Merge branch 'main' into hotfix/2.1.4

.github/docker/Dockerfile

@@ -17,6 +17,7 @@ RUN micromamba install -y -n base -c conda-forge \
       coverage">=7.1.0" \
       mpich \
       petsc"<=3.19" \
+      scipy \
       python=3.11 && \
    micromamba clean --all --yes
 

.github/workflows/codeql-analysis.yml

@@ -37,7 +37,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4.1.1
+      uses: actions/checkout@v4.1.7
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL

.github/workflows/docker.yml

@@ -16,7 +16,7 @@ jobs:
       TAG_PREFIX: ${{ steps.tag_name.outputs.TAG_PREFIX }}
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v4.1.7
 
       - name: Get tag name
         id: tag_name
@@ -47,7 +47,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v4.1.7
 
       - name: Log into the Dockerhub registry
         run: echo ${{ secrets.DOCKERHUB_TOKEN }} | docker login -u ${{ secrets.DOCKERHUB_USERNAME }} --password-stdin

.github/workflows/docker_ghcr.yml

@@ -30,7 +30,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v4.1.7
 
       - name: Log in to the Container registry
         uses: docker/login-action@v3
@@ -51,7 +51,7 @@ jobs:
             type=semver,pattern={{major}}.{{minor}}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           context: .
           file: ./.github/docker/Dockerfile

.github/workflows/ossar-analysis.yml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4.1.1
+      uses: actions/checkout@v4.1.7
 
     # Ensure a compatible version of dotnet is installed.
     # The [Microsoft Security Code Analysis CLI](https://aka.ms/mscadocs) is built with dotnet v3.1.201.

.github/workflows/publish.yml

@@ -22,7 +22,7 @@ jobs:
         rm -R /home/mambauser/cashocs
 
     - name: Checkout repository
-      uses: actions/checkout@v4.1.1 
+      uses: actions/checkout@v4.1.7 
 
     - name: Install cashocs
       shell: bash
@@ -45,7 +45,7 @@ jobs:
     steps:
 
     - name: Checkout repository
-      uses: actions/checkout@v4.1.1
+      uses: actions/checkout@v4.1.7
 
 
     - name: Get tag name
@@ -63,7 +63,7 @@ jobs:
 
     - name: Create Github release
       id: create_release
-      uses: softprops/action-gh-release@v1
+      uses: softprops/action-gh-release@v2
       with:
         name: cashocs ${{ steps.tag_name.outputs.TAG_PREFIX }}
         generate_release_notes: ${{ steps.check_version.outputs.is_stable == 'true' }}
@@ -80,7 +80,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4.1.1
+      uses: actions/checkout@v4.1.7
 
     - name: Set up Python 3.11
       uses: actions/setup-python@v5

.github/workflows/test_demos.yml

@@ -17,7 +17,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4.1.1
+      uses: actions/checkout@v4.1.7
 
     - name: Install micromamba
       uses: mamba-org/setup-micromamba@v1
@@ -30,6 +30,7 @@ jobs:
           gmsh>=4.8
           matplotlib
           petsc<=3.19
+          scipy
           python=3.11
 
     - name: Install package
@@ -55,7 +56,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4.1.1
+      uses: actions/checkout@v4.1.7
 
     - name: Install micromamba
       uses: mamba-org/setup-micromamba@v1
@@ -69,6 +70,7 @@ jobs:
           mpich
           matplotlib
           petsc<=3.19
+          scipy
           python=3.11
 
     - name: Install package

.github/workflows/tests.yml

@@ -27,7 +27,7 @@ jobs:
         rm -R /home/mambauser/cashocs
 
     - name: Checkout repository
-      uses: actions/checkout@v4.1.1 
+      uses: actions/checkout@v4.1.7 
 
     - name: Install cashocs
       shell: bash

.github/workflows/tests_macos.yml

@@ -20,7 +20,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4.1.1
+      uses: actions/checkout@v4.1.7
 
     - name: Install micromamba
       uses: mamba-org/setup-micromamba@v1
@@ -33,6 +33,7 @@ jobs:
           pytest>=7.2.0
           gmsh>=4.8
           petsc<=3.19
+          scipy
 
     - name: Install package
       run: |

.github/workflows/tests_parallel.yml

@@ -24,7 +24,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4.1.1
+      uses: actions/checkout@v4.1.7
 
