Fix memory leak in pickle creation (#213)

* fix a memory leak related to pickling Atom subclasses

The reason for the changes around __slotnames__ are not clear to me but are necessary

* cis: fix ruff invocation

* tests: update test so that it does show an improvement over main

.github/workflows/ci.yml

@@ -47,7 +47,7 @@ jobs:
       - name: Linting
         if: always()
         run: |
-          ruff atom examples tests
+          ruff check atom examples tests
       - name: Typing
         if: always()
         run: |

atom/src/catom.cpp

@@ -375,8 +375,9 @@ PyObject*
 CAtom_getstate( CAtom* self )
 {
     cppy::ptr stateptr = PyDict_New();
-    if ( !stateptr )
+    if ( !stateptr ) {
         return PyErr_NoMemory();  // LCOV_EXCL_LINE
+    }
 
     cppy::ptr selfptr(pyobject_cast(self), true);
 
@@ -391,26 +392,33 @@ CAtom_getstate( CAtom* self )
     // Copy __slots__ if present. This assumes copyreg._slotnames was called
     // during AtomMeta's initialization
     {
-        cppy::ptr typeptr = PyObject_Type(selfptr.get());
-        if (!typeptr)
-            return 0;
-        cppy::ptr slotnamesptr = typeptr.getattr("__slotnames__");
-        if (!slotnamesptr.get())
+        PyObject* typedict = Py_TYPE(selfptr.get())->tp_dict;
+        cppy::ptr slotnamesptr(PyDict_GetItemString(typedict, "__slotnames__"), true);
+        if ( !slotnamesptr ) {
             return 0;
-        if (!PyList_CheckExact(slotnamesptr.get()))
+        }
+        if ( !PyList_CheckExact(slotnamesptr.get()) ) {
             return cppy::system_error( "slot names" );
+        }
         for ( Py_ssize_t i=0; i < PyList_GET_SIZE(slotnamesptr.get()); i++ )
         {
             PyObject *name = PyList_GET_ITEM(slotnamesptr.get(), i);
             cppy::ptr value = selfptr.getattr(name);
-            if (!value || PyDict_SetItem(stateptr.get(), name, value.get()) )
+            if (!value ) {
+                // Following CPython impl it is not an error if the attribute is
+                // not present.
+                continue;
+            }
+            else if ( PyDict_SetItem(stateptr.get(), name, value.get()) ) {
                 return  0;
+            }
         }
     }
 
     cppy::ptr membersptr = selfptr.getattr(atom_members);
-    if ( !membersptr || !PyDict_CheckExact( membersptr.get() ) )
+    if ( !membersptr || !PyDict_CheckExact( membersptr.get() ) ) {
         return cppy::system_error( "atom members" );
+    }
 
     PyObject *name, *member;
     Py_ssize_t pos = 0;
@@ -421,9 +429,8 @@ CAtom_getstate( CAtom* self )
         }
         int test = PyObject_IsTrue( should_gs.get() );
         if ( test == 1) {
-            PyObject *value =  member_cast( member )->getattr( self );
-            if (!value || PyDict_SetItem( stateptr.get(), name, value ) ) {
-                Py_XDECREF( value );
+            cppy::ptr value =  member_cast( member )->getattr( self );
+            if (!value || PyDict_SetItem( stateptr.get(), name, value.get() ) ) {
                 return  0;
             }
         }
@@ -433,8 +440,9 @@ CAtom_getstate( CAtom* self )
     }
 
     // Frozen state
-    if ( self->is_frozen() && PyDict_SetItem(stateptr.get(), atom_flags, Py_None) )
+    if ( self->is_frozen() && PyDict_SetItem(stateptr.get(), atom_flags, Py_None) ) {
         return 0;
+    }
 
     return stateptr.release();
 }

docs/source/examples/example_doc_generator.py

@@ -87,7 +87,7 @@ def generate_example_doc(docs_path, script_path):
 
     # Add the script to the Python Path
     old_python_path = sys.path
-    sys.path = sys.path + [os.path.dirname(script_path)]
+    sys.path = [*sys.path, os.path.dirname(script_path)]
 
