Switch to gadopt-restructure version of tutorials

g-adopt · Feb 11, 2024 · 3c26415 · 3c26415
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -1,12 +1,12 @@
-name: Test notebook execution
+name: Test and deploy notebooks
 
 on:
   pull_request:
   workflow_dispatch:
 
 jobs:
   build:
-    name: Test notebook execution
+    name: Test and deploy notebooks
     runs-on: self-hosted
     container:
       image: firedrakeproject/firedrake:latest
@@ -19,7 +19,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Load pyrol wheel from cache
-        uses: actions/cache@v3
+        uses: actions/cache/restore@v3
         id: cache-pyrol
         with:
           path: /tmp/wheels
@@ -28,16 +28,47 @@ jobs:
       - name: Build pyrol wheel
         if: steps.cache-pyrol.outputs.cache-hit != 'true'
         run: |
-          /home/firedrake/firedrake/bin/pip wheel -r git+https://github.com/angus-g/[email protected] -w /tmp/wheels
+          /home/firedrake/firedrake/bin/pip wheel git+https://github.com/angus-g/[email protected] -w /tmp/wheels
 
-      - name: Install Python dependencies
+      - name: Save pyrol to cache
+        if: steps.cache-pyrol.outputs.cache-hit != 'true'
+        uses: actions/cache/save@v3
+        with:
+          path: /tmp/wheels
+          key: pyrol
+
+      - name: Install dependencies
         run: |
+          sudo apt update
+          sudo apt install -y libgl1-mesa-glx xvfb
           . /home/firedrake/firedrake/bin/activate
           python3 -m pip install --no-index -f /tmp/wheels pyroltrilinos
-          python3 -m pip install nbval
-          python3 -m pip install git+https://github.com/g-adopt/g-adopt@adjoint-cases-testing
+          python3 -m pip install nbval pyvista
+          python3 -m pip install git+https://github.com/g-adopt/g-adopt
 
