Merge branch 'dev/inequality_constraints' into curvature

sblauth · Feb 6, 2024 · da53216 · da53216
2 parents f1fd658 + 0133295
commit da53216
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diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -41,7 +41,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         config-file: ./.github/codeql/codeql-config.yml
@@ -53,7 +53,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      uses: github/codeql-action/autobuild@v3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 https://git.io/JvXDl
@@ -67,4 +67,4 @@ jobs:
     #   make release
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3
diff --git a/.github/workflows/ossar-analysis.yml b/.github/workflows/ossar-analysis.yml
@@ -40,6 +40,6 @@ jobs:
 
       # Upload results to the Security tab
     - name: Upload OSSAR results
-      uses: github/codeql-action/upload-sarif@v2
+      uses: github/codeql-action/upload-sarif@v3
       with:
         sarif_file: ${{ steps.ossar.outputs.sarifFile }}
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -56,7 +56,7 @@ jobs:
 
     - name: Check if release is a pre-release
       id: check_version
-      uses: nowsprinting/check-version-format-action@v3
+      uses: nowsprinting/check-version-format-action@v4
       with:
         prefix: 'v'
 

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -47,6 +47,7 @@ jobs:
         files: coverage.xml
 
     - name: Upload coverage to codacy
+      continue-on-error: true
       uses: codacy/codacy-coverage-reporter-action@v1
       with:
         project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,13 +7,13 @@ repos:
 
 
   - repo: https://github.com/psf/black
-    rev: 23.11.0
+    rev: 24.1.1
     hooks:
       - id: black
 
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
 
@@ -27,28 +27,28 @@ repos:
 
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
       - id: flake8
         files: cashocs/
 
 
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.7.5
+    rev: 1.7.7
     hooks:
       - id: bandit
         files: cashocs/
 
 
   - repo: https://github.com/PyCQA/pylint
-    rev: v3.0.1
+    rev: v3.0.3
     hooks:
       - id: pylint
         files: cashocs/
 
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.7.1
+    rev: v1.8.0
     hooks:
       - id: mypy
         files: cashocs/

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -8,8 +8,10 @@ build:
 sphinx:
   configuration: docs/source/conf.py
   builder: dirhtml
+  fail_on_warning: true
 
-formats: all
+formats:
+  - pdf
 
 python:
   install:

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 v2.1.0-dev",
-    "version": "v2.1.0-dev",
+    "title": "cashocs v2.2.0-dev",
+    "version": "v2.2.0-dev",
     "upload_type": "software", 
     "creators": [
         {

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -7,11 +7,28 @@ of the maintenance releases, please take a look at
 `<https://github.com/sblauth/cashocs/releases>`_.
 
 
-2.1.0 (in development)
+2..0 (in development)
 ----------------------
 
 * Add mesh quality constraints for shape optimization: These ensure that the angles of the triangles / dihedral angles of tetrahedrons cannot fall below a specified threshold.
 
+* New configuration file parameters:
+
+  * 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
+
+
+
+2.1.0 (February 6, 2024)
+------------------------
+
+* The class :py:class:`cashocs.DeformationHandler` cannot be used anymore. Instead, use the class by calling :py:class:`cashocs.geometry.DeformationHandler`. 
+
 * Add the keyword arguments :python:`pre_callback` and :python:`post_callback` to define callbacks when an optimization problem is instanciated.
 
 * Callbacks can now have one parameter - the parameter supplied when being called during runtime is the optimization problem itself
@@ -28,6 +45,12 @@ of the maintenance releases, please take a look at
 
 * :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`.
 
+* Add the kwargs `linear_solver` and (where applicable) `adjoint_linear_solver`. These can be used to define custom python KSP objects via petsc4py, most importantly, custom python-based preconditioners can be used with these. The feature is covered in the undocumented demo "demos/shape_optimization/python_pc".
+
+* Add the kwarg `newton_linearization` to the optimization problem classes. This can be used to specify which (alternative) linearization techniques can be used for solving the nonlinear state systems.
+
+* The function :py:func:`cashocs.newton_solve` does not change the user-specified tolerance (in the ksp_options) anymore, unless the kwarg `inexact=True` is set. This means, that the user can use custom "inexact Newton" schemes (e.g., gain one digit in accuracy) too. The old default was to use the relative tolerance of the nonlinear iteration multiplied with a safety factor (0.1).
+
 * New configuration file parameters:
 
   * Section LineSearch
@@ -42,13 +65,6 @@ of the maintenance releases, please take a look at
 
     * :ini:`remesh_iter` is used to perform a remeshing after a certain amount of iterations.
 
-  * 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
 
 
 2.0.0 (May 16, 2023)

diff --git a/README.rst b/README.rst
@@ -202,7 +202,7 @@ for the demo programs is located inside the "demos" folder.
 Citing
 ======
 
-If you use cashocs for your research, please cite the following paper
+If you use cashocs for your research, please cite the following papers
 
 .. code-block:: text
 
@@ -211,13 +211,14 @@ If you use cashocs for your research, please cite the following paper
 	SoftwareX, Volume 13, 2021
 	https://doi.org/10.1016/j.softx.2020.100646
 
-as well as the preprint
+as well as
 
 .. code-block:: text
 
 	Version 2.0 - cashocs: A Computational, Adjoint-Based Shape Optimization and Optimal Control Software
 	Sebastian Blauth
-	https://doi.org/10.48550/arXiv.2306.09828
+	SoftwareX, Volume 24, 2023
+	https://doi.org/10.1016/j.softx.2023.101577
 
 
 Additionally, if you are using the nonlinear conjugate gradient methods for shape optimization implemented in cashocs, please cite the following paper
@@ -266,13 +267,16 @@ If you are using BibTeX, you can use the following entries
 
