Support Python 3.12 and 3.13

.github/workflows/coverage.yml

@@ -6,24 +6,25 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
 
     - name: Install
       run: |
         python --version
-        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install --upgrade pip
         python -m pip install .[test]
 
     - name: Test coverage
       run: |
         python -m pytest --cov --cov-config=.coveragerc
 
     - name: Submit report to codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
       if: success()
-

.github/workflows/docs.yml

@@ -6,17 +6,17 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
 
     - name: Install
       run: |
         python --version
-        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install --upgrade pip
         python -m pip install .[docs]
 
     - name: Test documentation building

.github/workflows/style.yml

@@ -6,17 +6,17 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: 3.9
 
     - name: Install tools
       run: |
         python --version
-        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install --upgrade pip
         python -m pip install flake8 isort
 
     - name: Check code style

.github/workflows/unit-test-pinned.yml

@@ -2,21 +2,21 @@ name: Pinned requirements
 on: [pull_request]
 jobs:
   unit-test-pinned:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
-    - name: Set up Python 3.6
-      uses: actions/setup-python@v2
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.6
+        python-version: 3.9
 
     - name: Install pinned dependencies
       run: |
         python --version
-        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install --upgrade pip
         python -m pip install -r requirements/test.txt
 
     - name: Install

.github/workflows/unit-test.yml

@@ -5,22 +5,22 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, windows-latest, macos-latest]
-        python-version: [3.6, 3.7, 3.8, 3.9, "3.10", "3.11"]
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install
       run: |
         python --version
-        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install --upgrade pip
         python -m pip install .[test]
 
