From 3205327440a9cf61d73e446bb9ce7f444b7d92da Mon Sep 17 00:00:00 2001
From: Kwabena N Amponsah <kwabenantim@yahoo.com>
Date: Tue, 9 Jul 2024 23:45:20 +0100
Subject: [PATCH 1/7] Add python 3.12 to tests

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index ccf4c5de..6bd08513 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -5,7 +5,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
     steps:
     - name: Checkout repository and submodules
       uses: actions/checkout@v4

From 70dff316d26aa597e169393a0c638953a789168d Mon Sep 17 00:00:00 2001
From: Kwabena N Amponsah <kwabenantim@yahoo.com>
Date: Mon, 30 Sep 2024 05:01:57 +0100
Subject: [PATCH 2/7] #281 Add pyproject.toml

---
 pyproject.toml | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 pyproject.toml

diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000..fed528d4
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"

From ec8ea9ef6e8427a0c6c56851dc2b01e8522a9eae Mon Sep 17 00:00:00 2001
From: Kwabena N Amponsah <kwabenantim@yahoo.com>
Date: Mon, 30 Sep 2024 05:02:49 +0100
Subject: [PATCH 3/7] #281 Update dependency versions

---
 setup.py | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/setup.py b/setup.py
index e1b9cfa1..7a3cb58e 100644
--- a/setup.py
+++ b/setup.py
@@ -47,21 +47,21 @@
     # List of dependencies
     install_requires=[
         'py>=1.10.0',
-        'decorator>=4.4.2, <5',
-        'importlib-metadata>=1.7, <5',
+        'decorator>=4.4.2, <6',
+        'importlib-metadata>=1.7, <8',
         'isodate>=0.6.0, <1',
-        'lxml>=4.6.5, <5',
-        'MarkupSafe>=1.1.1, <2',
+        'lxml>=4.6.5, <6',
+        'MarkupSafe>=1.1.1, <3',
         'mpmath>=1.1.0, <2',
-        'networkx>=2.4, <3',
-        'packaging>=20.4, <21',
-        'Pint>=0.9, <0.20',
-        'pyparsing>=2.4.7, <3',
-        'rdflib>=5.0.0, <7',
+        'networkx>=2.4, <4',
+        'packaging>=20.4, <24',
+        'Pint>=0.9, <0.30',
+        'pyparsing>=2.4.7, <4',
+        'rdflib>=5.0.0, <8',
         'six>=1.15.0, <2',
         'sympy>=1.9, <1.11',
-        'zipp>=1.2.0, <2',
-        'Jinja2>=2.11.3, <4',
+        'zipp>=1.2.0, <4',
+        'Jinja2>=3.0.0, <4',
         'cellmlmanip>=0.3.6, <0.4',
         'Jinja2>=2.11.3, <4',
     ],

From 3d5414b2af366ecfe56a6af7e13c469ef74ccc93 Mon Sep 17 00:00:00 2001
From: Kwabena N Amponsah <kwabenantim@yahoo.com>
Date: Mon, 30 Sep 2024 05:08:19 +0100
Subject: [PATCH 4/7] #281 Switch from OrderedDict to dict

---
 chaste_codegen/_command_line_script.py                       | 5 ++---
 chaste_codegen/_lookup_tables.py                             | 4 +---
 chaste_codegen/data/tests/test_jacobian_equations_2.txt      | 2 +-
 .../data/tests/test_jacobian_equations_2.txt_python36        | 2 +-
 chaste_codegen/data/tests/test_jacobian_matrix_2.txt         | 2 +-
 .../data/tests/test_jacobian_matrix_2.txt_python36           | 2 +-
 chaste_codegen/tests/test_jacobian.py                        | 5 ++---
 7 files changed, 9 insertions(+), 13 deletions(-)

diff --git a/chaste_codegen/_command_line_script.py b/chaste_codegen/_command_line_script.py
index f70fb6d9..4c515e90 100644
--- a/chaste_codegen/_command_line_script.py
+++ b/chaste_codegen/_command_line_script.py
@@ -3,7 +3,6 @@
 ######################################################################
 import argparse
 import os
-from collections import OrderedDict
 
 import chaste_codegen as cg
 from chaste_codegen import LOGGER, CodegenError, load_model_with_conversions
@@ -17,7 +16,7 @@
 
