v0.8.0 (#166)

* Improve workflow handling (#118)

* Create common action for all workflows and split them into multiple files

* Dokken/update fspace and wmtgs (#127)

* fix runs-on

* Minor improvements in linearelasticity.md (#124)

* Fix various things on release branch

* Try adding trame

* Revert fundamentals

* Membrane code

* More updates due to autoformatting

* Lagrange -> CG back conversion

* Change to github image

---------

Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com>

* Update petsc arches

* Fix bounding boxes and more (#135)

* Start fixing code for nightly build

* rerun all files

* Try fixing subdomains

* Fix meshio

* PETSc python API update (#137)

* Resolve #136

* Fixes related to: FEniCS/dolfinx#2703

* Update changelog

* Make sure all notebooks run. Change to pathlib in some examples

* Api changes related to: FEniCS/dolfinx#2763 (#142)

* Bump version numbers

* Bump version numbers (#149)

* Fix petsc arch

* Prepare v0.7.1 (#154)

* Merge branch 'main' into release and bump versions

* Delete obsolete file

* Temporary shift path in nightly test

* Make sure there are no warnigns in build

* Tabulation

* Updates compatible with nightly branch of DOLFINx (#156)

* Replace VectorElement and FiniteElement with `basix.ufl.element`.
Replace `dolfinx.fem.FunctionSpace` with `dolfinx.fem.functionspace`

* More updates

* And more

* Last vector element updates

* Bump pyvista and dolfinx to v0.7.2 (#159)

* Bump pyvista and dolfinx to v0.7.2

* remove -r

* Add further pyvista deps

* Bump versions

* Update petsc solver and pc links. Resolves #143 (#160)

* Fix typo and issue Issue on page /fem.html #122 (#161)

* Compute entity-cell connectivity before calling locate_dofs_topological.
Remove soon to be deprecated pyvista syntax for updating time dependent fields.
Fix range->np.arange conversion

* Update backend in workflow

* Fix broken link (#140) + http:// to https:// (#162)

* Run book build prior to parallel run

* Add back write frame

* Fix wrong link

* Fix typo in changelog

* Merge main into release (#189)

* Merge main into release

* Apply suggestions from code review

* Various fixes when reading through the diff

* Further fixes

* add missing checkout (#191)

* add missing checkout

* Add test docker on release PR and release (only push on tag

* Remove unused import

---------

Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com>

Author: jorgensd

.github/workflows/book_stable.yml

@@ -4,8 +4,9 @@ on:
   workflow_dispatch:
   workflow_call:
   pull_request:
-    branches: ["main"]
-
+    branches: ["release"]
+  push:
+    branches: ["release"]
 env:
   HDF5_MPI: "ON"
   HDF5_DIR: "/usr/local/"
@@ -15,7 +16,7 @@ env:
 jobs:
   build-book:
     runs-on: ubuntu-latest
-    container: ghcr.io/fenics/dolfinx/lab:v0.7.3
+    container: ghcr.io/fenics/dolfinx/lab:v0.8.0
 
     env:
       PYVISTA_TRAME_SERVER_PROXY_PREFIX: "/proxy/"

.github/workflows/deploy.yml

@@ -3,7 +3,7 @@ name: Publish book
 on:
   push:
     branches:
-      - "main"
+      - "release"
   workflow_dispatch:
 
   # Weekly build on Mondays at 8 am
@@ -19,12 +19,6 @@ concurrency:
   group: "pages"
   cancel-in-progress: true
 
-env:
-  HDF5_MPI: "ON"
-  HDF5_DIR: "/usr/local/"
-  DISPLAY: ":99.0"
-  DEB_PYTHON_INSTALL_LAYOUT: deb_system
-
 jobs:
   run-tests:
     uses: ./.github/workflows/test_stable.yml

.github/workflows/publish_docker.yml

@@ -1,10 +1,13 @@
+name: Publish tutorial docker image
 on:
   push:
     branches:
-      - "!*"
+      - "release"
     tags:
       - "v*"
-
+  pull_request:
+    branches:
+      - "release"
   workflow_dispatch:
 
 env:
@@ -41,8 +44,22 @@ jobs:
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
 
