Modify tutorials for rendering on gadopt.org

.github/workflows/test.yml

@@ -33,13 +33,13 @@ jobs:
           export PYVISTA_OFF_SCREEN=true
           Xvfb $DISPLAY -screen 0 1024x768x24 > /dev/null 2>&1 &
           sleep 3
-          pytest --nbval *.ipynb
+          pytest --nbval 01-*.ipynb
 
       - name: Build Jupyter Book
         run: |
           . /home/firedrake/firedrake/bin/activate
           python3 -m pip install jupyter-book
-          for f in *.ipynb; do ln -s ../$f docs; done
+          for f in 01-*.ipynb; do ln -s ../$f docs; done
           ln -s ../stokes-control.msh docs
           export DISPLAY=:99
           export PYVISTA_OFF_SCREEN=true

01-spd-helmholtz.ipynb

@@ -122,7 +122,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "To start, we must make Firedrake available in the notebook.  It is available as a normal Python package, named `firedrake`.  To save on typing, we will import all of the public API into the current namespace"
+    "To start, we must make Firedrake available in the notebook.  We will import it through the `gadopt` package.  To save on typing, we will import all of the public API into the current namespace. For plotting within this notebook, we also explicitly import the `triplot` function."
    ]
   },
   {
@@ -131,7 +131,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from gadopt import *"
+    "from gadopt import *\n",
+    "from firedrake.pyplot import triplot, tripcolor"
    ]
   },
   {
@@ -363,7 +364,15 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": [
+     "exercise"
+    ]
+   },
    "source": [
     "## Exercises\n",
     "\n",
@@ -386,13 +395,29 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": [
+     "exercise"
+    ]
+   },
    "outputs": [],
    "source": []
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": [
+     "exercise"
+    ]
+   },
    "source": [
     "### Exercise 2: convergence of the method\n",
     "For solutions with sufficient smoothness (like the choice we have here), this method with a piecewise linear approximation space should converge in the $L_2$ error with rate $\\mathcal{O}(h^{-2})$, where $h$ is the typical mesh spacing.  Confirm this for the example in question by computing the $L_2$ error in the solution for a sequence of finer and finer meshes.\n",
@@ -411,7 +436,16 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": [
+     "skip-execution",
+     "exercise"
+    ]
+   },
    "outputs": [],
    "source": [
     "mesh = UnitSquareMesh(10, 10)\n",
@@ -433,7 +467,15 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": [
+     "exercise"
+    ]
+   },
    "outputs": [],
    "source": []
   },

02-poisson.ipynb

@@ -60,6 +60,7 @@
     "    !wget \"https://github.com/g-adopt/tutorials/releases/latest/download/firedrake-install-real.sh\" -O \"/tmp/firedrake-install.sh\" && bash \"/tmp/firedrake-install.sh\"\n",
     "    import firedrake\n",
     "from gadopt import *\n",
+    "from firedrake.pyplot import tripcolor\n",
     "mesh = UnitSquareMesh(10, 10)\n",
     "V = FunctionSpace(mesh, \"Lagrange\", 1)"
    ]
@@ -175,7 +176,15 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": [
+     "exercise"
+    ]
+   },
    "source": [
     "## Exercises\n",
     "\n",
@@ -198,7 +207,15 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": [
+     "exercise"
+    ]
+   },
    "outputs": [],
    "source": []
   }

03-elasticity.ipynb

@@ -56,6 +56,7 @@
     "    !wget \"https://github.com/g-adopt/tutorials/releases/latest/download/firedrake-install-real.sh\" -O \"/tmp/firedrake-install.sh\" && bash \"/tmp/firedrake-install.sh\"\n",
     "    import firedrake\n",
     "from gadopt import *\n",
+    "from firedrake.pyplot import triplot\n",
     "length = 1\n",
     "width = 0.2\n",
     "mesh = RectangleMesh(40, 20, length, width)"
@@ -199,7 +200,15 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": [
+     "exercise"
+    ]
+   },
    "source": [
     "## Exercises\n",
     "\n",
@@ -212,7 +221,15 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": [
+     "exercise"
+    ]
+   },
    "outputs": [],
    "source": []
   },
@@ -367,7 +384,15 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": [
+     "exercise"
+    ]
+   },
    "source": [
     "## Exercise\n",
     "\n",
@@ -377,7 +402,15 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": [
+     "exercise"
+    ]
+   },
    "outputs": [],
    "source": []
   }

04-burgers.ipynb

@@ -58,6 +58,7 @@
     "    !wget \"https://github.com/g-adopt/tutorials/releases/latest/download/firedrake-install-real.sh\" -O \"/tmp/firedrake-install.sh\" && bash \"/tmp/firedrake-install.sh\"\n",
     "    import firedrake\n",
     "from gadopt import *\n",
+    "from firedrake.pyplot import plot\n",
     "\n",
     "n = 100\n",
     "mesh = PeriodicIntervalMesh(n, length=2)\n",
@@ -305,7 +306,15 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": [
+     "exercise"
+    ]
+   },
    "source": [
     "## Exercise 1\n",
     "\n",
@@ -317,13 +326,29 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": [
+     "exercise"
+    ]
+   },
    "outputs": [],
    "source": []
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": [
+     "exercise"
+    ]
+   },
    "source": [
     "## Exercise 2\n",
     "\n",
@@ -344,7 +369,15 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": [
+     "exercise"
+    ]
+   },
    "outputs": [],
    "source": []
   }

05-pde-constrained-optimisation.ipynb

@@ -49,7 +49,8 @@
    "outputs": [],
    "source": [
     "from gadopt import *\n",
-    "from gadopt.inverse import *"
+    "from gadopt.inverse import *\n",
+    "from firedrake.pyplot import quiver, streamplot, tricontourf, triplot"
    ]
   },
   {
@@ -395,7 +396,15 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": [
+     "exercise"
+    ]
+   },
    "source": [
     "## Exercise:\n",
     "\n",