From 09c632f064817a3af0aa85a47996f7dd48cde802 Mon Sep 17 00:00:00 2001 From: Kwabena Amponsah Date: Thu, 6 Feb 2025 19:18:42 +0000 Subject: [PATCH 1/5] Add Python 3.13 and drop 3.6 to 3.8 --- .github/workflows/pytest.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 6bd08513..88d402eb 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -2,10 +2,10 @@ name: build on: [pull_request] jobs: build: - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.6", "3.7", "3.8", "3.9", "3.10", "3.11", "3.12"] + python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] steps: - name: Checkout repository and submodules uses: actions/checkout@v4 @@ -29,6 +29,6 @@ jobs: - name: Test with pytest run: | python -m pytest --cov --cov-config=.coveragerc - - uses: codecov/codecov-action@v4 + - uses: codecov/codecov-action@v5 with: token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos From e71f51ebb32a6ea5cbde83e615dd1be5f3c4883e Mon Sep 17 00:00:00 2001 From: Kwabena N Amponsah Date: Mon, 10 Feb 2025 11:36:38 +0000 Subject: [PATCH 2/5] #283 Update dependency versions --- dev-requirements/dev.txt | 93 ++++++++++++++++++++-------------------- setup.py | 30 ++++++------- 2 files changed, 61 insertions(+), 62 deletions(-) diff --git a/dev-requirements/dev.txt b/dev-requirements/dev.txt index 27571c0d..7d40b3b6 100644 --- a/dev-requirements/dev.txt +++ b/dev-requirements/dev.txt @@ -1,49 +1,48 @@ -atomicwrites==1.4.0 -attrs==21.2.0 -bleach==3.3.0 -build==0.3.1.post1 -cellmlmanip==0.3.6 -certifi==2024.7.4 -chardet==4.0.0 -colorama==0.4.4 -coverage==5.5 -decorator==4.4.2 -docutils==0.17.1 -flake8==3.9.2 -idna==3.7 -importlib-metadata==4.0.1 -iniconfig==1.1.1 -isodate==0.6.0 -isort==5.8.0 +alabaster==0.7.16 +babel==2.17.0 +cellmlmanip==0.3.7 +certifi==2025.1.31 +charset-normalizer==3.4.1 +coverage==7.6.11 +decorator==5.1.1 +docutils==0.21.2 +exceptiongroup==1.2.2 +flake8==7.1.1 +idna==3.10 +imagesize==1.4.1 +importlib_metadata==8.6.1 +iniconfig==2.0.0 +isodate==0.7.2 +isort==6.0.0 Jinja2==3.1.5 -lxml==4.9.1 -MarkupSafe==1.1.1 -mccabe==0.6.1 -mock==4.0.3 +lxml==5.3.1 +MarkupSafe==3.0.2 +mccabe==0.7.0 +mock==5.1.0 mpmath==1.3.0 -networkx==2.5.1 -packaging==20.9 -pep517==0.10.0 -Pint==0.17 -pkginfo==1.7.0 -pluggy==0.13.1 -py==1.10.0 -pycodestyle==2.7.0 -pyflakes==2.3.1 -Pygments==2.15.0 -pyparsing==2.4.7 -pytest==6.2.4 -pytest-cov==2.11.1 -pywin32-ctypes==0.2.0 -rdflib==5.0.0 -readme-renderer==29.0 -requests==2.32.0 -requests-toolbelt==0.9.1 -rfc3986==1.5.0 -six==1.16.0 -sympy==1.9 -toml==0.10.2 -tqdm==4.66.3 -urllib3==1.26.19 -webencodings==0.5.1 -zipp==3.19.1 +networkx==3.2.1 +packaging==24.2 +Pint==0.19.2 +pluggy==1.5.0 +py==1.11.0 +pycodestyle==2.12.1 +pyflakes==3.2.0 +Pygments==2.19.1 +pyparsing==3.2.1 +pytest==8.3.4 +pytest-cov==6.0.0 +rdflib==7.1.3 +requests==2.32.3 +six==1.17.0 +snowballstemmer==2.2.0 +Sphinx==7.4.7 +sphinx-automodapi==0.18.0 +sphinxcontrib-applehelp==2.0.0 +sphinxcontrib-devhelp==2.0.0 +sphinxcontrib-htmlhelp==2.1.