 # pass --<command_line_tag> to select this model type
 
-TRANSLATORS = OrderedDict(
+TRANSLATORS = dict(
     [('normal', (cg.NormalChasteModel, 'FromCellML', '', True, '')),
      ('cvode', (cg.CvodeChasteModel, 'FromCellMLCvode', 'Cvode', True, '')),
      ('cvode-data-clamp', (cg.CvodeChasteModel, 'FromCellMLCvodeDataClamp', 'CvodeDataClamp', True, '')),
@@ -29,7 +28,7 @@
                               ' in mastrcriptRT with added injection current(i_inj)')),
      ('rush-larsen-c', (cg.RushLarsenC, '', '', False, ' in C with added injection current(i_inj)'))])
 
-TRANSLATORS_OPT = OrderedDict(
+TRANSLATORS_OPT = dict(
     [('normal', (cg.OptChasteModel, 'FromCellMLOpt', 'Opt', True, '')),
      ('cvode', (cg.OptCvodeChasteModel, 'FromCellMLCvodeOpt', 'CvodeOpt', True, '')),
      ('cvode-data-clamp', (cg.OptCvodeChasteModel, 'FromCellMLCvodeDataClampOpt', 'CvodeDataClampOpt', True, '')),
diff --git a/chaste_codegen/_lookup_tables.py b/chaste_codegen/_lookup_tables.py
index 852d29ec..5777bbc8 100644
--- a/chaste_codegen/_lookup_tables.py
+++ b/chaste_codegen/_lookup_tables.py
@@ -1,5 +1,3 @@
-import collections
-
 from cellmlmanip.model import Quantity, Variable
 from sympy import (
     Piecewise,
@@ -71,7 +69,7 @@ def __init__(self, model, lookup_params=DEFAULT_LOOKUP_PARAMETERS):
                                          'lookup_epxrs': []} for param in lookup_params)
         self._model = model
         self._lookup_variables = set()
-        self._lookup_table_expr = collections.OrderedDict()
+        self._lookup_table_expr = dict()
         self._lookup_params_processed, self._lookup_params_printed = False, False
 
