Merge remote-tracking branch 'origin/main' into release

Author: jorgensd

.github/workflows/deploy.yml

@@ -41,13 +41,13 @@ jobs:
         uses: actions/configure-pages@v5
 
       - name: Download docs artifact
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           name: webpage
           path: "./public"
 
       - name: Upload page artifact
-        uses: actions/upload-pages-artifact@v3
+        uses: actions/upload-pages-artifact@v4
         with:
           path: "./public"
 

.github/workflows/publish_docker.yml

@@ -85,7 +85,7 @@ jobs:
       - build
     steps:
       - name: Download digests
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           path: ${{ runner.temp }}/digests
           pattern: digests-*

Changelog.md

@@ -1,14 +1,23 @@
 # Changelog
 
+## v0.10.0
+
+- Full refactoring of {py:class}`dolfinx.fem.petsc.NonlinearProblem`, which now uses the PETSc SNES backend. See [the non-linear poisson demo](./chapter2/nonlinpoisson_code.ipynb) for details.
+- {py:class}`dolfinx.fem.petsc.LinearProblem` now requires an additional argument, `petsc_options_prefix`. This should be a unique string identifier for each `LinearProblem` that is created.
+- Change how one reads in GMSH data with `gmshio`. See [the membrane code](./chapter1/membrane_code.ipynb) for more details.
+- {py:meth}`dolfinx.fem.FiniteElement.interpolation_points` -> {py:attr}`dolfinx.fem.FiniteElement.interpolation_points`.
+- {py:mod}`dolfinx.io.gmshio` has been renamed to {py:mod}`dolfinx.io.gmsh`
+- Input to {py:func}`dolfinx.fem.petsc.create_vector` has changed. One should now call {py:func}`dolfinx.fem.extract_function_spaces` on the input form first.
+
 ## v0.9.0
 
-- `scale` in `apply_lifting` has been renamed to `alpha`
+- `scale` in {py:func}`apply_lifting<dolfinx.fem.petsc.apply_lifting>` has been renamed to `alpha`
 - Use `dolfinx.fem.Function.x.petsc_vec` as opposed to `dolfinx.fem.Function.vector`
 
 ## v0.8.0
 
-- Replace all `ufl.FiniteElement` and `ufl.VectorElement` with the appropriate `basix.ufl.element`
-- Replace `dolfinx.fem.FunctionSpace` with `dolfinx.fem.functionspace`
+- Replace all `ufl.FiniteElement` and `ufl.VectorElement` with the appropriate {py:func}`basix.ufl.element`
+- Replace {py:class}`dolfinx.fem.FunctionSpace` with {py:func}`dolfinx.fem.functionspace`
 
 ## v0.7.2
 
@@ -22,12 +31,13 @@
 
 ## v0.7.0
 
-- Renamed `dolfinx.graph.create_adjacencylist` to `dolfinx.graph.adjacencylist`
-- Renamed `dolfinx.plot.create_vtk_mesh` to `dolfinx.plot.vtk_mesh`
-- `dolfinx.geometry.BoundingBoxTree` has been changed to `dolfinx.geometry.bb_tree`
+- Renamed `dolfinx.graph.create_adjacencylist` to {py:func}`dolfinx.graph.adjacencylist`
+- Renamed `dolfinx.plot.create_vtk_mesh` to {py:func}`dolfinx.plot.vtk_mesh`
+- Initialization of {py:class}`dolfinx.geometry.BoundingBoxTree` has been changed to {py:func}`dolfinx.geometry.bb_tree`
 - `create_mesh` with Meshio has been modified. Note that you now need to pass dtype `np.int32` to the cell_data.
-- Update dolfinx petsc API. Now one needs to explicitly import `dolfinx.fem.petsc` and `dolfinx.fem.nls`, as PETSc is no longer a strict requirement. Replace `petsc4py.PETSc.ScalarType` with `dolfinx.default_scalar_type` in demos where we do not use `petsc4py` explicitly.
-
+- Update dolfinx petsc API. Now one needs to explicitly import {py:mod}`dolfinx.fem.petsc` and {py:mod}`dolfinx.fem.nls`, as PETSc is no longer a strict requirement.
+  Replace `petsc4py.PETSc.ScalarType` with `dolfinx.default_scalar_type` in demos where we do not use {py:mod}`petsc4py` explicitly.
+  
 ## v0.6.0
 
 - Remove `ipygany` and `pythreejs` as plotting backends. Using `panel`.
@@ -41,7 +51,8 @@
 
 - Using new GMSH interface in DOLFINx (`dolfinx.io.gmshio`) in all demos using GMSH
 - Added a section on custom Newton-solvers, see [chapter4/newton-solver].
-- Various minor DOLFINx API updates. `dolfinx.mesh.compute_boundary_facets` -> `dolfinx.mesh.exterior_facet_indices` with slightly different functionality. Use `dolfinx.mesh.MeshTagsMetaClass.find` instead of `mt.indices[mt.values==value]`.
+- Various minor DOLFINx API updates. `dolfinx.mesh.compute_boundary_facets` -> {py:func}`dolfinx.mesh.exterior_facet_indices` with slightly different functionality.
+  Use `dolfinx.mesh.MeshTagsMetaClass.find` instead of `mt.indices[mt.values==value]`.
 - Various numpy updates, use `np.full_like`.
 - Change all notebooks to use [jupytext](https://jupytext.readthedocs.io/en/latest/install.html) to automatically sync `.ipynb` with `.py` files.
 - Add example of how to use `DOLFINx` in complex mode, see [chapter1/complex_mode].
@@ -53,11 +64,13 @@
 ## 0.4.0 (05.02.2021)
 
 - All `pyvista` plotting has been rewritten to use `ipygany` and `pythreejs` as well as using a cleaner interface.
-- `dolfinx.plot.create_vtk_topology` has been renamed to `dolfinx.plot.create_vtk_mesh` and can now be directly used as input to `pyvista.UnstructuredGrid`.
+- `dolfinx.plot.create_vtk_topology` has been renamed to `dolfinx.plot.create_vtk_mesh` and can now be directly used as input
+  to {py:class}`pyvista.UnstructuredGrid`.
 - `dolfinx.fem.Function.compute_point_values` has been deprecated. Interpolation into a CG-1 is now the way of getting vertex values.
-- API updates wrt. DOLFINx. `Form`->`form`, `DirichletBC`->`dirichletbc`.
+- Instead of initializing class with {py:class}`Form<dolfinx.fem.Form>`, use {py:func}`form<dolfinx.fem.form>`.
+- Instead of initializing class with {py:class}`DirichletBC<dolfinx.fem.DirichletBC>` use  {py:func}`dirichletbc<dolfinx.fem.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 interpolation of {py:class}`ufl.core.expr.Expr` 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
 

README.md

@@ -42,7 +42,7 @@ To run python scripts, either choose `PYVISTA_OFF_SCREEN=True` to get screenshot
 
 
 ```bash
-python3 -m jupytext --sync  */*.ipynb
+python3 -m jupytext --sync  */*.ipynb --set-formats ipynb,py:light
 ```
 or
 ```bash
@@ -86,4 +86,3 @@ from the root of this repository, and run
 ```
 
 from the main directory.
-

_config.yml

@@ -40,6 +40,24 @@ sphinx:
     # https://github.com/pydata/pydata-sphinx-theme/issues/1492
     # html_theme_options:
     #   navigation_with_keys: false
+    codeautolink_concat_default: True
+    intersphinx_mapping:
+      basix: ["https://docs.fenicsproject.org/basix/main/python/", null]
+      ffcx: ["https://docs.fenicsproject.org/ffcx/main/", null]
+      ufl: ["https://docs.fenicsproject.org/ufl/main/", null]
+      dolfinx: ["https://docs.fenicsproject.org/dolfinx/main/python", null]
+      petsc4py: ["https://petsc.org/release/petsc4py", null]
+      mpi4py: ["https://mpi4py.readthedocs.io/en/stable", null]
+      numpy: ["https://numpy.org/doc/stable/", null]
+      pyvista: ["https://docs.pyvista.org/", null]
+      packaging: ["https://packaging.pypa.io/en/stable/", null]
+      matplotlib: ["https://matplotlib.org/stable/", null]
+
+  extra_extensions:
+    - "sphinx.ext.autodoc"
+    - "sphinx.ext.intersphinx"
+    - "sphinx_codeautolink"
+
 parse:
   myst_enable_extensions:
     - "amsmath"
@@ -68,3 +86,4 @@ html:
     </div>
 
 exclude_patterns: [README.md, chapter2/advdiffreac.md]
+only_build_toc_files: true

_toc.yml

@@ -52,6 +52,7 @@ parts:
       - file: chapter3/em
   - caption: Improving your FEniCSx code
     chapters:
+      - file: chapter4/mixed_poisson
       - file: chapter4/solvers
       - file: chapter4/compiler_parameters
       - file: chapter4/convergence