Merge pull request #280 from ModellingWebLab/support-python-312

Support Python 3.12

Author: mirams

.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

.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
+        - docs

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.
 

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, '')),

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