         self._method_printed = None
diff --git a/chaste_codegen/data/tests/test_jacobian_equations_2.txt b/chaste_codegen/data/tests/test_jacobian_equations_2.txt
index 4b2ba638..2bd7dc2f 100644
--- a/chaste_codegen/data/tests/test_jacobian_equations_2.txt
+++ b/chaste_codegen/data/tests/test_jacobian_equations_2.txt
@@ -1 +1 @@
-[OrderedDict([('lhs', 'x0'), ('rhs', 'x0120.0*_sodium_channel_m_gate$m**3.0'), ('sympy_lhs', x0)]), OrderedDict([('lhs', 'x1'), ('rhs', 'x1_membrane$V - 40.0'), ('sympy_lhs', x1)]), OrderedDict([('lhs', 'x4'), ('rhs', 'x4(0.10000000000000001*_membrane$V + 5.0000000000000003 >= -9.9999999999999995e-8) & (0.10000000000000001*_membrane$V + 5.0000000000000003 <= 9.9999999999999995e-8)'), ('sympy_lhs', x4)]), OrderedDict([('lhs', 'x5'), ('rhs', 'x5exp_(-0.10000000000000001*_membrane$V - 5.0000000000000003)'), ('sympy_lhs', x5)]), OrderedDict([('lhs', 'x6'), ('rhs', 'x6exp_(-0.10000000000000001*_membrane$V - 5.0000000000000003) - 1.0'), ('sympy_lhs', x6)]), OrderedDict([('lhs', 'x7'), ('rhs', 'x71/(exp_(-0.10000000000000001*_membrane$V - 5.0000000000000003) - 1.0)'), ('sympy_lhs', x7)]), OrderedDict([('lhs', 'x8'), ('rhs', 'x8exp_(-0.055555555555555556*_membrane$V - 4.1666666666666667)'), ('sympy_lhs', x8)]), OrderedDict([('lhs', 'x9'), ('rhs', 'x9exp_(-0.05*_membrane$V - 3.75)'), ('sympy_lhs', x9)]), OrderedDict([('lhs', 'x10'), ('rhs', 'x10exp_(-0.1*_membrane$V - 4.5)'), ('sympy_lhs', x10)]), OrderedDict([('lhs', 'x11'), ('rhs', 'x11exp_(-0.1*_membrane$V - 4.5) + 1.0'), ('sympy_lhs', x11)]), OrderedDict([('lhs', 'x12'), ('rhs', 'x120.10000000000000001*_membrane$V + 6.5000000000000004'), ('sympy_lhs', x12)]), OrderedDict([('lhs', 'x13'), ('rhs', 'x13(0.10000000000000001*_membrane$V + 6.5000000000000004 >= -9.9999999999999995e-8) & (0.10000000000000001*_membrane$V + 6.5000000000000004 <= 9.9999999999999995e-8)'), ('sympy_lhs', x13)]), OrderedDict([('lhs', 'x14'), ('rhs', 'x14exp_(-0.10000000000000001*_membrane$V - 6.5000000000000004)'), ('sympy_lhs', x14)]), OrderedDict([('lhs', 'x15'), ('rhs', 'x15exp_(-0.10000000000000001*_membrane$V - 6.5000000000000004) - 1.0'), ('sympy_lhs', x15)]), OrderedDict([('lhs', 'x16'), ('rhs', 'x161/(exp_(-0.10000000000000001*_membrane$V - 6.5000000000000004) - 1.0)'), ('sympy_lhs', x16)]), OrderedDict([('lhs', 'x17'), ('rhs', 'x17exp_(0.0125*_membrane$V + 0.9375)'), ('sympy_lhs', x17)])]
\ No newline at end of file
+[{'lhs': 'x0', 'rhs': 'x0120.0*_sodium_channel_m_gate$m**3.0', 'sympy_lhs': x0}, {'lhs': 'x1', 'rhs': 'x1_membrane$V - 40.0', 'sympy_lhs': x1}, {'lhs': 'x4', 'rhs': 'x4(0.10000000000000001*_membrane$V + 5.0000000000000003 >= -9.9999999999999995e-8) & (0.10000000000000001*_membrane$V + 5.0000000000000003 <= 9.9999999999999995e-8)', 'sympy_lhs': x4}, {'lhs': 'x5', 'rhs': 'x5exp_(-0.10000000000000001*_membrane$V - 5.0000000000000003)', 'sympy_lhs': x5}, {'lhs': 'x6', 'rhs': 'x6exp_(-0.10000000000000001*_membrane$V - 5.0000000000000003) - 1.0', 'sympy_lhs': x6}, {'lhs': 'x7', 'rhs': 'x71/(exp_(-0.10000000000000001*_membrane$V - 5.0000000000000003) - 1.0)', 'sympy_lhs': x7}, {'lhs': 'x8', 'rhs': 'x8exp_(-0.055555555555555556*_membrane$V - 4.1666666666666667)', 'sympy_lhs': x8}, {'lhs': 'x9', 'rhs': 'x9exp_(-0.05*_membrane$V - 3.75)', 'sympy_lhs': x9}, {'lhs': 'x10', 'rhs': 'x10exp_(-0.1*_membrane$V - 4.5)', 'sympy_lhs': x10}, {'lhs': 'x11', 'rhs': 'x11exp_(-0.1*_membrane$V - 4.5) + 1.0', 'sympy_lhs': x11}, {'lhs': 'x12', 'rhs': 'x120.10000000000000001*_membrane$V + 6.5000000000000004', 'sympy_lhs': x12}, {'lhs': 'x13', 'rhs': 'x13(0.10000000000000001*_membrane$V + 6.5000000000000004 >= -9.9999999999999995e-8) & (0.10000000000000001*_membrane$V + 6.5000000000000004 <= 9.9999999999999995e-8)', 'sympy_lhs': x13}, {'lhs': 'x14', 'rhs': 'x14exp_(-0.10000000000000001*_membrane$V - 6.5000000000000004)', 'sympy_lhs': x14}, {'lhs': 'x15', 'rhs': 'x15exp_(-0.10000000000000001*_membrane$V - 6.5000000000000004) - 1.0', 'sympy_lhs': x15}, {'lhs': 'x16', 'rhs': 'x161/(exp_(-0.10000000000000001*_membrane$V - 6.5000000000000004) - 1.0)', 'sympy_lhs': x16}, {'lhs': 'x17', 'rhs': 'x17exp_(0.0125*_membrane$V + 0.9375)', 'sympy_lhs': x17}]
