Merge branch 'main' into hotfix/2.0.10

.github/dependabot.yml

@@ -8,11 +8,15 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      interval: "weekly"
+      interval: "daily"
+      time: "06:00"
+      timezone: Europe/Berlin
 
   - package-ecosystem: "pip"
     directory: "/"
     schedule:
-      interval: "weekly"
+      interval: "daily"
+      time: "06:00"
+      timezone: Europe/Berlin
     allow:
       - dependency-type: "all"

.github/workflows/codeql-analysis.yml

@@ -37,7 +37,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3.5.2
+      uses: actions/checkout@v3.5.3
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL

.github/workflows/docker_ghcr.yml

@@ -30,7 +30,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3.5.2
+        uses: actions/checkout@v3.5.3
 
       - name: Log in to the Container registry
         uses: docker/login-action@v2

.github/workflows/ossar-analysis.yml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3.5.2
+      uses: actions/checkout@v3.5.3
 
     # 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@v3.5.2 
+      uses: actions/checkout@v3.5.3 
 
     - name: Install cashocs
       shell: bash
@@ -45,7 +45,7 @@ jobs:
     steps:
 
     - name: Checkout repository
-      uses: actions/checkout@v3.5.2
+      uses: actions/checkout@v3.5.3
 
 
     - name: Get tag name
@@ -78,7 +78,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3.5.2
+      uses: actions/checkout@v3.5.3
 
     - name: Set up Python 3.11
       uses: actions/setup-python@v4

.github/workflows/test_demos.yml

@@ -17,18 +17,18 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3.5.2
+      uses: actions/checkout@v3.5.3
 
     - name: Install micromamba
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
         environment-file: .github/micromamba/testenv.yml
-        extra-specs: |
+        create-args: >-
           fenics=2019
-          meshio">=5.0.0"
-          pytest">=7.0.0"
-          gmsh">=4.8"
-          occt"<=7.7.0"
+          meshio>=5.0.0
+          pytest>=7.0.0
+          gmsh>=4.8
+          occt<=7.7.0
           matplotlib
           python=3.11
 
@@ -55,18 +55,18 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3.5.2
+      uses: actions/checkout@v3.5.3
 
     - name: Install micromamba
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
         environment-file: .github/micromamba/testenv.yml
-        extra-specs: |
+        create-args: >-
           fenics=2019
-          meshio">=5.0.0"
-          pytest">=7.0.0"
-          gmsh">=4.8"
-          occt"<=7.7.0"
+          meshio>=5.0.0
+          pytest>=7.0.0
+          gmsh>=4.8
+          occt<=7.7.0
           mpich
           matplotlib
           python=3.11

.github/workflows/tests_macos.yml

@@ -20,19 +20,19 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3.5.2
+      uses: actions/checkout@v3.5.3
 
     - name: Install micromamba
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
         environment-file: .github/micromamba/testenv.yml
-        extra-specs: |
+        create-args: >-
           python=${{ matrix.python-version }}
           fenics=2019
-          meshio">=5.0.0"
-          pytest">=7.0.0"
-          gmsh">=4.8"
-          occt"<=7.7.0"
+          meshio>=5.0.0
+          pytest>=7.0.0
+          gmsh>=4.8
+          occt<=7.7.0
 
     - name: Install package
       run: |

.github/workflows/tests_parallel.yml

@@ -24,18 +24,18 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3.5.2
+      uses: actions/checkout@v3.5.3
 
     - name: Install micromamba
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
         environment-file: .github/micromamba/testenv.yml
-        extra-specs: |
+        create-args: >-
           fenics=2019
-          meshio">=5.0.0"
-          pytest">=7.0.0"
-          gmsh">=4.8"
-          occt"<=7.7.0"
+          meshio>=5.0.0
+          pytest>=7.0.0
+          gmsh>=4.8
+          occt<=7.7.0
           ${{ matrix.mpi }}
           python=${{ matrix.python-version }}
 

.github/workflows/tests_serial.yml

@@ -21,18 +21,18 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3.5.2
+      uses: actions/checkout@v3.5.3
 
     - name: Install micromamba
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
         environment-file: .github/micromamba/testenv.yml
-        extra-specs: |
+        create-args: >-
           fenics=2019
-          meshio">=5.0.0"
-          pytest">=7.0.0"
-          gmsh">=4.8"
-          occt"<=7.7.0"
+          meshio>=5.0.0
+          pytest>=7.0.0
+          gmsh>=4.8
+          occt<=7.7.0
           python=${{ matrix.python-version }}
 
     - name: Install package

.gitignore

@@ -12,6 +12,7 @@ htmlcov
 *.vtu
 *.pvtu
 
+**/checkpoints/
 **/xdmf/
 
 ### pip

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
       - id: pyroma
 
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.7.0
     hooks:
       - id: black
 
@@ -26,7 +26,7 @@ repos:
 
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+    rev: 6.1.0
     hooks:
       - id: flake8
         files: cashocs/
@@ -40,14 +40,14 @@ repos:
 
 
   - repo: https://github.com/PyCQA/pylint
-    rev: v3.0.0a6
+    rev: v3.0.0a7
     hooks:
       - id: pylint
         files: cashocs/
 
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.3.0
+    rev: v1.5.1
     hooks:
       - id: mypy
         files: cashocs/

.pylintrc

@@ -64,6 +64,7 @@ disable=abstract-method,
         cmp-method,
         coerce-builtin,
         coerce-method,
+        cyclic-import,
         delslice-method,
         div-method,
         duplicate-code,

.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 v2.0.10",
-    "version": "v2.0.10",
+    "title": "cashocs v2.1.0-dev",
+    "version": "v2.1.0-dev",
     "upload_type": "software", 
     "creators": [
         {

CHANGELOG.rst

@@ -7,6 +7,35 @@ of the maintenance releases, please take a look at
 `<https://github.com/sblauth/cashocs/releases>`_.
 
 
+2.1.0 (in development)
+----------------------
+
+* Add the keyword arguments :python:`pre_callback` and :python:`post_callback` to define callbacks when an optimization problem is instanciated.
+
+* Add a new function :py:func:`cashocs.io.extract_mesh_from_xdmf` which extracts (any, not only Gmsh) meshes from some XDMF state file (e.g. written by cashocs) and saves the underlying mesh in Gmsh file format.
+
+* Add a new command line interface :bash:`cashocs-extract_mesh` which can be used to invoke :py:func:`cashocs.io.extract_mesh_from_xdmf`.
+
+* The output routines save the xdmf files not in a folder called `xdmf` anymore, but the folder is called `checkpoints`
+
+* The output parameter `save_mesh` does now not only save the optimized mesh, but also writes a Gmsh .msh file of the current iterated mesh for each iteration. This is very useful for restarting simulations.
+
+* Added the function :py:func:`cashocs.io.import_function` which can be used to load a XDMF Function with a function space. This is very useful for checkpointing (first, read the saved mesh, define the function space, then call :py:func:`cashocs.io.import_function`.
+
+* :py:func:`cashocs.import_mesh` can now also directly import a Gmsh mesh file. Internally, the mesh is directly converted to xdmf and then read. At the moment, this only supports the conversion mode `physical`.
+
+* New configuration file parameters:
+
+  * Section LineSearch
+
+    * :ini:`fail_if_not_converged` determines, whether the line search is cancelled once the state system cannot be solved or if a new iterate is tried instead.
+
+  * Section MeshQuality
+
+    * :ini:`remesh_iter` is used to perform a remeshing after a certain amount of iterations.
+
+
+
 2.0.0 (May 16, 2023)
 --------------------