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==2.0.0 +sphinxcontrib-serializinghtml==2.0.0 +sympy==1.12.1 +tomli==2.2.1 +urllib3==2.3. diff --git a/setup.py b/setup.py index f21cba50..7edac23a 100644 --- a/setup.py +++ b/setup.py @@ -47,22 +47,22 @@ # List of dependencies install_requires=[ 'py>=1.10.0', - 'decorator>=4.4.2, <6', - 'importlib-metadata>=1.7, <8', - 'isodate>=0.6.0, <1', - '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', + 'decorator>=4.5', + 'importlib-metadata>=1.7', + 'isodate>=0.6', + 'lxml>=4.7', + 'MarkupSafe>=1.2', + 'mpmath>=1.1', + 'networkx>=2.4', + 'packaging>=20.4', + 'Pint>=0.9, <0.20', 'pyparsing>=2.4.7, <4', - 'rdflib>=5.0.0, <8', - 'six>=1.15.0, <2', - 'sympy>=1.9, <1.11', - 'zipp>=1.2.0, <4', - 'Jinja2>=3.0.0, <4', - 'cellmlmanip>=0.3.6, <0.4', + 'rdflib>=5.0', + 'six>=1.15', + 'sympy>=1.9, <1.13', + 'zipp>=1.2', + 'Jinja2>=3.0', + 'cellmlmanip>=0.3.7', ], extras_require={ 'docs': [ From 3356a3c2f8929e78155622f18327ee47b670745c Mon Sep 17 00:00:00 2001 From: Kwabena N Amponsah Date: Mon, 10 Feb 2025 12:03:41 +0000 Subject: [PATCH 3/5] #283 Cap sympy at 1.11 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 7edac23a..e44359fe 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ 'pyparsing>=2.4.7, <4', 'rdflib>=5.0', 'six>=1.15', - 'sympy>=1.9, <1.13', + 'sympy>=1.9, <1.11', 'zipp>=1.2', 'Jinja2>=3.0', 'cellmlmanip>=0.3.7', From d15cafc6b068aba5475e3adde61ac529b32cec18 Mon Sep 17 00:00:00 2001 From: Kwabena N Amponsah Date: Mon, 10 Feb 2025 12:18:09 +0000 Subject: [PATCH 4/5] #283 Update dev requirements --- dev-requirements/dev.txt | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/dev-requirements/dev.txt b/dev-requirements/dev.txt index 7d40b3b6..b30fc64d 100644 --- a/dev-requirements/dev.txt +++ b/dev-requirements/dev.txt @@ -1,3 +1,4 @@ +# This list was generated in Python 3.9 with `pip freeze` alabaster==0.7.16 babel==2.17.0 cellmlmanip==0.3.7 @@ -43,6 +44,7 @@ sphinxcontrib-htmlhelp==2.1.0 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==2.0.0 sphinxcontrib-serializinghtml==2.0.0 -sympy==1.12.1 +sympy==1.10.1 tomli==2.2.1 -urllib3==2.3. +urllib3==2.3.0 +zipp==3.21.0 From a51be99beb1522dc02c7db2c99e1d2b0b6785041 Mon Sep 17 00:00:00 2001 From: Kwabena N Amponsah Date: Mon, 10 Feb 2025 12:21:48 +0000 Subject: [PATCH 5/5] #283 Add release notes for 0.10.6 --- RELEASE.md | 5 +++++ chaste_codegen/version.txt | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/RELEASE.md b/RELEASE.md index 25be5929..4e291fd1 100644 --- a/RELEASE.md +++ b/RELEASE.md @@ -1,3 +1,8 @@ +# Release 0.10.6 +- Added support for Python 3.13. +- Updated dependency versions: + - cellmlmanip>=0.3.7 + # Release 0.10.5 - Added support for Python 3.12. - Updated dependency versions: diff --git a/chaste_codegen/version.txt b/chaste_codegen/version.txt index 9028ec63..69da6ebc 100644 --- a/chaste_codegen/version.txt +++ b/chaste_codegen/version.txt @@ -1 +1 @@ -0.10.5 +0.10.6