Unused object warning

brian2/__init__.py

@@ -71,7 +71,7 @@ def _check_dependencies():
         )
         __version_tuple__ = tuple(int(x) for x in __version__.split(".")[:3])
     except ImportError:
-        logging.getLogger("brian2").warn(
+        logging.getLogger("brian2").warning(
             "Cannot determine Brian version, running from source and "
             "setuptools_scm is not installed."
         )

brian2/core/base.py

@@ -80,13 +80,8 @@ def __init__(
                 creation_stack.append(s)
         creation_stack = [""] + creation_stack
         #: A string indicating where this object was created (traceback with any parts of Brian code removed)
-        self._creation_stack = (
-            "Object was created here (most recent call only, full details in "
-            "debug log):\n" + creation_stack[-1]
-        )
-        self._full_creation_stack = "Object was created here:\n" + "\n".join(
-            creation_stack
-        )
+        self._creation_stack = creation_stack[-1]
+        self._full_creation_stack = "\n".join(creation_stack)
 
         if dt is not None and clock is not None:
             raise ValueError("Can only specify either a dt or a clock, not both.")
@@ -185,6 +180,22 @@ def __init__(
     #: dependent objects such as `StateUpdater`
     add_to_magic_network = False
 
+    def __del__(self):
+        # For objects that get garbage collected, raise a warning if they have
+        # never been part of a network
+        if (
+            getattr(self, "_network", "uninitialized") is None
+            and getattr(self, "group", None) is None
+        ):
+            logger.warn(
+                f"The object '{self.name}' is getting deleted, but was never included in a network. "
+                "This probably means that you did not store the object reference in a variable, "
+                "or that the variable was not used to construct the network.\n"
+                "The object was created here (most recent call only):\n"
+                + self._creation_stack,
+                name_suffix="unused_brian_object",
+            )
+
     def add_dependency(self, obj):
         """
         Add an object to the list of dependencies. Takes care of handling
@@ -365,11 +376,15 @@ class BrianObjectException(Exception):
     def __init__(self, message, brianobj):
         self._brian_message = message
         self._brian_objname = brianobj.name
-        self._brian_objcreate = brianobj._creation_stack
+        self._brian_objcreate = (
+            "Object was created here (most recent call only, full details in "
+            "debug log):\n" + brianobj._creation_stack
+        )
+        full_stack = "Object was created here:\n" + brianobj._full_creation_stack
         logger.diagnostic(
             "Error was encountered with object "
             f"'{self._brian_objname}':\n"
-            f"{brianobj._full_creation_stack}"
+            f"{full_stack}"
         )
 
     def __str__(self):

brian2/core/network.py

@@ -8,6 +8,7 @@
 
 """
 
+import gc
 import os
 import pickle as pickle
 import sys
@@ -1102,6 +1103,8 @@ def run(
         The simulation can be stopped by calling `Network.stop` or the
         global `stop` function.
         """
+        # This will trigger warnings for objects that have not been included in a network
+        gc.collect()
         device = get_device()  # Do not use the ProxyDevice -- slightly faster
 
         if profile is None:

brian2/groups/subgroup.py

@@ -121,3 +121,8 @@ def __repr__(self):
             f"<{classname} {self.name!r} of {self.source.name!r} "
             f"from {self.start} to {self.stop}>"
         )
+
+    def __del__(self):
+        # Do not raise a warning if the subgroup gets deleted (subgroups do not need
+        # to be part of a network to be useful)
+        pass

brian2/tests/test_network.py

@@ -1776,6 +1776,21 @@ def test_multiple_runs_function_change():
     assert_equal(mon.v[0], [1, 2, 3, 4])
 
 
+@pytest.mark.codegen_independent
+def test_unused_object_warning():
+    with catch_logs() as logs:
+        # Create a NeuronGroup that is not used in the network
+        NeuronGroup(1, "v:1", name="never_used")
+        # Make sure that it gets garbage collected
+        import gc
+
+        gc.collect()
+    assert len(logs) == 1
+    assert logs[0][0] == "WARNING"
+    assert logs[0][1].endswith("unused_brian_object")
+    assert "never_used" in logs[0][2]
+
+
 if __name__ == "__main__":
     BrianLogger.log_level_warn()
     for t in [

brian2/tests/test_neurongroup.py

@@ -807,7 +807,7 @@ def test_namespace_errors():
 
 @pytest.mark.codegen_independent
 def test_namespace_warnings():
-    G = NeuronGroup(
+    G1 = NeuronGroup(
         1,
         """
         x : 1
@@ -819,7 +819,7 @@ def test_namespace_warnings():
     # conflicting variable in namespace
     y = 5
     with catch_logs() as l:
-        G.x = "y"
+        G1.x = "y"
         assert len(l) == 1, f"got {str(l)} as warnings"
         assert l[0][1].endswith(".resolution_conflict")
 
