sure
     defaultclock.dt = 0.1 * ms
 

brian2/core/base.py

@@ -132,6 +132,7 @@ def __init__(
         #: Used to remember the `Network` in which this object has been included
         #: before, to raise an error if it is included in a new `Network`
         self._network = None
+        self._used_in_network = False
 
         #: The ID string determining when the object should be updated in `Network.run`.
         self.when = when
@@ -187,6 +188,7 @@ def __del__(self):
         if (
             prefs.logging.warn_for_unused_objects
             and getattr(self, "_network", "uninitialized") is None
+            and not getattr(self, "_used_in_network", False)
             and getattr(self, "group", None) is None
             and not BrianLogger.exception_occured  # No need to add a warning if something went wrong
         ):

brian2/core/clocks.py

@@ -84,6 +84,9 @@ def __init__(self, name):
         # We need a name right away because some devices (e.g. cpp_standalone)
         # need a name for the object when creating the variables
         Nameable.__init__(self, name=name)
+        from brian2.core.base import BrianObject
+
+        self._scope_key = BrianObject._scope_current_key
         self.variables = Variables(self)
         self.variables.add_array(
             "timestep", size=1, dtype=np.int64, read_only=True, scalar=True

brian2/core/magic.py

@@ -489,3 +489,7 @@ def start_scope():
     included by the magic functions such as `run`.
     """
     BrianObject._scope_current_key += 1
+
+    # Run garbage collection here to destroy stale objects from previous runs
+    # preventing them from squatting on auto-generated names in the InstanceFollower
+    gc.collect()

brian2/core/names.py

@@ -36,8 +36,20 @@ def find_name(name, names=None):
     name = name[:-1]
 
     if names is None:
+        from brian2.core.base import BrianObject
+
         instances = set(Nameable.__instances__())
-        allnames = {obj().name for obj in instances if hasattr(obj(), "name")}
+        allnames = set()
+        for obj_ref in instances:
+            obj = obj_ref()
+            if obj is not None and hasattr(obj, "name"):
+                obj_scope_key = getattr(obj, "_scope_key", None)
+                if (
+                    obj_scope_key is not None
+                    and obj_scope_key != BrianObject._scope_current_key
+                ):
+                    continue
+                allnames.add(obj.name)
     else:
         allnames = names
 

brian2/core/network.py

@@ -543,14 +543,15 @@ def add(self, *objs):
         """
         for obj in objs:
             if isinstance(obj, BrianObject):
-                if obj._network is not None:
+                if obj._network is not None and obj._network != self.id:
                     raise RuntimeError(
                         f"{obj.name} has already been simulated, cannot "
                         "add it to the network. If you were "
                         "trying to remove and add an object to "
                         "temporarily stop it from being run, "
                         "set its active flag to False instead."
                     )
+                obj._used_in_network = True
                 self.objects.add(obj)
             else:
                 # allow adding values from dictionaries

brian2/synapses/synapses.py

@@ -916,11 +916,15 @@ def __init__(
         self._connect_called = False
         self.codeobj_class = codeobj_class
 
+        if isinstance(source, SynapticSubgroup):
+            raise TypeError("SynapticSubgroup cannot be used as a source")
         self.source = source
         self.add_dependency(source)
         if target is None:
             self.target = self.source
         else:
+            if isinstance(target, SynapticSubgroup):
+                raise TypeError("SynapticSubgroup cannot be used as a target")
             self.target = target
             self.add_dependency(target)
 

brian2/tests/test_network.py

@@ -1922,6 +1922,33 @@ def test_negative_duration_in_net_run():
         net.run(-1 * second)
 
 
+@pytest.mark.codegen_independent
+def test_network_restore_loop():
+    # Issue 1814: Verify that running and restoring networks in a loop
+    # does not raise KeyError due to auto-generated clocks leaking iteratively
+    filename = tempfile.mktemp(suffix="state", prefix="brian_test")
+    try:
+        start_scope()
+        G = NeuronGroup(10, "v:1", name="G")
+        G.run_regularly("v += 0.1", dt=1 * ms)
+        net = Network(collect())
+        net.run(1 * ms)
+        net.store(filename=filename)
+
+        for i in range(2):
+            start_scope()
+            G = NeuronGroup(10, "v:1", name="G")
+            G.run_regularly("v += 0.1", dt=1 * ms)
+            net2 = Network(collect())
+            net2.restore(filename=filename)
+            net2.run(1 * ms)
+    finally:
+        try:
+            os.remove(filename)
+        except OSError:
+            pass
+
+
 if __name__ == "__main__":
     BrianLogger.log_level_warn()
     for t in [

brian2/tests/test_synapses.py

@@ -3697,6 +3697,24 @@ def test_synaptic_subgroups():
     assert connections == {(1, 0), (1, 1), (2, 0), (2, 1)}
 
 
+@pytest.mark.codegen_independent
+def test_synaptic_subgroup_type_error():
+    # Issue 1287: Ensure error is raised if passing SynapticSubgroup directly
+    source = NeuronGroup(5, "")
+    target = NeuronGroup(3, "")
+    syn1 = Synapses(source, target)
+    syn1.connect()
+    subgroup = syn1[0:2, :]
+
+    with pytest.raises(TypeError) as exc:
+        Synapses(subgroup, target)
+    assert "SynapticSubgroup cannot be used as a source" in str(exc.value)
+
+    with pytest.raises(TypeError) as exc:
+        Synapses(source, subgroup)
+    assert "SynapticSubgroup cannot be used as a target" in str(exc.value)
+
+
 @pytest.mark.codegen_independent
 def test_incorrect_connect_N_incoming_outgoing():
     # See github issue #1227