Use PETSc version 3.25.5

.github/actions/install_petsc4py/action.yml

@@ -18,7 +18,7 @@ runs:
       name: Download a specific release of PETSc
       shell: bash
       run: |
-        git clone --depth 1 --branch v3.25.0 https://gitlab.com/petsc/petsc.git
+        git clone --depth 1 --branch v3.25.5 https://gitlab.com/petsc/petsc.git
       # The branch "release" contains work towards the next version of PETSc,
       # and it may not be stable. If necessary, it can be cloned as follows:
       # git clone --depth 1 --branch release https://gitlab.com/petsc/petsc.git
@@ -50,5 +50,5 @@ runs:
       shell: bash
       working-directory: ./petsc
       run: | 
-        pip install wheel Cython numpy
+        pip install wheel numpy
         pip install src/binding/petsc4py

.github/workflows/deploy.yml

@@ -13,7 +13,7 @@ jobs:
     if: ${{ github.repository == 'pyccel/psydac' && github.event.workflow_run.conclusion == 'success' }}
     steps:
       - name: Set up Python 3.12
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: '3.12'
 

.github/workflows/deploy_check.yml

@@ -21,13 +21,13 @@ jobs:
           paths: '["psydac/**", "pyproject.toml", ".github/workflows/deploy_check.yml", ".github/actions/**"]'
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: '3.12'
 
       - name: Checkout repository
         if: steps.duplicate_check.outputs.should_skip != 'true'
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           submodules: true
 

.github/workflows/documentation.yml

@@ -28,12 +28,15 @@ jobs:
       OMP_NUM_THREADS: 2
     steps:
     - name: Checkout
-      uses: actions/checkout@v5
+      uses: actions/checkout@v6
+      with:
+        submodules: true
 
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.10'
+
     - name: Install non-Python dependencies on Ubuntu
       uses: awalsh128/cache-apt-pkgs-action@latest
       with:

.github/workflows/testing.yml

@@ -40,10 +40,12 @@ jobs:
       OMP_NUM_THREADS: 2
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
+        with:
+          submodules: true
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'

CHANGELOG.md

@@ -26,6 +26,7 @@ All notable changes to this project will be documented in this file.
 
 ### Changed
 
+-   #595 : Use PETSc 3.25.5 whose Python bindings `petsc4py` are built correctly with `cython>=3`
 -   #580 : Use PETSc 3.25.0 whose Python bindings `petsc4py` install correctly with `setuptools>=81.0`
 -   #579 : Require `pyccel>=2.2.3` which can compile all kernels with C
 -   #579 : Require `numpy>=2.1` to support Python >= 3.10

docs/installation.md

@@ -160,9 +160,9 @@ Although PSYDAC provides several iterative linear solvers which work with our na
 (`petsc4py` is a Python package which provides Python bindings to PETSc.) After solving the linear system with a PETSc solver, the function `petsc_to_psydac` allows converting the solution vector back to the PSYDAC format.
 
 In order to use these additional feature, PETSc and petsc4py must be installed as follows.
-First, we download the latest release of PETSc from its [official Git repository](https://gitlab.com/petsc/petsc):
+First, we download a recent release of PETSc from its [official Git repository](https://gitlab.com/petsc/petsc):
 ```sh
-git clone --depth 1 --branch v3.25.0 https://gitlab.com/petsc/petsc.git
+git clone --depth 1 --branch v3.25.5 https://gitlab.com/petsc/petsc.git
 ```
 Next, we specify a configuration for complex numbers, and install PETSc in a local directory:
 ```sh