\ No newline at end of file
diff --git a/chaste_codegen/data/tests/test_jacobian_equations_2.txt_python36 b/chaste_codegen/data/tests/test_jacobian_equations_2.txt_python36
index 56c9658b..8ce18d06 100644
--- a/chaste_codegen/data/tests/test_jacobian_equations_2.txt_python36
+++ b/chaste_codegen/data/tests/test_jacobian_equations_2.txt_python36
@@ -1 +1 @@
-[OrderedDict([('lhs', 'x0'), ('rhs', 'x0120.0*_sodium_channel_m_gate$m**3.0'), ('sympy_lhs', x0)]), OrderedDict([('lhs', 'x1'), ('rhs', 'x1_membrane$V - 40.0'), ('sympy_lhs', x1)]), OrderedDict([('lhs', 'x2'), ('rhs', 'x2(_membrane$V >= -50.000001) & (_membrane$V <= -49.999999)'), ('sympy_lhs', x2)]), OrderedDict([('lhs', 'x4'), ('rhs', 'x4-0.10000000000000001*_membrane$V - 5.0000000000000003'), ('sympy_lhs', x4)]), OrderedDict([('lhs', 'x5'), ('rhs', 'x5exp_(-0.10000000000000001*_membrane$V - 5.0000000000000003)'), ('sympy_lhs', x5)]), OrderedDict([('lhs', 'x6'), ('rhs', 'x6exp_(-0.10000000000000001*_membrane$V - 5.0000000000000003) - 1.0'), ('sympy_lhs', x6)]), OrderedDict([('lhs', 'x7'), ('rhs', 'x71/(exp_(-0.10000000000000001*_membrane$V - 5.0000000000000003) - 1.0)'), ('sympy_lhs', x7)]), OrderedDict([('lhs', 'x8'), ('rhs', 'x8exp_(-0.055555555555555556*_membrane$V - 4.1666666666666667)'), ('sympy_lhs', x8)]), OrderedDict([('lhs', 'x9'), ('rhs', 'x9exp_(-0.05*_membrane$V - 3.75)'), ('sympy_lhs', x9)]), OrderedDict([('lhs', 'x10'), ('rhs', 'x10exp_(-0.1*_membrane$V - 4.5)'), ('sympy_lhs', x10)]), OrderedDict([('lhs', 'x11'), ('rhs', 'x11exp_(-0.1*_membrane$V - 4.5) + 1.0'), ('sympy_lhs', x11)]), OrderedDict([('lhs', 'x12'), ('rhs', 'x12(_membrane$V >= -65.000001) & (_membrane$V <= -64.999999)'), ('sympy_lhs', x12)]), OrderedDict([('lhs', 'x13'), ('rhs', 'x13-0.10000000000000001*_membrane$V - 6.5000000000000004'), ('sympy_lhs', x13)]), OrderedDict([('lhs', 'x14'), ('rhs', 'x14exp_(-0.10000000000000001*_membrane$V - 6.5000000000000004)'), ('sympy_lhs', x14)]), OrderedDict([('lhs', 'x15'), ('rhs', 'x15exp_(-0.10000000000000001*_membrane$V - 6.5000000000000004) - 1.0'), ('sympy_lhs', x15)]), OrderedDict([('lhs', 'x16'), ('rhs', 'x161/(exp_(-0.10000000000000001*_membrane$V - 6.5000000000000004) - 1.0)'), ('sympy_lhs', x16)]), OrderedDict([('lhs', 'x17'), ('rhs', 'x17exp_(0.0125*_membrane$V + 0.9375)'), ('sympy_lhs', x17)])]
\ No newline at end of file
+[{'lhs': 'x0', 'rhs': 'x0120.0*_sodium_channel_m_gate$m**3.0', 'sympy_lhs': x0}, {'lhs': 'x1', 'rhs': 'x1_membrane$V - 40.0', 'sympy_lhs': x1}, {'lhs': 'x2', 'rhs': 'x2(_membrane$V >= -50.000001) & (_membrane$V <= -49.999999)', 'sympy_lhs': x2}, {'lhs': 'x4', 'rhs': 'x4-0.10000000000000001*_membrane$V - 5.0000000000000003', 'sympy_lhs': x4}, {'lhs': 'x5', 'rhs': 'x5exp_(-0.10000000000000001*_membrane$V - 5.0000000000000003)', 'sympy_lhs': x5}, {'lhs': 'x6', 'rhs': 'x6exp_(-0.10000000000000001*_membrane$V - 5.0000000000000003) - 1.0', 'sympy_lhs': x6}, {'lhs': 'x7', 'rhs': 'x71/(exp_(-0.10000000000000001*_membrane$V - 5.0000000000000003) - 1.0)', 'sympy_lhs': x7}, {'lhs': 'x8', 'rhs': 'x8exp_(-0.055555555555555556*_membrane$V - 4.1666666666666667)', 'sympy_lhs': x8}, {'lhs': 'x9', 'rhs': 'x9exp_(-0.05*_membrane$V - 3.75)', 'sympy_lhs': x9}, {'lhs': 'x10', 'rhs': 