       - name: Run test
         run: |
           . /home/firedrake/firedrake/bin/activate
+          export DISPLAY=:99
+          export PYVISTA_OFF_SCREEN=true
+          Xvfb $DISPLAY -screen 0 1024x768x24 > /dev/null 2>&1 &
+          sleep 3
           pytest --nbval *.ipynb
+
+      - name: Build Jupyter Book
+        run: |
+          . /home/firedrake/firedrake/bin/activate
+          python3 -m pip install jupyter-book
+          for f in *.ipynb; do ln -s ../$f docs; done
+          ln -s ../stokes-control.msh docs
+          export DISPLAY=:99
+          export PYVISTA_OFF_SCREEN=true
+          Xvfb $DISPLAY -screen 0 1024x768x24 > /dev/null 2>&1 &
+          sleep 3
+          jupyter-book build docs
+
+      - name: Archive built book
+        uses: actions/upload-artifact@v3
+        with:
+          name: tutorials-html
+          path: docs/_build/html
diff --git a/01-spd-helmholtz.ipynb b/01-spd-helmholtz.ipynb
@@ -7,14 +7,14 @@
    "outputs": [],
    "source": [
     "# This magic makes plots appear in the browser\n",
-    "%matplotlib notebook\n",
+    "%matplotlib inline\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
     "# Load Firedrake on Colab\n",
     "try:\n",
     "    import firedrake\n",
     "except ImportError:\n",
-    "    !wget \"https://fem-on-colab.github.io/releases/firedrake-install-real.sh\" -O \"/tmp/firedrake-install.sh\" && bash \"/tmp/firedrake-install.sh\"\n",
+    "    !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"
    ]
   },
@@ -52,7 +52,9 @@
   {
    "cell_type": "markdown",
    "metadata": {
-    "collapsed": true
+    "jupyter": {
+     "outputs_hidden": true
+    }
    },
    "source": [
     "$$ \\int_\\Omega \\nabla u\\cdot\\nabla v  + uv\\ \\mathrm{d}x = \\int_\\Omega\n",
@@ -129,7 +131,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from firedrake import *"
+    "from gadopt import *"
    ]
   },
   {
@@ -187,10 +189,13 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "nbval-ignore-output"
+    ]
+   },
    "outputs": [],
    "source": [
-    "# NBVAL_IGNORE_OUTPUT\n",
     "# We test the output of the notebooks with out continuous integration system to\n",
     "# make sure they run.\n",
     "# Unfortunately we can't compare the plots from run to run, so the above line\n",
@@ -312,10 +317,13 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "nbval-ignore-output"
+    ]
+   },
    "outputs": [],
    "source": [
-    "# NBVAL_IGNORE_OUTPUT\n",
     "fig, axes = plt.subplots()\n",
     "collection = tripcolor(uh, axes=axes, cmap='coolwarm')\n",
     "fig.colorbar(collection);"
@@ -340,10 +348,13 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "nbval-ignore-output"
+    ]
+   },
    "outputs": [],
    "source": [
-    "# NBVAL_IGNORE_OUTPUT\n",
     "difference = assemble(interpolate(u_exact, V) - uh)\n",
     "fig, axes = plt.subplots()\n",
     "collection = tripcolor(difference, axes=axes, cmap='coolwarm')\n",
@@ -354,17 +365,17 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Exercises\n",
+    "## Exercises\n",
     "\n",
-    "## Exercise 1: \n",
+    "### Exercise 1: \n",
     "\n",
-    "### 1a: use a higher approximation degree\n",
+    "#### 1a: use a higher approximation degree\n",
     "\n",
     "Solve the same problem, only this time, use a piecewise quadratic approximation space.\n",
     "\n",
     "- Hint: check the help for `FunctionSpace` to see how to specify the degree.\n",
     "\n",
-    "### 1b: use a quadrilateral mesh\n",
+    "#### 1b: use a quadrilateral mesh\n",
     "\n",
     "Solve the same problem, but using quadrilateral, rather than triangular, cells.\n",
     "\n",
@@ -383,14 +394,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Exercise 2: convergence of the method\n",
+    "### 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",
     "\n",
     "- Hint 1: You can compute errors using [errornorm](http://firedrakeproject.org/firedrake.html#firedrake.norms.errornorm)\n",
     "- Hint 2: If the error is $\\mathcal{O}(h^{-2})$ then $\\log_2 (e_H/e_h) \\approx 2$.\n",
     "  The Python module `math` contains an implementation of `log`.\n",
     "  \n",
-    "### What works better?  Mesh refinement, or increasing the approximation degree?\n",
+    "#### What works better?  Mesh refinement, or increasing the approximation degree?\n",
     "\n",
     "Instead of (or as well as!) refining the mesh, we can increase the degree of the approximating polynomial space.\n",
     "\n",
@@ -430,7 +441,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Part II: inhomogeneous Neuman conditions\n",
+    "## Part II: inhomogeneous Neuman conditions\n",
     "\n",
     "Let us recall again the statement of our problem.  We seek $u \\in V$ satisfying\n",
     "\n",
@@ -449,7 +460,9 @@
   {
    "cell_type": "markdown",
    "metadata": {
-    "collapsed": true
+    "jupyter": {
+     "outputs_hidden": true
+    }
    },
    "source": [
     "As previously, we introduce a test function $v \\in V$, multiply and integrate.  After integrating by parts, we obtain\n",
@@ -548,11 +561,6 @@
   }
  ],
  "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
@@ -563,9 +571,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.2"
+   "version": "3.11.4"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }
diff --git a/02-poisson.ipynb b/02-poisson.ipynb
@@ -10,7 +10,9 @@
   {
    "cell_type": "markdown",
    "metadata": {
-    "collapsed": true
+    "jupyter": {
+     "outputs_hidden": true
+    }
    },
    "source": [
     "Let's move on from the Helmholtz problem to Poisson:\n",
@@ -49,15 +51,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matplotlib notebook\n",
+    "%matplotlib inline\n",
     "import matplotlib.pyplot as plt\n",
     "# Load Firedrake on Colab\n",
     "try:\n",
     "    import firedrake\n",
     "except ImportError:\n",
-    "    !wget \"https://fem-on-colab.github.io/releases/firedrake-install-real.sh\" -O \"/tmp/firedrake-install.sh\" && bash \"/tmp/firedrake-install.sh\"\n",
+    "    !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 firedrake import *\n",
+    "from gadopt import *\n",
     "mesh = UnitSquareMesh(10, 10)\n",
     "V = FunctionSpace(mesh, \"Lagrange\", 1)"
    ]
@@ -159,10 +161,13 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "nbval-ignore-output"
+    ]
+   },
    "outputs": [],
    "source": [
-    "# NBVAL_IGNORE_OUTPUT\n",
     "fig, axes = plt.subplots()\n",
     "collection = tripcolor(uh, axes=axes)\n",
     "fig.colorbar(collection);"
@@ -172,7 +177,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Exercises\n",
+    "## Exercises\n",
     "\n",
     "Most of the time, we don't want to impose the same Dirichlet condition everywhere.  Instead of solving with homogeneous Dirichlet conditions everywhere, solve the following problem.\n",
     "\n",
@@ -199,11 +204,6 @@
   }
  ],
  "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
@@ -214,9 +214,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.11.4"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }