cashocs v2.1.0

What's Changed

• Bump jupytext from 1.14.5 to 1.14.6 by @dependabot in #243
• Fix a bug when computing the transfer matrix with remeshing by @sblauth in #244
• Add configuration file parameter [LineSearch][fail_if_not_converged] by @sblauth in #245
• Fix for computing the global deformation function by @sblauth in #246
• Add keyword arguments pre_callback and post_callback to optimization problems by @sblauth in #248
• Hotfix/2.0.4 - Add preconditioner forms to topology optimization by @sblauth in #249
• Fix an issue with the fail_if_not_converged parameter by @sblauth in #250
• Bump actions/checkout from 3.5.2 to 3.5.3 by @dependabot in #251
• Fix a bug in the Newton solver with MPI by @sblauth in #252
• Fix PETSc version to <= 3.17.4 as a temporary workaround by @sblauth in #257
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #255
• Update from provision-with-micromamba to setup-micromamba by @sblauth in #256
• Bump jupytext from 1.14.6 to 1.14.7 by @dependabot in #260
• Hotfix/2.0.7 by @sblauth in #261
• Change np.alltrue to np.all by @sblauth in #262
• Bump myst-parser from 1.0.0 to 2.0.0 by @dependabot in #254
• Use a different criterion for the BFGS curvature test by @sblauth in #263
• Hotfix/2.0.8 by @sblauth in #265
• Add configuration parameter "remesh_iter" to Section "MeshQuality" by @sblauth in #267
• Hotfix/2.0.9 by @sblauth in #269
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #270
• Bump sphinx-design from 0.4.1 to 0.5.0 by @dependabot in #273
• Bump jupytext from 1.14.7 to 1.15.0 by @dependabot in #272
• Bump sphinx from 6.2.1 to 7.1.1 by @dependabot in #274
• Bump docutils from 0.19 to 0.20.1 by @dependabot in #238
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #275
• Move to mambaorg/micromamba as docker base image for CI by @sblauth in #276
• Add new function cashocs.io.extract_mesh_from_xdmf and corresponding CLI by @sblauth in #277
• Fix extract_mesh_from_xdmf so that it can also be run in parallel by @sblauth in #278
• Bump sphinx from 7.1.1 to 7.1.2 by @dependabot in #279
• Add the option to extract more sophisticated meshes when using Gmsh by @sblauth in #282
• Raises a warning if remeshing fails due to wrong Gmsh file by @sblauth in #283
• Add the possibility for checkpointing by @sblauth in #286
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #287
• Bump sphinx from 7.1.2 to 7.2.2 by @dependabot in #289
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #291
• Bump sphinx from 7.2.2 to 7.2.3 by @dependabot in #292
• Hotfix/2.0.10 by @sblauth in #294
• Bump actions/checkout from 3.5.3 to 3.6.0 by @dependabot in #295
• Bump sphinx from 7.2.3 to 7.2.4 by @dependabot in #296
• Bump jupytext from 1.15.0 to 1.15.1 by @dependabot in #297
• Bump sphinx from 7.2.4 to 7.2.5 by @dependabot in #298
• Bump actions/checkout from 3.6.0 to 4.0.0 by @dependabot in #300
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #302
• Bump docker/login-action from 2 to 3 by @dependabot in #305
• Bump docker/build-push-action from 4 to 5 by @dependabot in #304
• Bump docker/metadata-action from 4 to 5 by @dependabot in #303
• Hotfix/2.0.11 by @sblauth in #309
• Bump sphinx from 7.2.5 to 7.2.6 by @dependabot in #310
• Bump pydata-sphinx-theme from 0.13.3 to 0.14.0 by @dependabot in #313
• Bump jupytext from 1.15.1 to 1.15.2 by @dependabot in #312
• Add version warning banners and (more) colors to the docs by @sblauth in #314
• Bump pydata-sphinx-theme from 0.14.0 to 0.14.1 by @dependabot in #315
• Bump actions/checkout from 4.0.0 to 4.1.0 by @dependabot in #317
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #318
• FIX: Pin PETSc to <= 3.19. DOCS: Add tutorials for topology optimization problems by @sblauth in #323
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #319
• CI: Remove occt pin, update pins for meshio and pytest by @sblauth in #326
• FIX: Fix the bugs in the parallel demos by @sblauth in #329
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #330
• Pin mpi4py to versions <= 3.1.4 by @sblauth in #338
• Bump actions/checkout from 4.1.0 to 4.1.1 by @dependabot in #332
• FEAT: Improve the visualization of the shape in topology optimization by @sblauth in #339
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #335
• FEAT: Json output is now nicer to read for humans by @sblauth in #331
• FEAT: Adds the possibility of passing an argument to callback functions by @sblauth in #328
• FIX: Fixes a bug where the mesh files were not written properly by @sblauth in #340
• Bump pydata-sphinx-theme from 0.14.1 to 0.14.2 by @dependabot in #341
• Remove the pin on mpi4py by @sblauth in #342
• [Snyk] Fix for 4 vulnerabilities by @sblauth in #345
• Bump pydata-sphinx-theme from 0.14.2 to 0.14.3 by @dependabot in #347
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #346
• Add a config file parameter "global_deformation" for the deformation by @sblauth in #348
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #349
• Bump pydata-sphinx-theme from 0.14.3 to 0.14.4 by @dependabot in #352
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #351
• Rename APosterioriTester to IntersectionTester and add a config parameter by @sblauth in #355
• Bump jupytext from 1.15.2 to 1.16.0 by @dependabot in #357
• Fix a bug when computing the mesh quality in parallel by @sblauth in #360
• Bump actions/setup-python from 4 to 5 by @dependabot in #362
• [Snyk] Security upgrade numpy from 1.21.3 to 1.22.2 by @sblauth in #361
• CI: Improve and update GitHub actions workflows by @sblauth in #363
• Add compatibility for ufl 2023 and ufl_legacy by @sblauth in #364
• Fix two bugs regarding the remeshing in cashocs by @sblauth in #365
• Fix the docs at demos/documented/misc/xdmf_io/demo_xdmf_io by @sblauth in #366
• Add the parameter "inhomogeneous_exponent" to the Section ShapeGradient by @sblauth in #367
• FIX: Change the way the temporary files are deleted when remeshing by @sblauth in #368
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #369
• Bump github/codeql-action from 2 to 3 by @dependabot in #370
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #371
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #373
• [Snyk] Security upgrade fonttools from 4.38.0 to 4.43.0 by @sblauth in #372
• Fix broken autodoc handling of docs by @sblauth in #374
• Bump pydata-sphinx-theme from 0.14.4 to 0.15.1 by @dependabot in #375
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #376
• Bump jupytext from 1.16.0 to 1.16.1 by @dependabot in #378
• Bump pydata-sphinx-theme from 0.15.1 to 0.15.2 by @dependabot in #379
• FEAT: Add the kwargs linear_solver and adjoint_linear_solver by @sblauth in #380
• Bump nowsprinting/check-version-format-action from 3 to 4 by @dependabot in #382
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #381
• Bump meshio from 5.3.4 to 5.3.5 by @dependabot in #383
• Hotfix/2.0.14 by @sblauth in #386
• Prevent upload to codacy action blocking PRs from forks by @sblauth in #387
• Add the kwarg newton_linearization to the optimization problems by @sblauth in #390
• Add the possibility to specify the preconditioner form as bilinear form in Newton's method by @sblauth in #392
• ENH: Newton's method now uses the user-specified relative tolerance by @sblauth in #393

Full Changelog: v2.0.14...v2.1.0