'x10exp_(-0.1*_membrane$V - 4.5)', 'sympy_lhs': x10}, {'lhs': 'x11', 'rhs': 'x11exp_(-0.1*_membrane$V - 4.5) + 1.0', 'sympy_lhs': x11}, {'lhs': 'x12', 'rhs': 'x12(_membrane$V >= -65.000001) & (_membrane$V <= -64.999999)', 'sympy_lhs': x12}, {'lhs': 'x13', 'rhs': 'x13-0.10000000000000001*_membrane$V - 6.5000000000000004', 'sympy_lhs': x13}, {'lhs': 'x14', 'rhs': 'x14exp_(-0.10000000000000001*_membrane$V - 6.5000000000000004)', 'sympy_lhs': x14}, {'lhs': 'x15', 'rhs': 'x15exp_(-0.10000000000000001*_membrane$V - 6.5000000000000004) - 1.0', 'sympy_lhs': x15}, {'lhs': 'x16', 'rhs': 'x161/(exp_(-0.10000000000000001*_membrane$V - 6.5000000000000004) - 1.0)', 'sympy_lhs': x16}, {'lhs': 'x17', 'rhs': 'x17exp_(0.0125*_membrane$V + 0.9375)', 'sympy_lhs': x17}]
\ No newline at end of file
diff --git a/chaste_codegen/data/tests/test_jacobian_matrix_2.txt b/chaste_codegen/data/tests/test_jacobian_matrix_2.txt
index f532b494..8f824f21 100644
--- a/chaste_codegen/data/tests/test_jacobian_matrix_2.txt
+++ b/chaste_codegen/data/tests/test_jacobian_matrix_2.txt
@@ -1 +1 @@
-[OrderedDict([('i', 0), ('j', 0), ('entry', '-0.29999999999999999 - 36 * pow(potassium_channel_n_gate$n, 4) - x0 * sodium_channel_h_gate$h')]), OrderedDict([('i', 1), ('j', 0), ('entry', '(1 - sodium_channel_m_gate$m) * ((x4) ? (0.050000000000000003) : (-0.10000000000000001 * x7 - 0.10000000000000001 * x3 * x5 / pow(x6, 2))) + 0.22222222222222221 * x8 * sodium_channel_m_gate$m')]), OrderedDict([('i', 2), ('j', 0), ('entry', '-0.050000000000000003 * x9 * (0.070000000000000007 - 0.070000000000000007 * sodium_channel_h_gate$h) - 0.10000000000000001 * x10 * sodium_channel_h_gate$h / pow(x11, 2)')]), OrderedDict([('i', 3), ('j', 0), ('entry', '(1 - potassium_channel_n_gate$n) * ((x13) ? (0.0050000000000000001) : (-0.01 * x16 - 0.01 * x12 * x14 / pow(x15, 2))) - 0.0015625000000000001 * x17 * potassium_channel_n_gate$n')]), OrderedDict([('i', 0), ('j', 1), ('entry', '-360 * x1 * pow(sodium_channel_m_gate$m, 2) * sodium_channel_h_gate$h')]), OrderedDict([('i', 1), ('j', 1), ('entry', '-((x4) ? (3.5 + 0.050000000000000003 * membrane$V) : (-x3 * x7)) - 4 * x8')]), OrderedDict([('i', 0), ('j', 2), ('entry', '-x0 * x1')]), OrderedDict([('i', 2), ('j', 2), ('entry', '-1 / x11 - 0.070000000000000007 * x9')]), OrderedDict([('i', 0), ('j', 3), ('entry', '-144 * pow(potassium_channel_n_gate$n, 3) * (87 + membrane$V)')]), OrderedDict([('i', 3), ('j', 3), ('entry', '-((x13) ? (0.42499999999999999 + 0.0050000000000000001 * membrane$V) : (-0.099999999999999992 * x12 * x16)) - 0.125 * x17')])]
\ No newline at end of file
+[{'i': 0, 'j': 0, 'entry': '-0.29999999999999999 - 36 * pow(potassium_channel_n_gate$n, 4) - x0 * sodium_channel_h_gate$h'}, {'i': 1, 'j': 0, 'entry': '(1 - sodium_channel_m_gate$m) * ((x4) ? (0.050000000000000003) : (-0.10000000000000001 * x7 - 0.10000000000000001 * x3 * x5 / pow(x6, 2))) + 0.22222222222222221 * x8 * sodium_channel_m_gate$m'}, {'i': 2, 'j': 0, 'entry': '-0.050000000000000003 * x9 * (0.070000000000000007 - 0.070000000000000007 * sodium_channel_h_gate$h) - 0.10000000000000001 * x10 * sodium_channel_h_gate$h / pow(x11, 2)'}, {'i': 3, 'j': 0, 'entry': '(1 - potassium_channel_n_gate$n) * ((x13) ? (0.0050000000000000001) : (-0.01 * x16 - 0.01 * x12 * x14 / pow(x15, 2))) - 0.0015625000000000001 * x17 * potassium_channel_n_gate$n'}, {'i': 0, 'j': 1, 'entry': '-360 * x1 * pow(sodium_channel_m_gate$m, 2) * sodium_channel_h_gate$h'}, {'i': 1, 'j': 1, 'entry': '-((x4) ? (3.5 + 0.050000000000000003 * membrane$V) : (-x3 * x7)) - 4 * x8'}, {'i': 0, 'j': 2, 'entry': '-x0 * x1'}, {'i': 2, 'j': 2, 'entry': '-1 / x11 - 0.070000000000000007 * x9'}, {'i': 0, 'j': 3, 'entry': '-144 * pow(potassium_channel_n_gate$n, 3) * (87 + membrane$V)'}, {'i': 3, 'j': 3, 'entry': '-((x13) ? (0.42499999999999999 + 0.0050000000000000001 * membrane$V) : (-0.099999999999999992 * x12 * x16)) - 0.125 * x17'}]