     - name: Run unit tests

README.md

@@ -12,7 +12,7 @@ Users install `cellmlmanip` using pip.
 pip install cellmlmanip
 ```
 
-Cellmlmanip is tested and developed on Python 3.5 and higher.
+Cellmlmanip is tested and developed on Python 3.9 and higher.
 
 ## Release notes
 For release notes see [RELEASE.md](./RELEASE.md)

RELEASE.md

@@ -1,3 +1,8 @@
+# Release 0.3.7
+- Added support for Python 3.12 and 3.13.
+- Dropped support for Python 3.6, 3.7 and 3.8 as they are at end of life.
+- Pinned sympy to be < 1.13. See https://github.com/ModellingWebLab/cellmlmanip/issues/376.
+
 # Release 0.3.6
 - Added the ability to exclude a collection of tags from being used as variable names, by adding the `exclude_terms` parameter to  `model.get_display_name`. This can be used for example to prevent ontology annotation that can be used multiple times from appearing as the display name of a variable.
 

cellmlmanip/version.txt

@@ -1 +1 @@
-0.3.6
+0.3.7

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=64", "wheel"]
+build-backend = "setuptools.build_meta"

requirements/base.in

@@ -1,6 +1,5 @@
-lxml>4.2.1
-pint==0.9 ; python_version < '3.8'
-pint==0.10 ; python_version >= '3.8'
-rdflib
-networkx
-sympy
+lxml>=4.7
+pint>=0.9, <0.20
+rdflib>=4
+networkx>=2.1
+sympy>=1.4, <1.13

requirements/base.txt

@@ -1,26 +1,28 @@
 #
-# This file is autogenerated by pip-compile
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.9
+# by the following command:
 #
 #    pip-compile --output-file=base.txt base.in
 #
 decorator==4.4.2
     # via networkx
 isodate==0.6.0
     # via rdflib
-lxml==4.6.2
+lxml==5.3.0
     # via -r base.in
 mpmath==1.1.0
     # via sympy
 networkx==2.5
     # via -r base.in
-pint==0.9 ; python_version < "3.8"
+pint==0.19.2
     # via -r base.in
 pyparsing==2.4.7
     # via rdflib
 rdflib==5.0.0
     # via -r base.in
 six==1.15.0
-    # via rdflib
+    # via
+    #   isodate
+    #   rdflib
 sympy==1.7.1
     # via -r base.in

requirements/dev.txt

@@ -1,33 +1,21 @@
 #
-# This file is autogenerated by pip-compile
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.9
+# by the following command:
 #
 #    pip-compile --output-file=dev.txt dev.in
 #
 attrs==20.3.0
     # via pytest
-certifi==2020.12.5
-    # via requests
-chardet==4.0.0
-    # via requests
 click==7.1.2
     # via pip-tools
 coverage==5.4
-    # via
-    #   pytest-cov
+    # via pytest-cov
 decorator==4.4.2
     # via networkx
 flake8==3.8.4
     # via
     #   -r dev.in
     #   -r test.in
-idna==2.10
-    # via requests
-importlib-metadata==3.4.0
-    # via
-    #   flake8
-    #   pluggy
-    #   pytest
 iniconfig==1.1.1
     # via pytest
 isodate==0.6.0
@@ -36,7 +24,7 @@ isort==5.7.0
     # via
     #   -r dev.in
     #   -r test.in
-lxml==4.6.2
+lxml==5.3.0
     # via -r base.in
 mccabe==0.6.1
     # via flake8
@@ -46,7 +34,7 @@ networkx==2.5
     # via -r base.in
 packaging==20.8
     # via pytest
-pint==0.9 ; python_version < "3.8"
+pint==0.19.2
     # via -r base.in
 pip-tools==5.5.0
     # via -r dev.in
@@ -62,15 +50,14 @@ pyparsing==2.4.7
     # via
     #   packaging
     #   rdflib
-pytest-cov==2.11.1
-    # via -r test.in
 pytest==6.2.2
     # via
     #   -r test.in
     #   pytest-cov
+pytest-cov==2.11.1
+    # via -r test.in
 rdflib==5.0.0
     # via -r base.in
-requests==2.25.1
 six==1.15.0
     # via
     #   isodate
@@ -79,12 +66,6 @@ sympy==1.7.1
     # via -r base.in
 toml==0.10.2
     # via pytest
-typing-extensions==3.7.4.3
-    # via importlib-metadata
-urllib3==1.26.3
-    # via requests
-zipp==3.4.0
-    # via importlib-metadata
 
 # The following packages are considered to be unsafe in a requirements file:
 # pip

requirements/test.txt

@@ -1,36 +1,24 @@
 #
-# This file is autogenerated by pip-compile
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.9
+# by the following command:
 #
 #    pip-compile --output-file=test.txt test.in
 #
 attrs==20.3.0
     # via pytest
-certifi==2020.12.5
-    # via requests
-chardet==4.0.0
-    # via requests
 coverage==5.4
-    # via
-    #   pytest-cov
+    # via pytest-cov
 decorator==4.4.2
     # via networkx
 flake8==3.8.4
     # via -r test.in
-idna==2.10
-    # via requests
-importlib-metadata==3.4.0
-    # via
-    #   flake8
-    #   pluggy
-    #   pytest
 iniconfig==1.1.1
     # via pytest
 isodate==0.6.0
     # via rdflib
 isort==5.7.0
     # via -r test.in
-lxml==4.6.2
+lxml==5.3.0
     # via -r base.in
 mccabe==0.6.1
     # via flake8
@@ -40,7 +28,7 @@ networkx==2.5
     # via -r base.in
 packaging==20.8
     # via pytest
-pint==0.9 ; python_version < "3.8"
+pint==0.19.2
     # via -r base.in
 pluggy==0.13.1
     # via pytest
@@ -54,15 +42,14 @@ pyparsing==2.4.7
     # via
     #   packaging
     #   rdflib
-pytest-cov==2.11.1
-    # via -r test.in
 pytest==6.2.2
     # via
     #   -r test.in
     #   pytest-cov
+pytest-cov==2.11.1
+    # via -r test.in
 rdflib==5.0.0
     # via -r base.in
-requests==2.25.1
 six==1.15.0
     # via
     #   isodate
@@ -71,9 +58,3 @@ sympy==1.7.1
     # via -r base.in
 toml==0.10.2
     # via pytest
-typing-extensions==3.7.4.3
-    # via importlib-metadata
-urllib3==1.26.3
-    # via requests
-zipp==3.4.0
-    # via importlib-metadata

setup.py

@@ -28,13 +28,13 @@
 
     packages=find_packages(exclude=('tests', 'docs')),
     include_package_data=True,
-    python_requires='>=3.6',
+    python_requires='>=3.9',
     install_requires=[
-        'lxml>=4.6.5, <5',
+        'lxml>=4.7',
         'networkx>=2.1',
         'Pint>=0.9, <0.20',
         'rdflib>=4',
-        'sympy>=1.4',
+        'sympy>=1.4, <1.13',
     ],
     extras_require={
         'docs': [