Prepare for release

jorgensd · jorgensd · commit 84ef93bcd4a1 · 2025-10-20T12:58:31.000+02:00
diff --git a/chapter1/complex_mode.py b/chapter1/complex_mode.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (DOLFINx complex)
 #     language: python
diff --git a/chapter1/fundamentals.md b/chapter1/fundamentals.md
@@ -52,7 +52,7 @@ As we have already covered step 1, we shall now cover steps 2-4.
 FEniCSx is based on the finite element method, which is a general and
 efficient mathematical technique for the numerical solution of
 PDEs. The starting point for finite element methods is a PDE
-expressed in _variational form_. For readers not familiar with variational problems, we suggest reading a proper treatment on the finite element method, as this tutorial is meant as a brief introduction to the subject. See the original tutorial {cite}`FenicsTutorial` (Chapter 1.6.2).
+expressed in _variational form_. For readers not familiar with variational problems, we suggest reading a proper treatment on the finite element method, as this tutorial is meant as a brief introduction to the subject. See the original tutorial {cite}`fd-FenicsTutorial` (Chapter 1.6.2).
 
 The basic recipe for turning a PDE into a variational problem is:
 
@@ -80,7 +80,7 @@ $-\int_\Omega (\nabla^2 u)v~\mathrm{d}x
 
 where $\frac{\partial u}{\partial n}=\nabla u \cdot \vec{n}$ is the derivative of $u$ in the outward normal direction $\vec{n}$ on the boundary.
 
-Another feature of variational formulations is that the test function $v$ is required to vanish on the parts of the boundary where the solution $u$ is known. See for instance {cite}`Langtangen_Mardal_FEM_2019`.
+Another feature of variational formulations is that the test function $v$ is required to vanish on the parts of the boundary where the solution $u$ is known. See for instance {cite}`fd-Langtangen_Mardal_FEM_2019`.
 
 In the present problem, this means that $v$ is $0$ on the whole boundary $\partial\Omega$. Thus, the second term in the integration by parts formula vanishes, and we have that
 
@@ -138,5 +138,7 @@ To solve a linear PDE in FEniCSx, such as the Poisson equation, a user thus need
 ## References
 
 ```{bibliography}
-   :filter: cited and ({"chapter1/fundamentals"} >= docnames)
+   :filter: cited
+   :labelprefix:
+   :keyprefix: fd-
 ```
diff --git a/chapter1/fundamentals_code.ipynb b/chapter1/fundamentals_code.ipynb
@@ -9,7 +9,7 @@
     "\n",
     "Author: Jørgen Schartum Dokken\n",
     "\n",
-    "This implementation is an adaptation of the work in {cite}`FenicsTutorial` to DOLFINx.\n",
+    "This implementation is an adaptation of the work in {cite}`fundamentals-FenicsTutorial` to DOLFINx.\n",
     "\n",
     "In this section, you will learn:\n",
     "- How to use the built-in meshes in DOLFINx\n",
@@ -249,7 +249,7 @@
     "so it is sufficient to use a common space for the trial and test function.\n",
     "\n",
     "We use the {py:mod}`Unified Form Language<ufl>` (UFL) to specify the varitional formulations.\n",
-    "See {cite}`ufl2014` for more details."
+    "See {cite}`fundamentals-ufl2014` for more details."
    ]
   },
   {
@@ -646,7 +646,9 @@
    "metadata": {},
    "source": [
     "```{bibliography}\n",
-    "   :filter: cited and ({\"chapter1/fundamentals_code\"} >= docnames)\n",
+    "   :filter: cited\n",
+    "   :labelprefix:\n",
+    "   :keyprefix: fundamentals-\n",
     "```"
    ]
   }
diff --git a/chapter1/fundamentals_code.py b/chapter1/fundamentals_code.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
@@ -17,7 +17,7 @@
 #
 # Author: Jørgen Schartum Dokken
 #
-# This implementation is an adaptation of the work in {cite}`FenicsTutorial` to DOLFINx.
+# This implementation is an adaptation of the work in {cite}`fundamentals-FenicsTutorial` to DOLFINx.
 #
 # In this section, you will learn:
 # - How to use the built-in meshes in DOLFINx
@@ -176,7 +176,7 @@
 # so it is sufficient to use a common space for the trial and test function.
 #
 # We use the {py:mod}`Unified Form Language<ufl>` (UFL) to specify the varitional formulations.
-# See {cite}`ufl2014` for more details.
+# See {cite}`fundamentals-ufl2014` for more details.
 