\ No newline at end of file
diff --git a/chaste_codegen/data/tests/test_jacobian_matrix_2.txt_python36 b/chaste_codegen/data/tests/test_jacobian_matrix_2.txt_python36
index e8a06f18..5c141c27 100644
--- a/chaste_codegen/data/tests/test_jacobian_matrix_2.txt_python36
+++ b/chaste_codegen/data/tests/test_jacobian_matrix_2.txt_python36
@@ -1 +1 @@
-[OrderedDict([('i', 0), ('j', 0), ('entry', '-0.29999999999999999 - 36 * pow(potassium_channel_n_gate$n, 4) - x0 * sodium_channel_h_gate$h')]), OrderedDict([('i', 1), ('j', 0), ('entry', '(1 - sodium_channel_m_gate$m) * ((x2) ? (0.050000000000000003) : (-0.10000000000000001 * x7 + 0.10000000000000001 * x4 * x5 / pow(x6, 2))) + 0.22222222222222221 * x8 * sodium_channel_m_gate$m')]), OrderedDict([('i', 2), ('j', 0), ('entry', '-0.050000000000000003 * x9 * (0.070000000000000007 - 0.070000000000000007 * sodium_channel_h_gate$h) - 0.10000000000000001 * x10 * sodium_channel_h_gate$h / pow(x11, 2)')]), OrderedDict([('i', 3), ('j', 0), ('entry', '(1 - potassium_channel_n_gate$n) * ((x12) ? (0.0050000000000000001) : (-0.01 * x16 + 0.01 * x13 * x14 / pow(x15, 2))) - 0.0015625000000000001 * x17 * potassium_channel_n_gate$n')]), OrderedDict([('i', 0), ('j', 1), ('entry', '-360 * x1 * pow(sodium_channel_m_gate$m, 2) * sodium_channel_h_gate$h')]), OrderedDict([('i', 1), ('j', 1), ('entry', '-((x2) ? (3.5 + 0.050000000000000003 * membrane$V) : (x4 * x7)) - 4 * x8')]), OrderedDict([('i', 0), ('j', 2), ('entry', '-x0 * x1')]), OrderedDict([('i', 2), ('j', 2), ('entry', '-1 / x11 - 0.070000000000000007 * x9')]), OrderedDict([('i', 0), ('j', 3), ('entry', '-144 * pow(potassium_channel_n_gate$n, 3) * (87 + membrane$V)')]), OrderedDict([('i', 3), ('j', 3), ('entry', '-((x12) ? (0.42499999999999999 + 0.0050000000000000001 * membrane$V) : (0.099999999999999992 * x13 * x16)) - 0.125 * x17')])]
\ No newline at end of file
+[{'i': 0, 'j': 0, 'entry': '-0.29999999999999999 - 36 * pow(potassium_channel_n_gate$n, 4) - x0 * sodium_channel_h_gate$h'}, {'i': 1, 'j': 0, 'entry': '(1 - sodium_channel_m_gate$m) * ((x2) ? (0.050000000000000003) : (-0.10000000000000001 * x7 + 0.10000000000000001 * x4 * x5 / pow(x6, 2))) + 0.22222222222222221 * x8 * sodium_channel_m_gate$m'}, {'i': 2, 'j': 0, 'entry': '-0.050000000000000003 * x9 * (0.070000000000000007 - 0.070000000000000007 * sodium_channel_h_gate$h) - 0.10000000000000001 * x10 * sodium_channel_h_gate$h / pow(x11, 2)'}, {'i': 3, 'j': 0, 'entry': '(1 - potassium_channel_n_gate$n) * ((x12) ? (0.0050000000000000001) : (-0.01 * x16 + 0.01 * x13 * x14 / pow(x15, 2))) - 0.0015625000000000001 * x17 * potassium_channel_n_gate$n'}, {'i': 0, 'j': 1, 'entry': '-360 * x1 * pow(sodium_channel_m_gate$m, 2) * sodium_channel_h_gate$h'}, {'i': 1, 'j': 1, 'entry': '-((x2) ? (3.5 + 0.050000000000000003 * membrane$V) : (x4 * x7)) - 4 * x8'}, {'i': 0, 'j': 2, 'entry': '-x0 * x1'}, {'i': 2, 'j': 2, 'entry': '-1 / x11 - 0.070000000000000007 * x9'}, {'i': 0, 'j': 3, 'entry': '-144 * pow(potassium_channel_n_gate$n, 3) * (87 + membrane$V)'}, {'i': 3, 'j': 3, 'entry': '-((x12) ? (0.42499999999999999 + 0.0050000000000000001 * membrane$V) : (0.099999999999999992 * x13 * x16)) - 0.125 * x17'}]
\ No newline at end of file
diff --git a/chaste_codegen/tests/test_jacobian.py b/chaste_codegen/tests/test_jacobian.py
index 3bc5fe8d..74c0bbb2 100644
--- a/chaste_codegen/tests/test_jacobian.py
+++ b/chaste_codegen/tests/test_jacobian.py
@@ -1,4 +1,3 @@
-import collections
 import os
 
