Merge branch 'main' into dev/scotch7_support

sblauth · Sep 30, 2024 · 5bd1e03 · 5bd1e03
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
diff --git a/.github/ISSUE_TEMPLATE/ci-cd.md b/.github/ISSUE_TEMPLATE/ci-cd.md
diff --git a/.github/ISSUE_TEMPLATE/development-related-matters.md b/.github/ISSUE_TEMPLATE/development-related-matters.md
diff --git a/.github/ISSUE_TEMPLATE/documentation.md b/.github/ISSUE_TEMPLATE/documentation.md
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
diff --git a/.github/ISSUE_TEMPLATE/question---support-request.md b/.github/ISSUE_TEMPLATE/question---support-request.md
diff --git a/.github/release.yml b/.github/release.yml
@@ -0,0 +1,17 @@
+changelog:
+  exclude:
+    authors:
+      - snyk-bot
+  categories:
+    - title: New Features and Improvements
+      labels:
+        - enhancement
+    - title: Bug Fixes
+      labels:
+        - bug
+    - title: Configuration changes
+      labels:
+        - config
+    - title: Changes to the documentation
+      labels:
+        - documentation
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -37,7 +37,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.0
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -16,7 +16,7 @@ jobs:
       TAG_PREFIX: ${{ steps.tag_name.outputs.TAG_PREFIX }}
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4.1.7
+        uses: actions/checkout@v4.2.0
 
       - name: Get tag name
         id: tag_name
@@ -47,7 +47,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4.1.7
+        uses: actions/checkout@v4.2.0
 
       - name: Log into the Dockerhub registry
         run: echo ${{ secrets.DOCKERHUB_TOKEN }} | docker login -u ${{ secrets.DOCKERHUB_USERNAME }} --password-stdin

diff --git a/.github/workflows/docker_ghcr.yml b/.github/workflows/docker_ghcr.yml
@@ -30,7 +30,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4.1.7
+        uses: actions/checkout@v4.2.0
 
       - name: Log in to the Container registry
         uses: docker/login-action@v3

diff --git a/.github/workflows/ossar-analysis.yml b/.github/workflows/ossar-analysis.yml
@@ -21,7 +21,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.0
 
     # 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.

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -22,7 +22,7 @@ jobs:
         rm -R /home/mambauser/cashocs
 
     - name: Checkout repository
-      uses: actions/checkout@v4.1.7 
+      uses: actions/checkout@v4.2.0 
 
     - name: Install cashocs
       shell: bash
@@ -45,7 +45,7 @@ jobs:
     steps:
 
     - name: Checkout repository
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.0
 
 
     - name: Get tag name
@@ -80,7 +80,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.0
 
     - name: Set up Python 3.11
       uses: actions/setup-python@v5

diff --git a/.github/workflows/test_demos.yml b/.github/workflows/test_demos.yml
@@ -17,7 +17,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.0
 
     - name: Install micromamba
       uses: mamba-org/setup-micromamba@v1
@@ -55,7 +55,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.0
 
     - name: Install micromamba
       uses: mamba-org/setup-micromamba@v1

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -27,7 +27,7 @@ jobs:
         rm -R /home/mambauser/cashocs
 
     - name: Checkout repository
-      uses: actions/checkout@v4.1.7 
+      uses: actions/checkout@v4.2.0 
 
     - name: Install cashocs
       shell: bash

diff --git a/.github/workflows/tests_macos.yml b/.github/workflows/tests_macos.yml
@@ -20,7 +20,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.0
 
     - name: Install micromamba
       uses: mamba-org/setup-micromamba@v1

diff --git a/.github/workflows/tests_parallel.yml b/.github/workflows/tests_parallel.yml
@@ -24,7 +24,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.0
 
     - name: Install micromamba
       uses: mamba-org/setup-micromamba@v1

diff --git a/.github/workflows/tests_serial.yml b/.github/workflows/tests_serial.yml
@@ -21,7 +21,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.0
 