     # Restore Python path.
     sys.path = old_python_path

tests/test_atom_from_annotations.py

@@ -168,7 +168,7 @@ class A(Atom, use_annotations=True):
         assert A.a.validate_mode[1] == (annotation.__origin__,)
     elif member is Subclass:
         if isinstance(annotation.__args__[0], TypeVar):
-            assert A.a.validate_mode[1] == object
+            assert A.a.validate_mode[1] is object
         else:
             assert A.a.validate_mode[1] == annotation.__args__[0]
     else:
@@ -254,9 +254,9 @@ class A(Atom, use_annotations=True, type_containers=depth):
                 assert type(v) is type(mv)
                 assert f(A()) == mf(A())
         else:
-            assert type(A.a.item) is type(member.item)  # noqa: E721
+            assert type(A.a.item) is type(member.item)
             if isinstance(member.item, List):
-                assert type(A.a.item.item) is type(member.item.item)  # noqa: E721
+                assert type(A.a.item.item) is type(member.item.item)
 
 
 @pytest.mark.parametrize(

tests/test_mem.py

@@ -1,14 +1,16 @@
 # --------------------------------------------------------------------------------------
-# Copyright (c) 2023, Nucleic Development Team.
+# Copyright (c) 2023-2024, Nucleic Development Team.
 #
 # Distributed under the terms of the Modified BSD License.
 #
 # The full license is in the file LICENSE, distributed with this software.
 # --------------------------------------------------------------------------------------
 import gc
 import os
+import pickle
 import sys
 import time
+import tracemalloc
 from multiprocessing import Process
 
 import pytest
@@ -53,6 +55,13 @@ class RefObj(Atom):
     "atomref": RefObj,
 }
 
+PICKLE_MEM_TESTS = {
+    "dict": DictObj,
+    "defaultdict": DefaultDictObj,
+    "list": ListObj,
+    "set": SetObj,
+}
+
 
 def memtest(cls):
     # Create object in a loop
@@ -105,3 +114,34 @@ def test_mem_usage(label):
     finally:
         p.kill()
         p.join()
+
+
+@pytest.mark.parametrize("label", PICKLE_MEM_TESTS.keys())
+def test_pickle_mem_usage(label):
+    TestClass = PICKLE_MEM_TESTS[label]
+
+    obj = TestClass()
+
+    for _ in range(100):
+        pickle.loads(pickle.dumps(obj))
+
+    gc.collect()
+    tracemalloc.start()
+    for i in range(10000):
+        pck = pickle.dumps(obj)
+        pickle.loads(pck)
+        del pck
+    gc.collect()
+    for stat in (
+        tracemalloc.take_snapshot()
+        .filter_traces(
+            [
+                tracemalloc.Filter(True, "*/atom/*"),
+                tracemalloc.Filter(False, "*/tests/*"),
+            ]
+        )
+        .statistics("lineno")
+    ):
+        # not sure why I sometimes see a 2 here but the original buggy version
+        # reported values > 50
+        assert stat.count < 5