 import pytest
@@ -91,10 +90,10 @@ def test_format_jacobian(jacobian):
     equations, jacobian = format_jacobian(jacobian_equations, sp.Matrix([jacobian_matrix]), ChastePrinter(),
                                           lambda x, y: str(x) + str(y))
     # order dictionary for printing
-    equations = [collections.OrderedDict([('lhs', eq['lhs']), ('rhs', eq['rhs']), ('sympy_lhs', eq['sympy_lhs'])])
+    equations = [dict([('lhs', eq['lhs']), ('rhs', eq['rhs']), ('sympy_lhs', eq['sympy_lhs'])])
                  for eq in equations]
     # order dictionary for printing
-    jacobian = [collections.OrderedDict([('i', jac['i']), ('j', jac['j']), ('entry', jac['entry'])])
+    jacobian = [dict([('i', jac['i']), ('j', jac['j']), ('entry', jac['entry'])])
                 for jac in jacobian]
 
     expected = open(os.path.join(TESTS_FOLDER, 'test_jacobian_equations_2.txt'), 'r').read()

From 003de78dca9fb63da75dba842a0b4cd5278a7f6d Mon Sep 17 00:00:00 2001
From: Kwabena N Amponsah <kwabenantim@yahoo.com>
Date: Mon, 30 Sep 2024 08:38:28 +0100
Subject: [PATCH 5/7] #281 Increasee version to 0.10.4

