Merge pull request #201 from NeuralEnsemble/feat-use-caching

Feat: use caching for methods that return the same value each time

neuroml/nml/gds_imports-template.py

@@ -1,6 +1,7 @@
 import inspect
 import math
 import typing
+from functools import cached_property, lru_cache
 from math import pi, sqrt
 from operator import attrgetter
 

neuroml/nml/generatedssupersuper.py

@@ -535,6 +535,7 @@ def parentinfo(self, return_format="string"):
             "GdsCollector_",
             "GeneratedsSuperSuper",
             "attrgetter",
+            "cached_property",
         ]
 
         # do not show parameters here, they are indicated by members below

neuroml/nml/helper_methods.py

@@ -911,6 +911,7 @@ def __str__(self):
     source='''\
 
     # Get segment object by its id
+    @lru_cache(maxsize=1000)
     def get_segment(self, segment_id: int) -> Segment:
         """Get segment object by its id
 
@@ -947,6 +948,7 @@ def get_segments_by_substring(self, substring: str) -> typing.Dict[str, Segment]
 
     # Get the proximal point of a segment, even the proximal field is None and
     # so the proximal point is on the parent (at a point set by fraction_along)
+    @lru_cache(maxsize=1000)
     def get_actual_proximal(self, segment_id: str):
         """Get the proximal point of a segment.
 
@@ -976,6 +978,7 @@ def get_actual_proximal(self, segment_id: str):
 
             return p
 
+    @lru_cache(maxsize=1000)
     def get_segment_length(self, segment_id: str) -> float:
         """Get the length of the segment.
 
@@ -993,6 +996,7 @@ def get_segment_length(self, segment_id: str) -> float:
 
             return length
 
+    @lru_cache(maxsize=1000)
     def get_segment_surface_area(self, segment_id: str) -> float:
         """Get the surface area of the segment.
 
@@ -1010,6 +1014,7 @@ def get_segment_surface_area(self, segment_id: str) -> float:
 
             return temp_seg.surface_area
 
+    @lru_cache(maxsize=1000)
     def get_segment_volume(self, segment_id: str) -> float:
         """Get volume of segment
 
@@ -1029,6 +1034,14 @@ def get_segment_volume(self, segment_id: str) -> float:
     def get_segment_ids_vs_segments(self) -> typing.Dict[str, Segment]:
         """Get a dictionary of segment IDs and the segments in the cell.
 
+        :return: dictionary with segment ID as key, and segment as value
+        """
+        return self.segment_ids_vs_segments
+
+    @cached_property
+    def segment_ids_vs_segments(self) -> typing.Dict[str, Segment]:
+        """Get a dictionary of segment IDs and the segments in the cell.
+
         :return: dictionary with segment ID as key, and segment as value
         """
 
@@ -1038,6 +1051,7 @@ def get_segment_ids_vs_segments(self) -> typing.Dict[str, Segment]:
 
         return segments
 
+    @lru_cache(maxsize=1000)
     def get_all_segments_in_group(self,
                                   segment_group: typing.Union[str, SegmentGroup],
                                   assume_all_means_all: bool = True) -> typing.List[int]:
@@ -1235,6 +1249,7 @@ def get_ordered_segments_in_groups(self,
 
         return ord_segs
 
+    @lru_cache(maxsize=1000)
     def get_segment_group(self, sg_id: str) -> SegmentGroup:
         """Return the SegmentGroup object for the specified segment group id.
 

neuroml/nml/nml.py

@@ -2,8 +2,8 @@
 # -*- coding: utf-8 -*-
 
 #
-# Generated Tue Aug 20 10:23:13 2024 by generateDS.py version 2.44.1.
-# Python 3.11.9 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)]
+# Generated Wed Sep 11 16:30:43 2024 by generateDS.py version 2.44.1.
+# Python 3.11.9 (main, Aug 23 2024, 00:00:00) [GCC 14.2.1 20240801 (Red Hat 14.2.1-1)]
 #
 # Command line options:
 #   ('-o', 'nml.py')
@@ -36,6 +36,7 @@
 import os
 import re as re_
 import typing
+from functools import cached_property, lru_cache
 from math import pi, sqrt
 from operator import attrgetter
 
@@ -48429,6 +48430,7 @@ def _buildChildren(
         super(Cell, self)._buildChildren(child_, node, nodeName_, True)
 
     # Get segment object by its id
+    @lru_cache(maxsize=1000)
     def get_segment(self, segment_id: int) -> Segment:
         """Get segment object by its id
 
@@ -48471,6 +48473,7 @@ def get_segments_by_substring(self, substring: str) -> typing.Dict[str, Segment]
 
     # Get the proximal point of a segment, even the proximal field is None and
     # so the proximal point is on the parent (at a point set by fraction_along)
+    @lru_cache(maxsize=1000)
     def get_actual_proximal(self, segment_id: str):
         """Get the proximal point of a segment.
 
@@ -48504,6 +48507,7 @@ def get_actual_proximal(self, segment_id: str):
 
             return p
 
+    @lru_cache(maxsize=1000)
     def get_segment_length(self, segment_id: str) -> float:
         """Get the length of the segment.
 
@@ -48521,6 +48525,7 @@ def get_segment_length(self, segment_id: str) -> float:
 
             return length
 
+    @lru_cache(maxsize=1000)
     def get_segment_surface_area(self, segment_id: str) -> float:
         """Get the surface area of the segment.
 
@@ -48538,6 +48543,7 @@ def get_segment_surface_area(self, segment_id: str) -> float:
 
             return temp_seg.surface_area
 
+    @lru_cache(maxsize=1000)
     def get_segment_volume(self, segment_id: str) -> float:
         """Get volume of segment
 
@@ -48557,6 +48563,14 @@ def get_segment_volume(self, segment_id: str) -> float:
     def get_segment_ids_vs_segments(self) -> typing.Dict[str, Segment]:
         """Get a dictionary of segment IDs and the segments in the cell.
 
+        :return: dictionary with segment ID as key, and segment as value
+        """
+        return self.segment_ids_vs_segments
+
+    @cached_property
+    def segment_ids_vs_segments(self) -> typing.Dict[str, Segment]:
+        """Get a dictionary of segment IDs and the segments in the cell.
+
         :return: dictionary with segment ID as key, and segment as value
         """
 
@@ -48566,6 +48580,7 @@ def get_segment_ids_vs_segments(self) -> typing.Dict[str, Segment]:
 
         return segments
 
+    @lru_cache(maxsize=1000)
     def get_all_segments_in_group(
         self,
         segment_group: typing.Union[str, SegmentGroup],
@@ -48773,6 +48788,7 @@ def get_ordered_segments_in_groups(
 
         return ord_segs
 
+    @lru_cache(maxsize=1000)
     def get_segment_group(self, sg_id: str) -> SegmentGroup:
         """Return the SegmentGroup object for the specified segment group id.
 

neuroml/nml/regenerate-nml.sh

@@ -56,6 +56,7 @@ reformat () {
     if command -v ruff > /dev/null 2>&1
     then
         echo "Formatting new nml.py with ruff"
+        ruff check --select I --fix nml.py
         ruff format nml.py
     else
         echo "ruff is not installed"

neuroml/test/test_cell.py

@@ -392,6 +392,11 @@ def test_get_morphology_root(self):
             root_seg = acell.get_segment(0)
             new_id = 99999
             root_seg.id = new_id
+
+            # clear the cache, otherwise it'll return the old value again in
+            # other function calls also
+            acell.get_segment.cache_clear()
+
             # also update all descendents to ensure cell remains valid
             for seg in acell.morphology.segments:
                 par = seg.parent