     - name: Install micromamba
       uses: mamba-org/setup-micromamba@v1
@@ -36,6 +36,7 @@ jobs:
           pytest>=7.2.0
           gmsh>=4.8
           petsc<=3.19
+          scipy
           ${{ matrix.mpi }}
           python=${{ matrix.python-version }}
 

.github/workflows/tests_serial.yml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4.1.1
+      uses: actions/checkout@v4.1.7
 
     - name: Install micromamba
       uses: mamba-org/setup-micromamba@v1
@@ -33,6 +33,7 @@ jobs:
           pytest>=7.2.0
           gmsh>=4.8
           petsc<=3.19
+          scipy
           python=${{ matrix.python-version }}
 
     - name: Install package

.pre-commit-config.yaml

@@ -1,60 +1,47 @@
-repos:
+default_language_version:
+  python: python3.11
 
+repos:
   - repo: https://github.com/regebro/pyroma
     rev: "4.2"
     hooks:
       - id: pyroma
-
   - repo: https://github.com/psf/black
-    rev: 24.1.1
+    rev: 24.4.2
     hooks:
       - id: black
-
-
   - repo: https://github.com/PyCQA/isort
     rev: 5.13.2
     hooks:
       - id: isort
-
-
   - repo: https://github.com/PyCQA/pydocstyle
     rev: 6.3.0
     hooks:
       - id: pydocstyle
         additional_dependencies: ["tomli"]
         files: cashocs/
-
-
   - repo: https://github.com/PyCQA/flake8
-    rev: 7.0.0
+    rev: 7.1.0
     hooks:
       - id: flake8
         files: cashocs/
-
-
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.7.7
+    rev: 1.7.9
     hooks:
       - id: bandit
         files: cashocs/
-
-
   - repo: https://github.com/PyCQA/pylint
-    rev: v3.0.3
+    rev: v3.2.5
     hooks:
       - id: pylint
         files: cashocs/
-
-
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.8.0
+    rev: v1.10.1
     hooks:
       - id: mypy
         files: cashocs/
         additional_dependencies: ["numpy"]
         args: [--config-file, pyproject.toml]
-
-
   - repo: https://github.com/PyCQA/prospector
     rev: v1.10.3
     hooks:

.zenodo.json

@@ -1,8 +1,8 @@
 {
     "description": "<p>cashocs is a computational, adjoint-based shape optimization and optimal control software.</p>", 
     "license": "GPL-3.0+", 
-    "title": "cashocs v2.1.4",
-    "version": "v2.1.4",
+    "title": "cashocs v2.2.0-dev",
+    "version": "v2.2.0-dev",
     "upload_type": "software", 
     "creators": [
         {

CHANGELOG.rst

@@ -7,6 +7,33 @@ of the maintenance releases, please take a look at
 `<https://github.com/sblauth/cashocs/releases>`_.
 
 
+2.2.0 (in development)
+----------------------
+
+* Add a wrapper for PETSc's SNES solver for nonlinear equations. This is used internally in cashocs whenever possible. For the solution of the state system, our own Newton solver is the default for backwards compatibility. Users can use the new SNES backend by specifying :ini:`backend = petsc` in the Section StateSystem of the configuration.
+
+* Allows nesting of PETSc Fieldsplit PCs with the command line option "pc_fieldsplit_%d_fields <a,b,...>, as explained at `<https://petsc.org/main/manualpages/PC/PCFieldSplitSetFields/>`_
+
+* Increase the precision of the Gmsh output from cashocs
+
+* Add mesh quality constraints for shape optimization: These ensure that the angles of the (solid) angles of triangles and tetrahedrons cannot fall below a specified threshold.
+
+* New configuration file parameters:
+
+  * Section StateSystem
+
+    * :ini:`backend` specifies which backend is used for solving nonlinear equations. The default is :ini:`backend = cashocs`, which is the "old" behavior, and :ini:`backend = petsc` uses the new PETSc SNES interface.
+
+  * Section ShapeGradient
+
+    * :ini:`test_for_intersections` is used to disable the (post mesh movement) check for intersections of the mesh, which ensures physically reasonable designs. This should not be set to `False`.
+
+  * Section MeshQualityConstraints
+
+    * This section includes parameters for the new mesh quality constraints for shape optimization. These are described in the documentation at `<https://cashocs.readthedocs.io/en/stable/user/demos/shape_optimization/doc_config/#section-meshqualityconstraints>`_
+
+
+
 2.1.0 (February 6, 2024)
 ------------------------