@@ -829,7 +829,7 @@ def test_namespace_warnings():
     i = 5
     N = 3
     with catch_logs() as l:
-        G.x = "i // N"
+        G1.x = "i // N"
         assert len(l) == 2, f"got {str(l)} as warnings"
         assert l[0][1].endswith(".resolution_conflict")
         assert l[1][1].endswith(".resolution_conflict")
@@ -838,7 +838,7 @@ def test_namespace_warnings():
     del N
     # conflicting variables in equations
     y = 5 * Hz
-    G = NeuronGroup(
+    G2 = NeuronGroup(
         1,
         """
         y : Hz
@@ -848,7 +848,7 @@ def test_namespace_warnings():
         name=f"neurongroup_{str(uuid.uuid4()).replace('-', '_')}",
     )
 
-    net = Network(G)
+    net = Network(G2)
     with catch_logs() as l:
         net.run(0 * ms)
         assert len(l) == 1, f"got {str(l)} as warnings"
@@ -857,13 +857,13 @@ def test_namespace_warnings():
 
     i = 5
     # i is referring to the neuron number:
-    G = NeuronGroup(
+    G3 = NeuronGroup(
         1,
         "dx/dt = i*Hz : 1",
         # unique names to get warnings every time:
         name=f"neurongroup_{str(uuid.uuid4()).replace('-', '_')}",
     )
-    net = Network(G)
+    net = Network(G3)
     with catch_logs() as l:
         net.run(0 * ms)
         assert len(l) == 1, f"got {str(l)} as warnings"
@@ -875,13 +875,13 @@ def test_namespace_warnings():
     N = 3
     i = 5
     dt = 1 * ms
-    G = NeuronGroup(
+    G4 = NeuronGroup(
         1,
         "dx/dt = x/(10*ms) : 1",
         # unique names to get warnings every time:
         name=f"neurongroup_{str(uuid.uuid4()).replace('-', '_')}",
     )
-    net = Network(G)
+    net = Network(G4)
     with catch_logs() as l:
         net.run(0 * ms)
         assert len(l) == 0, f"got {str(l)} as warnings"
@@ -893,22 +893,22 @@ def test_threshold_reset():
     Test that threshold and reset work in the expected way.
     """
     # Membrane potential does not change by itself
-    G = NeuronGroup(3, "dv/dt = 0 / second : 1", threshold="v > 1", reset="v=0.5")
-    G.v = np.array([0, 1, 2])
+    G1 = NeuronGroup(3, "dv/dt = 0 / second : 1", threshold="v > 1", reset="v=0.5")
+    G1.v = np.array([0, 1, 2])
     run(defaultclock.dt)
-    assert_allclose(G.v[:], np.array([0, 1, 0.5]))
+    assert_allclose(G1.v[:], np.array([0, 1, 0.5]))
 
     with catch_logs() as logs:
-        G = NeuronGroup(1, "v : 1", threshold="True")
+        G2 = NeuronGroup(1, "v : 1", threshold="True")
         assert len(logs) == 1
         assert logs[0][0] == "WARNING" and logs[0][1].endswith("only_threshold")
 
     with catch_logs() as logs:
-        G = NeuronGroup(1, "v : 1", threshold="True", reset="")
+        G3 = NeuronGroup(1, "v : 1", threshold="True", reset="")
         assert len(logs) == 0
 
     with catch_logs() as logs:
-        G = NeuronGroup(1, "v : 1", threshold="True", refractory=1 * ms)
+        G4 = NeuronGroup(1, "v : 1", threshold="True", refractory=1 * ms)
         assert len(logs) == 0
 
 

brian2/utils/logger.py

@@ -240,6 +240,7 @@ def clean_up_logging():
     Shutdown the logging system and delete the debug log file if no error
     occured.
     """
+    BrianLogger.initialized = False
     logging.shutdown()
     if not BrianLogger.exception_occured and prefs["logging.delete_log_on_exit"]:
         if BrianLogger.tmp_log is not None:
@@ -343,6 +344,9 @@ class BrianLogger:
         ``brian2``.
     """
 
+    #: Global flag to know whether the logging system is in a usable state
+    initialized = False
+
     #: Class attribute to remember whether any exception occured
     exception_occured = False
 
@@ -392,6 +396,9 @@ def _log(self, log_level, msg, name_suffix, once):
         once : bool
             Whether to suppress identical messages if they are logged again.
         """
+        if not BrianLogger.initialized:
+            # Prevent logging errors on exit
+            return
         name = self.name
         if name_suffix:
             name += f".{name_suffix}"
@@ -482,6 +489,8 @@ def warn(self, msg, name_suffix=None, once=False):
         """
         self._log("WARNING", msg, name_suffix, once)
 
+    warning = warn
+
     def error(self, msg, name_suffix=None, once=False):
         """
         Log an error message.
@@ -711,6 +720,8 @@ def initialize():
         # Handle uncaught exceptions
         sys.excepthook = brian_excepthook
 
+        BrianLogger.initialized = True
+
 
 def get_logger(module_name="brian2"):
     """