-      - name: Build and push Docker image
+      - name: Build Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          load: true
+          push: false
+          file: docker/Dockerfile
+          platforms: linux/amd64
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+  
+
+
+      - name: Build (arm) and push (amd/arm) Docker image
         uses: docker/build-push-action@v5
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
         with:
           context: .
           push: true

.github/workflows/test_nightly.yml

@@ -4,11 +4,11 @@ name: Test release branch against DOLFINx nightly build
 on:
   pull_request:
     branches:
-      - release
+      - main
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
-
+  workflow_call:
   schedule:
     - cron: "0 9 * * *"
 
@@ -23,68 +23,67 @@ jobs:
       HDF5_MPI: "ON"
       PYVISTA_OFF_SCREEN: true
       DISPLAY: ":99.0"
-      PYVISTA_JUPYTER_BACKEND: panel
+      PYVISTA_JUPYTER_BACKEND: html
 
-    # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-      # Checkout release branch to work on schedule
-      - name: Checkout release branch
-        uses: actions/checkout@v4
-        if: ${{ github.event_name == 'schedule' }}
-        with:
-          ref: release
-
-      - name: Use current branch
-        uses: actions/checkout@v4
-        if: ${{ github.event_name != 'schedule' }}
+      - uses: actions/checkout@v4
 
       - name: Special handling of some installation
         uses: ./.github/actions/install-dependencies
 
       - name: Install requirements
         run: python3 -m pip install --no-cache-dir --no-binary=h5py . --upgrade
 
+      - name: Test building the book
+        run: PYVISTA_OFF_SCREEN=false jupyter-book build  -W .
+
       - name: Test complex notebooks in parallel
+        working-directory: chapter1
         run: |
           export PKG_CONFIG_PATH=/usr/local/dolfinx-complex/lib/pkgconfig:$PKG_CONFIG_PATH
           export PETSC_ARCH=linux-gnu-complex128-32
           export PYTHONPATH=/usr/local/dolfinx-complex/lib/python3.10/dist-packages:$PYTHONPATH
           export LD_LIBRARY_PATH=/usr/local/dolfinx-complex/lib:$LD_LIBRARY_PATH
-          cd chapter1
           python3 complex_mode.py
           mpirun -n 2 python3 complex_mode.py
 
-      - name: Test real notebooks in parallel
+      - name: Test chapter 1
+        working-directory: chapter1
         run: |
-          cd chapter1
-          python3 -c "from pyvista import start_xvfb; start_xvfb(0.1)"
-          mpirun -n 2 python3 fundamentals_code.py
-          mpirun -n 2 python3 nitsche.py
-          mpirun -n 2 python3 membrane_code.py
-          cd ../chapter2
+            python3 -c "from pyvista import start_xvfb; start_xvfb(0.1)"
+            mpirun -n 2 python3 fundamentals_code.py
+            mpirun -n 2 python3 nitsche.py
+            mpirun -n 2 python3 membrane_code.py
+
+      - name: Test chapter 2
+        working-directory: chapter2
+        run: |    
           mpirun -n 2 python3 diffusion_code.py
           mpirun -n 2 python3 heat_code.py
           mpirun -n 2 python3 linearelasticity_code.py
           mpirun -n 2 python3 hyperelasticity.py
           mpirun -n 2 python3 nonlinpoisson_code.py
           mpirun -n 2 python3 ns_code1.py
           mpirun -n 2 python3 ns_code2.py
-          cd ../chapter3
+       
+      - name: Test chapter 3
+        working-directory: chapter3
+        run: |
           mpirun -n 2 python3 neumann_dirichlet_code.py
           mpirun -n 2 python3 multiple_dirichlet.py
           mpirun -n 2 python3 subdomains.py
           mpirun -n 2 python3 robin_neumann_dirichlet.py
           mpirun -n 2 python3 component_bc.py
           mpirun -n 2 python3 em.py
-          cd ../chapter4
+  
+      - name: Test chapter 4
+        working-directory: chapter4
+        run: |
           mpirun -n 2 python3 solvers.py
           mpirun -n 2 python3 convergence.py
           mpirun -n 2 python3 compiler_parameters.py
           mpirun -n 2 python3 newton-solver.py
 
-      - name: Test building the book
-        run: PYVISTA_OFF_SCREEN=false jupyter-book build  -W .
-
       - uses: actions/upload-artifact@v4
         if: always()
         with:

.github/workflows/test_stable.yml

@@ -1,26 +1,20 @@
-name: Check that all python files run in parallel
+name: Test stable release
 
-# Controls when the action will run.
 on:
-  # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
   workflow_call:
   pull_request:
-    branches: ["main"]
+    branches: ["release"]
 env:
-  # Directory that will be published on github pages
   HDF5_MPI: "ON"
   HDF5_DIR: "/usr/local/"
   DISPLAY: ":99.0"
   DEB_PYTHON_INSTALL_LAYOUT: deb_system
 
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # This workflow contains a single job called "build"
   test:
-    # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: ghcr.io/fenics/dolfinx/lab:v0.7.2
+    container: ghcr.io/fenics/dolfinx/lab:v0.8.0
     env:
       PYVISTA_OFF_SCREEN: true
 
@@ -35,41 +29,51 @@ jobs:
           python3 -m pip install --no-binary=h5py .
 
       - name: Test complex notebooks in parallel
+        working-directory: chapter1
         run: |
           export PKG_CONFIG_PATH=/usr/local/dolfinx-complex/lib/pkgconfig:$PKG_CONFIG_PATH
           export PETSC_ARCH=linux-gnu-complex128-32
           export PYTHONPATH=/usr/local/dolfinx-complex/lib/python3.10/dist-packages:$PYTHONPATH
           export LD_LIBRARY_PATH=/usr/local/dolfinx-complex/lib:$LD_LIBRARY_PATH
-          python3 -c "from pyvista import start_xvfb; start_xvfb(0.1)"
-          cd chapter1
           python3 complex_mode.py
           mpirun -n 2 python3 complex_mode.py
-
-      - name: Test notebooks in parallel
+  
+      - name: Test chapter 1
+        working-directory: chapter1
         run: |
-          python3 -c "from pyvista import start_xvfb; start_xvfb(0.1)"
-          cd chapter1
-          mpirun -n 2 python3 fundamentals_code.py
-          mpirun -n 2 python3 membrane_code.py
-          cd ../chapter2
+            python3 -c "from pyvista import start_xvfb; start_xvfb(0.1)"
+            mpirun -n 2 python3 fundamentals_code.py
+            mpirun -n 2 python3 nitsche.py
+            mpirun -n 2 python3 membrane_code.py
+
+      - name: Test chapter 2
+        working-directory: chapter2
+        run: |    
           mpirun -n 2 python3 diffusion_code.py
           mpirun -n 2 python3 heat_code.py
           mpirun -n 2 python3 linearelasticity_code.py
           mpirun -n 2 python3 hyperelasticity.py
           mpirun -n 2 python3 nonlinpoisson_code.py
           mpirun -n 2 python3 ns_code1.py
           mpirun -n 2 python3 ns_code2.py
-          cd ../chapter3
+        
+      - name: Test chapter 3
+        working-directory: chapter3
+        run: |
           mpirun -n 2 python3 neumann_dirichlet_code.py
           mpirun -n 2 python3 multiple_dirichlet.py
           mpirun -n 2 python3 subdomains.py
           mpirun -n 2 python3 robin_neumann_dirichlet.py
           mpirun -n 2 python3 component_bc.py
           mpirun -n 2 python3 em.py
-          cd ../chapter4
+  
+      - name: Test chapter 4
+        working-directory: chapter4
+        run: |
           mpirun -n 2 python3 solvers.py
           mpirun -n 2 python3 convergence.py
           mpirun -n 2 python3 compiler_parameters.py
+          mpirun -n 2 python3 newton-solver.py
 
       - name: Upload Navier-Stokes DFG 2D 3 plots
         uses: actions/upload-artifact@v4

Changelog.md

@@ -1,12 +1,19 @@
 # Changelog
 
+## v0.8.0
+
+- Replace all `ufl.FiniteElement` and `ufl.VectorElement` with the appropriate `basix.ufl.element`
+- Replace `dolfinx.fem.FunctionSpace` with `dolfinx.fem.functionspace`
+
 ## v0.7.2
- - Change pyvista backend to `html`, using Pyvista main branch
- - Using DOLFINx v0.7.2 https://github.com/FEniCS/dolfinx/releases/tag/v0.7.2 as base
+
+- Change pyvista backend to `html`, using Pyvista main branch
+- Using DOLFINx v0.7.2 https://github.com/FEniCS/dolfinx/releases/tag/v0.7.2 as base
 