 
 # +
@@ -389,5 +389,7 @@
 # -
 
 # ```{bibliography}
-#    :filter: cited and ({"chapter1/fundamentals_code"} >= docnames)
+#    :filter: cited
+#    :labelprefix:
+#    :keyprefix: fundamentals-
 # ```
diff --git a/chapter1/membrane_code.py b/chapter1/membrane_code.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/chapter1/nitsche.py b/chapter1/nitsche.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/chapter2/amr.py b/chapter2/amr.py
@@ -7,7 +7,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 # ---
 
 # # Adaptive mesh refinement with NetGen and DOLFINx
diff --git a/chapter2/diffusion_code.py b/chapter2/diffusion_code.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/chapter2/heat_code.py b/chapter2/heat_code.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/chapter2/helmholtz_code.py b/chapter2/helmholtz_code.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (DOLFINx complex)
 #     language: python
diff --git a/chapter2/hyperelasticity.py b/chapter2/hyperelasticity.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/chapter2/linearelasticity_code.py b/chapter2/linearelasticity_code.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/chapter2/nonlinpoisson_code.py b/chapter2/nonlinpoisson_code.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/chapter2/ns_code1.py b/chapter2/ns_code1.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/chapter2/ns_code2.py b/chapter2/ns_code2.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/chapter2/singular_poisson.py b/chapter2/singular_poisson.py
@@ -7,7 +7,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 # ---
 
 # # Singular Poisson problem
diff --git a/chapter3/component_bc.py b/chapter3/component_bc.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/chapter3/em.py b/chapter3/em.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/chapter3/multiple_dirichlet.py b/chapter3/multiple_dirichlet.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/chapter3/neumann_dirichlet_code.py b/chapter3/neumann_dirichlet_code.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/chapter3/robin_neumann_dirichlet.py b/chapter3/robin_neumann_dirichlet.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/chapter3/subdomains.py b/chapter3/subdomains.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/chapter4/compiler_parameters.py b/chapter4/compiler_parameters.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/chapter4/convergence.py b/chapter4/convergence.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/chapter4/mixed_poisson.ipynb b/chapter4/mixed_poisson.ipynb
@@ -8,7 +8,7 @@
     "# Mixed Poisson with a Schur complement pre-conditioner\n",
     "This example demonstrates how to use PETSC fieldsplits with custom preconditions in DOLFINx.\n",
     "This example is heavily insipired by the [FEniCSx PCTools example](https://rafinex-external-rifle.gitlab.io/fenicsx-pctools/demo/demo_mixed-poisson.html)\n",
-    "which was presented in {cite}`rehor2025pctools`."
+    "which was presented in {cite}`mp-rehor2025pctools`."
    ]
   },
   {
@@ -611,17 +611,24 @@
     ")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "3b3b48be",
+   "metadata": {},
+   "source": [
+    "```{admonition} NEST matrices\n",
+    "Note that instead of using `kind=\"mpi\"` we use `kind=\"nest\"` to indicate that we want to use a nested matrix structure\n",
+    "and employ the power of [PETSc fieldsplit](https://petsc.org/release/manual/ksp/#solving-block-matrices-with-pcfieldsplit).\n",
+    "```"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "id": "32",
    "metadata": {},
    "outputs": [],
    "source": [
-    "# ```{admonition} NEST matrices\n",
-    "# Note that instead of using `kind=\"mpi\"` we use `kind=\"nest\"` to indicate that we want to use a nested matrix structure\n",
-    "# and employ the power of [PETSc fieldsplit](https://petsc.org/release/manual/ksp/#solving-block-matrices-with-pcfieldsplit).\n",
-    "# ```\n",
     "start_it = time.perf_counter()\n",
     "problem.solve()\n",
     "end_it = time.perf_counter()\n",
@@ -689,7 +696,9 @@
    "metadata": {},
    "source": [
     "```{bibliography}\n",
-    "   :filter: cited and ({\"chapter4/mixed_poisson\"} >= docnames)\n",
+    "   :filter: cited\n",
+    "   :labelprefix:\n",
+    "   :keyprefix: mp-\n",
     "```"
    ]
   }
diff --git a/chapter4/mixed_poisson.py b/chapter4/mixed_poisson.py
@@ -7,13 +7,13 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 # ---
 
 # # Mixed Poisson with a Schur complement pre-conditioner
 # This example demonstrates how to use PETSC fieldsplits with custom preconditions in DOLFINx.
 # This example is heavily insipired by the [FEniCSx PCTools example](https://rafinex-external-rifle.gitlab.io/fenicsx-pctools/demo/demo_mixed-poisson.html)
-# which was presented in {cite}`rehor2025pctools`.
+# which was presented in {cite}`mp-rehor2025pctools`.
 
 # We start with the mixed formulation of the Poisson equation, which is given by
 # \begin{align}
@@ -414,6 +414,7 @@ def __del__(self):
 # Note that instead of using `kind="mpi"` we use `kind="nest"` to indicate that we want to use a nested matrix structure
 # and employ the power of [PETSc fieldsplit](https://petsc.org/release/manual/ksp/#solving-block-matrices-with-pcfieldsplit).
 # ```
+
 start_it = time.perf_counter()
 problem.solve()
 end_it = time.perf_counter()
@@ -444,5 +445,7 @@ def __del__(self):
 
 
 # ```{bibliography}
-#    :filter: cited and ({"chapter4/mixed_poisson"} >= docnames)
+#    :filter: cited
+#    :labelprefix:
+#    :keyprefix: mp-
 # ```
diff --git a/chapter4/newton-solver.py b/chapter4/newton-solver.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/chapter4/solvers.py b/chapter4/solvers.py
@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.17.3
+#       jupytext_version: 1.18.1
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
diff --git a/docker/Dockerfile b/docker/Dockerfile
diff --git a/fem.md b/fem.md
diff --git a/pyproject.toml b/pyproject.toml