     - name: Install micromamba
       uses: mamba-org/setup-micromamba@v1

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ repos:
     hooks:
       - id: pyroma
   - repo: https://github.com/psf/black
-    rev: 24.4.2
+    rev: 24.8.0
     hooks:
       - id: black
   - repo: https://github.com/PyCQA/isort
@@ -21,7 +21,7 @@ repos:
         additional_dependencies: ["tomli"]
         files: cashocs/
   - repo: https://github.com/PyCQA/flake8
-    rev: 7.1.0
+    rev: 7.1.1
     hooks:
       - id: flake8
         files: cashocs/
@@ -31,12 +31,12 @@ repos:
       - id: bandit
         files: cashocs/
   - repo: https://github.com/PyCQA/pylint
-    rev: v3.2.5
+    rev: v3.2.7
     hooks:
       - id: pylint
         files: cashocs/
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.1
+    rev: v1.11.2
     hooks:
       - id: mypy
         files: cashocs/

diff --git a/.zenodo.json b/.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 v2.2.0-dev",
-    "version": "v2.2.0-dev",
+    "title": "cashocs v2.3.0-dev",
+    "version": "v2.3.0-dev",
     "upload_type": "software", 
     "creators": [
         {

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -6,18 +6,19 @@ here as they add new functionality or might change the API. For a documentation
 of the maintenance releases, please take a look at
 `<https://github.com/sblauth/cashocs/releases>`_.
 
-
-2.2.0 (in development)
+2.3.0 (in development)
 ----------------------
 
+
+2.2.0 (August 28, 2024)
+-----------------------
+
 * 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
@@ -28,10 +29,6 @@ of the maintenance releases, please take a look at
 
     * :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)

diff --git a/cashocs/__init__.py b/cashocs/__init__.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2024 Sebastian Blauth
+# Copyright (C) 2020-2024 Fraunhofer ITWM and Sebastian Blauth
 #
 # This file is part of cashocs.
 #
@@ -60,7 +60,7 @@
 from cashocs.nonlinear_solvers import picard_iteration
 from cashocs.nonlinear_solvers import snes_solve
 
-__version__ = "2.2.0-dev"
+__version__ = "2.3.0-dev"
 
 __citation__ = """
 @Article{Blauth2021cashocs,

diff --git a/cashocs/_cli/__init__.py b/cashocs/_cli/__init__.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2024 Sebastian Blauth
+# Copyright (C) 2020-2024 Fraunhofer ITWM and Sebastian Blauth
 #
 # This file is part of cashocs.
 #

diff --git a/cashocs/_cli/_convert.py b/cashocs/_cli/_convert.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (C) 2020-2024 Sebastian Blauth
+# Copyright (C) 2020-2024 Fraunhofer ITWM and Sebastian Blauth
 #
 # This file is part of cashocs.
 #

diff --git a/cashocs/_cli/_extract_mesh.py b/cashocs/_cli/_extract_mesh.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# Copyright (C) 2020-2024 Sebastian Blauth
+# Copyright (C) 2020-2024 Fraunhofer ITWM and Sebastian Blauth
 #
 # This file is part of cashocs.
 #

diff --git a/cashocs/_constraints/__init__.py b/cashocs/_constraints/__init__.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2024 Sebastian Blauth
+# Copyright (C) 2020-2024 Fraunhofer ITWM and Sebastian Blauth
 #
 # This file is part of cashocs.
 #

diff --git a/cashocs/_constraints/constrained_problems.py b/cashocs/_constraints/constrained_problems.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2024 Sebastian Blauth
+# Copyright (C) 2020-2024 Fraunhofer ITWM and Sebastian Blauth
 #
 # This file is part of cashocs.
 #

diff --git a/cashocs/_constraints/constraints.py b/cashocs/_constraints/constraints.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2024 Sebastian Blauth
+# Copyright (C) 2020-2024 Fraunhofer ITWM and Sebastian Blauth
 #
 # This file is part of cashocs.
 #

diff --git a/cashocs/_constraints/solvers.py b/cashocs/_constraints/solvers.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2024 Sebastian Blauth
+# Copyright (C) 2020-2024 Fraunhofer ITWM and Sebastian Blauth
 #
 # This file is part of cashocs.
 #

diff --git a/cashocs/_database/__init__.py b/cashocs/_database/__init__.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2024 Sebastian Blauth
+# Copyright (C) 2020-2024 Fraunhofer ITWM and Sebastian Blauth
 #
 # This file is part of cashocs.
 #

diff --git a/cashocs/_database/database.py b/cashocs/_database/database.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2024 Sebastian Blauth
+# Copyright (C) 2020-2024 Fraunhofer ITWM and Sebastian Blauth
 #
 # This file is part of cashocs.
 #