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

Support Python 3.12
ModellingWebLab · Sep 30, 2024 · af9c0bf · af9c0bf
2 parents 0ef92bb + e00ba4a
commit af9c0bf
Show file tree

Hide file tree

Showing 13 changed files with 52 additions and 35 deletions.
diff --git 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

diff --git 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
+        - docs
diff --git 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/_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
@@ -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
diff --git a/chaste_codegen/data/tests/test_jacobian_equations_2.txt_python36 b/chaste_codegen/data/tests/test_jacobian_equations_2.txt_python36
diff --git a/chaste_codegen/data/tests/test_jacobian_matrix_2.txt b/chaste_codegen/data/tests/test_jacobian_matrix_2.txt
diff --git a/chaste_codegen/data/tests/test_jacobian_matrix_2.txt_python36 b/chaste_codegen/data/tests/test_jacobian_matrix_2.txt_python36
diff --git a/chaste_codegen/tests/test_jacobian.py b/chaste_codegen/tests/test_jacobian.py
diff --git a/chaste_codegen/version.txt b/chaste_codegen/version.txt
@@ -1 +1 @@
-0.10.3
+0.10.5
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
diff --git a/setup.py b/setup.py
@@ -47,23 +47,22 @@
     # 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',
     ],
     extras_require={
         'docs': [