 .. code-block:: bibtex
 
-	@Misc{Blauth2023Version,
-	  author        = {Sebastian Blauth},
-	  title         = {{Version 2.0 -- cashocs: A Computational, Adjoint-Based Shape Optimization and Optimal Control Software}},
-	  year          = {2023},
-	  archiveprefix = {arXiv},
-	  eprint        = {2306.09828},
-	  primaryclass  = {math.OC},
+	@Article{Blauth2023Version,
+	  author   = {Sebastian Blauth},
+	  journal  = {SoftwareX},
+	  title    = {{Version 2.0 - cashocs: A Computational, Adjoint-Based Shape Optimization and Optimal Control Software}},
+	  year     = {2023},
+	  issn     = {2352-7110},
+	  pages    = {101577},
+	  volume   = {24},
+	  doi      = {https://doi.org/10.1016/j.softx.2023.101577},
+	  keywords = {PDE constrained optimization, Shape optimization, Topology optimization, Space mapping},
 	}
 
 
@@ -281,7 +285,7 @@ If you are using BibTeX, you can use the following entries
 	@Article{Blauth2021Nonlinear,
 	  author   = {Sebastian Blauth},
 	  journal  = {SIAM J. Optim.},
-	  title    = {{N}onlinear {C}onjugate {G}radient {M}ethods for {PDE} {C}onstrained {S}hape {O}ptimization {B}ased on {S}teklov-{P}oincaré-{T}ype {M}etrics},
+	  title    = {{Nonlinear Conjugate Gradient Methods for PDE Constrained Shape Optimization Based on Steklov-Poincaré-Type Metrics}},
 	  year     = {2021},
 	  number   = {3},
 	  pages    = {1658--1689},
@@ -296,7 +300,7 @@ If you are using BibTeX, you can use the following entries
 	@Article{Blauth2023Space,
 	  author   = {Blauth, Sebastian},
 	  journal  = {SIAM J. Optim.},
-	  title    = {Space {M}apping for {PDE} {C}onstrained {S}hape {O}ptimization},
+	  title    = {{Space Mapping for PDE Constrained Shape Optimization}},
 	  year     = {2023},
 	  issn     = {1052-6234,1095-7189},
 	  number   = {3},
@@ -314,7 +318,7 @@ If you are using BibTeX, you can use the following entries
 	@Article{Blauth2023Quasi,
 	  author   = {Blauth, Sebastian and Sturm, Kevin},
 	  journal  = {Struct. Multidiscip. Optim.},
-	  title    = {Quasi-{N}ewton methods for topology optimization using a level-set method},
+	  title    = {{Quasi-Newton methods for topology optimization using a level-set method}},
 	  year     = {2023},
 	  issn     = {1615-147X,1615-1488},
 	  number   = {9},

diff --git a/cashocs/__init__.py b/cashocs/__init__.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 Sebastian Blauth
 #
 # This file is part of cashocs.
 #
@@ -49,7 +49,6 @@
 from cashocs._utils import interpolate_levelset_function_to_cells
 from cashocs._utils import Interpolator
 from cashocs.geometry import compute_mesh_quality
-from cashocs.geometry import DeformationHandler
 from cashocs.geometry import interval_mesh
 from cashocs.geometry import regular_box_mesh
 from cashocs.geometry import regular_mesh
@@ -60,7 +59,7 @@
 from cashocs.nonlinear_solvers import newton_solve
 from cashocs.nonlinear_solvers import picard_iteration
 
-__version__ = "2.1.0-dev"
+__version__ = "2.2.0-dev"
 
 __citation__ = """
 @Article{Blauth2021cashocs,
@@ -132,7 +131,6 @@
     "LogLevel",
     "regular_mesh",
     "regular_box_mesh",
-    "DeformationHandler",
     "compute_mesh_quality",
     "newton_solve",
     "picard_iteration",

diff --git a/cashocs/_cli/__init__.py b/cashocs/_cli/__init__.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 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) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 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) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 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) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 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) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 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) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 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) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 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) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 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) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 Sebastian Blauth
 #
 # This file is part of cashocs.
 #

diff --git a/cashocs/_database/form_database.py b/cashocs/_database/form_database.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 Sebastian Blauth
 #
 # This file is part of cashocs.
 #

diff --git a/cashocs/_database/function_database.py b/cashocs/_database/function_database.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 Sebastian Blauth
 #
 # This file is part of cashocs.
 #

diff --git a/cashocs/_database/geometry_database.py b/cashocs/_database/geometry_database.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 Sebastian Blauth
 #
 # This file is part of cashocs.
 #

diff --git a/cashocs/_database/parameter_database.py b/cashocs/_database/parameter_database.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 Sebastian Blauth
 #
 # This file is part of cashocs.
 #

diff --git a/cashocs/_exceptions.py b/cashocs/_exceptions.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 Sebastian Blauth
 #
 # This file is part of cashocs.
 #

diff --git a/cashocs/_forms/__init__.py b/cashocs/_forms/__init__.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 Sebastian Blauth
 #
 # This file is part of cashocs.
 #

diff --git a/cashocs/_forms/control_form_handler.py b/cashocs/_forms/control_form_handler.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 Sebastian Blauth
 #
 # This file is part of cashocs.
 #

diff --git a/cashocs/_forms/form_handler.py b/cashocs/_forms/form_handler.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 Sebastian Blauth
 #
 # This file is part of cashocs.
 #

diff --git a/cashocs/_forms/general_form_handler.py b/cashocs/_forms/general_form_handler.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2020-2023 Sebastian Blauth
+# Copyright (C) 2020-2024 Sebastian Blauth
 #
 # This file is part of cashocs.
 #