Fix garbage collection (#1119)

Co-authored-by: ilan-gold <[email protected]>
Co-authored-by: Philipp A. <[email protected]>

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
+
+    # custom because `memory_profiler` is a line-by-line profiler (also: https://github.com/pythonprofilers/memory_profiler/issues/402)
+    def track_peakmem_garbage_collection(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)

docs/_templates/autosummary/class.rst

@@ -13,7 +13,7 @@
    .. autosummary::
       :toctree: .
    {% for item in attributes %}
-      ~{{ fullname }}.{{ item }}
+      ~{{ name }}.{{ item }}
    {%- endfor %}
    {% endif %}
    {% endblock %}
@@ -26,7 +26,7 @@
       :toctree: .
    {% for item in methods %}
       {%- if item != '__init__' %}
-      ~{{ fullname }}.{{ item }}
+      ~{{ name }}.{{ item }}
       {%- endif -%}
    {%- endfor %}
    {% endif %}

docs/conf.py

@@ -27,7 +27,7 @@
 # default settings
 templates_path = ["_templates"]
 html_static_path = ["_static"]
-source_suffix = [".rst", ".md"]
+source_suffix = {".rst": "restructuredtext", ".md": "markdown"}
 master_doc = "index"
 default_role = "literal"
 exclude_patterns = [