tests/type_checking/test_subclass.yml

@@ -1,60 +1,61 @@
 #------------------------------------------------------------------------------
-# Copyright (c) 2021, Nucleic Development Team.
+# Copyright (c) 2021-2024, Nucleic Development Team.
 #
 # Distributed under the terms of the Modified BSD License.
 #
 # The full license is in the file LICENSE, distributed with this software.
 #------------------------------------------------------------------------------
 - case: subclass
+  skip: sys.version_info < (3, 9)  # 3.8 uses Type[] while 3.9+ uses type[]
   parametrized:
     - member: Subclass
       member_instance: Subclass(A)
-      member_type: atom.subclass.Subclass[Type[main.A]]
-      member_value_type: Type[main.A]
+      member_type: atom.subclass.Subclass[type[main.A]]
+      member_value_type: type[main.A]
     - member: Subclass
       member_instance: Subclass(A, B)
-      member_type: atom.subclass.Subclass[Type[main.A]]
-      member_value_type: Type[main.A]
+      member_type: atom.subclass.Subclass[type[main.A]]
+      member_value_type: type[main.A]
     - member: Subclass
       member_instance: Subclass((A,))
-      member_type: atom.subclass.Subclass[Type[main.A]]
-      member_value_type: Type[main.A]
+      member_type: atom.subclass.Subclass[type[main.A]]
+      member_value_type: type[main.A]
     - member: Subclass
       member_instance: Subclass((A,), B)
-      member_type: atom.subclass.Subclass[Type[main.A]]
-      member_value_type: Type[main.A]
+      member_type: atom.subclass.Subclass[type[main.A]]
+      member_value_type: type[main.A]
     - member: Subclass
       member_instance: Subclass((int, A))
-      member_type: atom.subclass.Subclass[Union[Type[builtins.int], Type[main.A]]]
-      member_value_type: Union[Type[builtins.int], Type[main.A]]
+      member_type: atom.subclass.Subclass[Union[type[builtins.int], type[main.A]]]
+      member_value_type: Union[type[builtins.int], type[main.A]]
     - member: Subclass
       member_instance: Subclass((int, A), B)
-      member_type: atom.subclass.Subclass[Union[Type[builtins.int], Type[main.A]]]
-      member_value_type: Union[Type[builtins.int], Type[main.A]]
+      member_type: atom.subclass.Subclass[Union[type[builtins.int], type[main.A]]]
+      member_value_type: Union[type[builtins.int], type[main.A]]
     - member: Subclass
       member_instance: Subclass((int, A, str))
-      member_type: atom.subclass.Subclass[Union[Type[builtins.int], Type[main.A], Type[builtins.str]]]
-      member_value_type: Union[Type[builtins.int], Type[main.A], Type[builtins.str]]
+      member_type: atom.subclass.Subclass[Union[type[builtins.int], type[main.A], type[builtins.str]]]
+      member_value_type: Union[type[builtins.int], type[main.A], type[builtins.str]]
     - member: Subclass
       member_instance: Subclass((int, A, str), B)
-      member_type: atom.subclass.Subclass[Union[Type[builtins.int], Type[main.A], Type[builtins.str]]]
-      member_value_type: Union[Type[builtins.int], Type[main.A], Type[builtins.str]]
+      member_type: atom.subclass.Subclass[Union[type[builtins.int], type[main.A], type[builtins.str]]]
+      member_value_type: Union[type[builtins.int], type[main.A], type[builtins.str]]
     - member: ForwardSubclass
       member_instance: ForwardSubclass(resolve1)
-      member_type: atom.subclass.ForwardSubclass[Type[main.A]]
-      member_value_type: Type[main.A]
+      member_type: atom.subclass.ForwardSubclass[type[main.A]]
+      member_value_type: type[main.A]
     - member: ForwardSubclass
       member_instance: ForwardSubclass(resolve2)
-      member_type: atom.subclass.ForwardSubclass[Type[main.A]]
-      member_value_type: Type[main.A]
+      member_type: atom.subclass.ForwardSubclass[type[main.A]]
+      member_value_type: type[main.A]
     - member: ForwardSubclass
       member_instance: ForwardSubclass(resolve3)
-      member_type: atom.subclass.ForwardSubclass[Union[Type[builtins.int], Type[main.A]]]
-      member_value_type: Union[Type[builtins.int], Type[main.A]]
+      member_type: atom.subclass.ForwardSubclass[Union[type[builtins.int], type[main.A]]]
+      member_value_type: Union[type[builtins.int], type[main.A]]
     - member: ForwardSubclass
       member_instance: ForwardSubclass(resolve4)
-      member_type: atom.subclass.ForwardSubclass[Union[Type[builtins.int], Type[main.A], Type[builtins.str]]]
-      member_value_type: Union[Type[builtins.int], Type[main.A], Type[builtins.str]]
+      member_type: atom.subclass.ForwardSubclass[Union[type[builtins.int], type[main.A], type[builtins.str]]]
+      member_value_type: Union[type[builtins.int], type[main.A], type[builtins.str]]
   main: |
     import io
     from typing import Tuple, Type