---
 RELEASE.md                 | 16 ++++++++++++++++
 chaste_codegen/version.txt |  2 +-
 setup.py                   |  1 -
 3 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/RELEASE.md b/RELEASE.md
index bd3d188e..25be5929 100644
--- a/RELEASE.md
+++ b/RELEASE.md
@@ -1,3 +1,19 @@
+# Release 0.10.5
+- Added support for Python 3.12.
+- Updated dependency versions:
+  - decorator>=4.4.2, <6
+  - importlib-metadata>=1.7, <8
+  - lxml>=4.6.5, <6
+  - MarkupSafe>=1.1.1, <3
+  - mpmath>=1.1.0, <2
+  - networkx>=2.4, <4
+  - packaging>=20.4, <24
+  - Pint>=0.9, <0.30
+  - pyparsing>=2.4.7, <4
+  - rdflib>=5.0.0, <8
+  - zipp>=1.2.0, <4
+  - Jinja2>=3.0.0, <4
+
 # Release 0.10.4
 - Improved the developer documentation with regards to updating python packages, the ontology and releasing new versions of chaste_codegen.
 
diff --git a/chaste_codegen/version.txt b/chaste_codegen/version.txt
index a3f5a8ed..9b40aa6c 100644
--- a/chaste_codegen/version.txt
+++ b/chaste_codegen/version.txt
@@ -1 +1 @@
-0.10.3
+0.10.4
diff --git a/setup.py b/setup.py
index 7a3cb58e..f21cba50 100644
--- a/setup.py
+++ b/setup.py
@@ -63,7 +63,6 @@
         'zipp>=1.2.0, <4',
         'Jinja2>=3.0.0, <4',
         'cellmlmanip>=0.3.6, <0.4',
-        'Jinja2>=2.11.3, <4',
     ],
     extras_require={
         'docs': [

From de41094da675df017ec4c02741a4405a4a8cd1a5 Mon Sep 17 00:00:00 2001
From: Kwabena N Amponsah <kwabenantim@yahoo.com>
Date: Mon, 30 Sep 2024 08:40:58 +0100
Subject: [PATCH 6/7] #281 Increment to version 0.10.5

---
 chaste_codegen/version.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/chaste_codegen/version.txt b/chaste_codegen/version.txt
index 9b40aa6c..9028ec63 100644
--- a/chaste_codegen/version.txt
+++ b/chaste_codegen/version.txt
@@ -1 +1 @@
-0.10.4
+0.10.5

From e00ba4aaeb51fa39c5c0c1987ff06cfe66642d90 Mon Sep 17 00:00:00 2001
From: Kwabena N Amponsah <kwabenantim@yahoo.com>
Date: Mon, 30 Sep 2024 11:18:09 +0100
Subject: [PATCH 7/7] #281 Update readthedocs config

---
 .readthedocs.yml | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index e3023e3b..85e96429 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -5,23 +5,26 @@
 # Required
 version: 2
 
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
 
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
-
-# Optionally build your docs in additional formats such as PDF
+# Optionally build your docs in additional formats such as PDF and ePub
 formats:
   - pdf
 
-# Optionally set the version of Python and requirements required to build your docs
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
-  version: 3.7
   install:
     - method: pip
       path: .
       extra_requirements:
-        - docs
\ No newline at end of file
+        - docs