 ## v0.7.1
- - No API changes, release due to various bug-fixes from the 0.7.0 release, see:
-   https://github.com/FEniCS/dolfinx/releases/tag/v0.7.1 for more information
+
+- No API changes, release due to various bug-fixes from the 0.7.0 release, see:
+  https://github.com/FEniCS/dolfinx/releases/tag/v0.7.1 for more information
 
 ## v0.7.0
 
@@ -46,7 +53,7 @@
 - API updates wrt. DOLFINx. `Form`->`form`, `DirichletBC`->`dirichletbc`.
 - Updates on error computations in [Error control: Computing convergence rates](chapter4/convergence).
 - Added tutorial on interpolation of `ufl.Expression` in [Deflection of a membrane](chapter1/membrane_code).
-- Added tutorial on how to apply constant-valued Dirichet conditions in [Deflection of a membrane](chapter1/membrane_code).
+- Added tutorial on how to apply constant-valued Dirichlet conditions in [Deflection of a membrane](chapter1/membrane_code).
 - Various API changes relating to the import structure of DOLFINx
 
 ## 0.3.0 (09.09.2021)

chapter1/complex_mode.ipynb

@@ -11,7 +11,7 @@
     "\n",
     "Many PDEs, such as the [Helmholtz equation](https://docs.fenicsproject.org/dolfinx/v0.4.1/python/demos/demo_helmholtz.html) require complex-valued fields.\n",
     "\n",
-    "For simplicity, let us consider a Poisson equation of the form:\n",
+    "For simplicity, let us consider a Poisson equation of the form: \n",
     "\n",
     "$$-\\Delta u = f \\text{ in } \\Omega,$$\n",
     "$$ f = -1 - 2j \\text{ in } \\Omega,$$\n",
@@ -57,7 +57,7 @@
     "import dolfinx\n",
     "import numpy as np\n",
     "mesh = dolfinx.mesh.create_unit_square(MPI.COMM_WORLD, 10, 10)\n",
-    "V = dolfinx.fem.FunctionSpace(mesh, (\"Lagrange\", 1))\n",
+    "V = dolfinx.fem.functionspace(mesh, (\"Lagrange\", 1))\n",
     "u_r = dolfinx.fem.Function(V, dtype=np.float64) \n",
     "u_r.interpolate(lambda x: x[0])\n",
     "u_c = dolfinx.fem.Function(V, dtype=np.complex128)\n",
@@ -75,7 +75,7 @@
     "\n",
     "Unfortunately, PETSc only supports one floating type in their matrices, thus we need to install two versions of PETSc, one that supports `float64` and one that supports `complex128`. In the [docker images](https://hub.docker.com/r/dolfinx/dolfinx) for DOLFINx, both versions are installed, and one can switch between them by calling `source dolfinx-real-mode` or `source dolfinx-complex-mode`. For the `dolfinx/lab` images, one can change the Python kernel to be either the real or complex mode, by going to `Kernel->Change Kernel...` and choosing `Python3 (ipykernel)` (for real mode) or `Python3 (DOLFINx complex)` (for complex mode).\n",
     "\n",
-    "We check that we are using the correct installation of PETSc by inspecting the scalar type.\n"
+    "We check that we are using the correct installation of PETSc by inspecting the scalar type."
    ]
   },
   {
@@ -105,8 +105,7 @@
    "metadata": {},
    "source": [
     "## Variational problem\n",
-    "\n",
-    "We are now ready to define our variational problem\n"
+    "We are now ready to define our variational problem"
    ]
   },
   {
@@ -133,7 +132,7 @@
     "\n",
     "Secondly, note that we are using `ufl.inner` to describe multiplication of $f$ and $v$, even if they are scalar values. This is because `ufl.inner` takes the conjugate of the second argument, as decribed by the $L^2$ inner product. One could alternatively write this out explicitly\n",
     "\n",
-    "### Inner-products and derivatives\n"
+    "### Inner-products and derivatives"
    ]
   },
   {
@@ -252,8 +251,7 @@
    "metadata": {},
    "source": [
     "We define our Dirichlet condition and setup and solve the variational problem.\n",
-    "\n",
-    "## Solve variational problem\n"
+    "## Solve variational problem"
    ]
   },
   {