From f493de2eaf333bd49d13aa4ef588bbe662bb3b72 Mon Sep 17 00:00:00 2001
From: Dr Maurice Hendrix <52317399+MauriceHendrix@users.noreply.github.com>
Date: Thu, 20 Jan 2022 16:16:21 +0000
Subject: [PATCH] performance improvement to linearity check for rush-larsen
 using caching (#224)

* performance improvement to linearity check for rush-larsen using caching
---
 CITATION.cff                       | 2 +-
 RELEASE.md                         | 3 +++
 chaste_codegen/_linearity_check.py | 5 ++++-
 chaste_codegen/version.txt         | 2 +-
 4 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index 044d9dc9f..c55f9d3b4 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -23,7 +23,7 @@ authors:
   given-names: "Gary R."
 
 title: "chaste-codegen"
-version: 0.9.1
+version: 0.9.3
 doi: 10.5281/zenodo.5517000
 date-released: 2021-09-20
 url: "https://github.com/ModellingWebLab/chaste-codegen"
diff --git a/RELEASE.md b/RELEASE.md
index 0a065db34..0cead5b78 100644
--- a/RELEASE.md
+++ b/RELEASE.md
@@ -1,3 +1,6 @@
+# Release 0.9.3
+- Performance upgrade for `--rush-larsen` using caching on linearity checking.
+
 # Release 0.9.2
 - Corrected a typo in command line argument `--skip-ingularity-fixes` renaming it to `--skip-singularity-fixes`
 
diff --git a/chaste_codegen/_linearity_check.py b/chaste_codegen/_linearity_check.py
index 44bb2aada..7aab3ca05 100644
--- a/chaste_codegen/_linearity_check.py
+++ b/chaste_codegen/_linearity_check.py
@@ -1,4 +1,5 @@
 from enum import Enum
+from functools import lru_cache
 
 from cellmlmanip.model import Variable
 from sympy import (
@@ -26,6 +27,7 @@ class KINDS(Enum):
     NONLINEAR = 3
 
 
+@lru_cache(maxsize=128)
 def _check_expr(expr, state_var, membrane_voltage_var, state_vars):
     """Check the kind of expression given (NONE, LINEAR or NONLINEAR)
 
@@ -38,6 +40,7 @@ def _check_expr(expr, state_var, membrane_voltage_var, state_vars):
     :param state_vars: the state variables in the model the expression comes from
     :return: the kind of expr (NONE, LINEAR or NONLINEAR)
     """
+    @lru_cache(maxsize=128)
     def max_kind(state_var, operands):
         result = KINDS.NONE
         for op in operands:
@@ -126,7 +129,7 @@ def get_non_linear_state_vars(derivative_equations, membrane_voltage_var, state_
     return set([eq.lhs.args[0] for eq in derivative_equations
                 if isinstance(eq.lhs, Derivative) and
                 eq.lhs.args[0] != membrane_voltage_var and
-                _check_expr(eq.rhs, eq.lhs.args[0], membrane_voltage_var, state_vars) != KINDS.LINEAR])
+                _check_expr(eq.rhs, eq.lhs.args[0], membrane_voltage_var, tuple(state_vars)) != KINDS.LINEAR])
 
 
 def subst_deriv_eqs_non_linear_vars(y_derivatives, non_linear_state_vars, membrane_voltage_var, state_vars,
diff --git a/chaste_codegen/version.txt b/chaste_codegen/version.txt
index 2003b639c..965065db5 100644
--- a/chaste_codegen/version.txt
+++ b/chaste_codegen/version.txt
@@ -1 +1 @@
-0.9.2
+0.9.3