Fix garbage collection

benchmarks/benchmarks/anndata.py

@@ -0,0 +1,33 @@
+from __future__ import annotations
+
+import tracemalloc
+
+import numpy as np
+
+from .utils import gen_adata
+
+
+class GarbargeCollectionSuite:
+    runs = 10
+
+    # https://github.com/pythonprofilers/memory_profiler/issues/402 and other backend does not pick this up
+    def track_peakmem_write_compressed(self, *_):
+        def display_top(snapshot, key_type="lineno"):
+            snapshot = snapshot.filter_traces(
+                (
+                    tracemalloc.Filter(False, "<frozen importlib._bootstrap>"),
+                    tracemalloc.Filter(False, "<unknown>"),
+                )
+            )
+            top_stats = snapshot.statistics(key_type)
+            total = sum(stat.size for stat in top_stats)
+            return total
+
+        total = np.zeros(self.runs)
+        tracemalloc.start()
+        for i in range(self.runs):
+            data = gen_adata(10000, 10000, "X-csc")  # noqa: F841
+            snapshot = tracemalloc.take_snapshot()
+            total[i] = display_top(snapshot)
+        tracemalloc.stop()
+        return max(total)

src/anndata/_core/aligned_mapping.py

@@ -20,7 +20,13 @@
 from anndata._warnings import ExperimentalFeatureWarning, ImplicitModificationWarning
 from anndata.compat import AwkArray
 
-from ..utils import axis_len, deprecated, ensure_df_homogeneous, warn_once
+from ..utils import (
+    axis_len,
+    convert_to_dict,
+    deprecated,
+    ensure_df_homogeneous,
+    warn_once,
+)
 from .access import ElementRef
 from .index import _subset
 from .views import as_view, view_update
@@ -115,7 +121,7 @@
         return self._parent
 
     def copy(self):
-        d = self._actual_class(self.parent, self._axis)
+        d = self._actual_class(self.parent, self._axis, {})
         for k, v in self.items():
             if isinstance(v, AwkArray):
                 # Shallow copy since awkward array buffers are immutable
@@ -272,6 +278,7 @@
         return (self.parent.obs_names, self.parent.var_names)[self._axis]
 
 
+# TODO: vals can't be None
 class AxisArrays(AlignedActualMixin, AxisArraysBase):
     def __init__(
         self,
@@ -283,9 +290,9 @@
         if axis not in (0, 1):
             raise ValueError()
         self._axis = axis
-        self._data = dict()
-        if vals is not None:
-            self.update(vals)
+        for k, v in vals.items():
+            vals[k] = self._validate_value(v, k)
+        self._data = vals
 
 
 class AxisArraysView(AlignedViewMixin, AxisArraysBase):
@@ -317,18 +324,21 @@
 
     # TODO: I thought I had a more elegant solution to overriding this...
     def copy(self) -> Layers:
-        d = self._actual_class(self.parent)
+        d = self._actual_class(self.parent, vals={})
         for k, v in self.items():
             d[k] = v.copy()
         return d
 
 
 class Layers(AlignedActualMixin, LayersBase):
-    def __init__(self, parent: AnnData, vals: Mapping | None = None):
+    def __init__(
+        self, parent: AnnData, axis: tuple[int] = (0, 1), vals: Mapping | None = None
+    ):
+        assert axis == (0, 1), axis
         self._parent = parent
-        self._data = dict()
-        if vals is not None:
-            self.update(vals)
+        for k, v in vals.items():
+            vals[k] = self._validate_value(v, k)
+        self._data = vals
 
 
 class LayersView(AlignedViewMixin, LayersBase):
@@ -382,9 +392,9 @@
         if axis not in (0, 1):
             raise ValueError()
         self._axis = axis
-        self._data = dict()
-        if vals is not None:
-            self.update(vals)
+        for k, v in vals.items():
+            vals[k] = self._validate_value(v, k)
+        self._data = vals
 
 
 class PairwiseArraysView(AlignedViewMixin, PairwiseArraysBase):
@@ -396,9 +406,39 @@
     ):
         self.parent_mapping = parent_mapping
         self._parent = parent_view
-        self.subset_idx = (subset_idx, subset_idx)
+        self.subset_idx = subset_idx
         self._axis = parent_mapping._axis
 
 
 PairwiseArraysBase._view_class = PairwiseArraysView
 PairwiseArraysBase._actual_class = PairwiseArrays
+
+
+class AlignedMappingProperty:
+    def __init__(self, name, cls, axis):
+        self.name = name
+        self.axis = axis
+        self.cls = cls
+
+    def __get__(self, obj, objtype=None):
+        if obj is None:  # None check needed for AnnData.layers accessors
+            return self.cls
+        if obj.is_view:
+            parent_anndata = obj._adata_ref
+            idxs = (obj._oidx, obj._vidx)
+            parent_aligned_mapping = getattr(parent_anndata, self.name)
+            return parent_aligned_mapping._view(
+                obj, tuple(idxs[ax] for ax in parent_aligned_mapping.axes)
+            )
+        else:
+            return self.cls(obj, self.axis, getattr(obj, "_" + self.name))
+
+    def __set__(self, obj, value):
+        value = convert_to_dict(value)
+        _ = self.cls(obj, self.axis, value)  # Validate
+        if obj.is_view:
+            obj._init_as_actual(obj.copy())
+        setattr(obj, "_" + self.name, value)
+
+    def __delete__(self, obj):
+        setattr(obj, self.name, dict())