Try removing xvfb for most tutorials (#278)

* Try removing xvfb for most tutorials

Author: jorgensd

.github/actions/install-dependencies/action.yml

@@ -6,4 +6,4 @@ runs:
     - name: Install apt dependencies and upgrade pip
       shell: bash -el {0}
       run: |
-        apt-get update && apt-get install -y libxrender1 xvfb
+        apt-get update && apt-get install -y libxrender1

.github/workflows/book_stable.yml

@@ -10,7 +10,6 @@ on:
 env:
   HDF5_MPI: "ON"
   HDF5_DIR: "/usr/local/"
-  DISPLAY: ":99.0"
   DEB_PYTHON_INSTALL_LAYOUT: deb_system
   LIBGL_ALWAYS_SOFTWARE: 1
 
@@ -20,8 +19,6 @@ jobs:
     container: ghcr.io/fenics/dolfinx/lab:stable
 
     env:
-      PYVISTA_TRAME_SERVER_PROXY_PREFIX: "/proxy/"
-      PYVISTA_TRAME_SERVER_PROXY_ENABLED: "True"
       PYVISTA_OFF_SCREEN: false
       PYVISTA_JUPYTER_BACKEND: "html"
 

.github/workflows/test_nightly.yml

@@ -1,4 +1,4 @@
-name: Test release branch against DOLFINx nightly build
+name: Test against DOLFINx nightly build
 
 # Controls when the action will run.
 on:
@@ -22,7 +22,6 @@ jobs:
     env:
       HDF5_MPI: "ON"
       PYVISTA_OFF_SCREEN: true
-      DISPLAY: ":99.0"
       PYVISTA_JUPYTER_BACKEND: html
       LIBGL_ALWAYS_SOFTWARE: 1
 
@@ -56,7 +55,6 @@ jobs:
       - name: Test chapter 1
         working-directory: chapter1
         run: |
-          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

.github/workflows/test_stable.yml

@@ -45,7 +45,6 @@ jobs:
       - name: Test chapter 1
         working-directory: chapter1
         run: |
-          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

README.md

@@ -10,15 +10,36 @@ If you have any comments, corrections or questions, please submit an issue in th
 
 ## Contributing
 
-If you want to contribute to this tutorial, please make a fork of the repository, make your changes, and test that the CI passes. You can do this locally by downloading [act](https://github.com/nektos/act) and call
+If you want to contribute to this tutorial, please make a fork of the repository, make your changes, and test that the CI passes. 
 
+Alternatively, if you want to add a separate chapter, a Jupyter notebook can be added to a pull request, without integrating it into the tutorial. If so, the notebook will be reviewed and modified to be included in the tutorial.
+
+Any code added to the tutorial should work in parallel. If any changes are made to `ipynb` files, please ensure that these changes are reflected in the corresponding `py` files by using [`jupytext`](https://jupytext.readthedocs.io/en/latest/faq.html#can-i-use-jupytext-with-jupyterhub-binder-nteract-colab-saturn-or-azure):
+
+
+## Building the book and running code
+The book is built using [jupyterbook](https://jupyterbook.org/). The following environment variables should be set if you want to build the book
 ```bash
-act -j test-nightly
+PYVISTA_OFF_SCREEN=false
+PYVISTA_JUPYTER_BACKEND="html"
+JUPYTER_EXTENSION_ENABLED=true
+LIBGL_ALWAYS_SOFTWARE=1
 ```
 
-Alternatively, if you want to add a separate chapter, a Jupyter notebook can be added to a pull request, without integrating it into the tutorial. If so, the notebook will be reviewed and modified to be included in the tutorial.
+If you run the tutorial using `jupyter-lab`, for instance through `conda`, one should set the following environment variables
+```bash
+PYVISTA_OFF_SCREEN=false
+PYVISTA_JUPYTER_BACKEND="trame"
+JUPYTER_EXTENSION_ENABLED=true
+LIBGL_ALWAYS_SOFTWARE=1
+```
+If you use docker to run your code, you should set the following variables:
+```bash
+docker run -ti -e DISPLAY=$DISPLAY -e LIBGL_ALWAYS_SOFTWARE=1 -e PYVISTA_OFF_SCREEN=false -e PYVISTA_JUPYTER_BACKEND="trame" -e JUPYTER_EXTENSION_ENABLED=true --network=host -v $(pwd):/root/shared -w /root/shared  ....
+```
+
+To run python scripts, either choose `PYVISTA_OFF_SCREEN=True` to get screenshots, or render interactive plots with `PYVISTA_OFF_SCREEN=False`
 
-Any code added to the tutorial should work in parallel. If any changes are made to `ipynb` files, please ensure that these changes are reflected in the corresponding `py` files by using [`jupytext`](https://jupytext.readthedocs.io/en/latest/faq.html#can-i-use-jupytext-with-jupyterhub-binder-nteract-colab-saturn-or-azure):
 
 ```bash
 python3 -m jupytext --sync  */*.ipynb

chapter1/complex_mode.ipynb

@@ -219,7 +219,7 @@
    "outputs": [],
    "source": [
     "import pyvista\n",
-    "pyvista.start_xvfb()\n",
+    "\n",
     "mesh.topology.create_connectivity(mesh.topology.dim, mesh.topology.dim)\n",
     "p_mesh = pyvista.UnstructuredGrid(*dolfinx.plot.vtk_mesh(mesh, mesh.topology.dim))\n",
     "pyvista_cells, cell_types, geometry = dolfinx.plot.vtk_mesh(V)\n",

chapter1/complex_mode.py

@@ -125,7 +125,6 @@
 #
 
 import pyvista
-pyvista.start_xvfb()
 mesh.topology.create_connectivity(mesh.topology.dim, mesh.topology.dim)
 p_mesh = pyvista.UnstructuredGrid(*dolfinx.plot.vtk_mesh(mesh, mesh.topology.dim))
 pyvista_cells, cell_types, geometry = dolfinx.plot.vtk_mesh(V)

chapter1/fundamentals_code.ipynb

@@ -407,9 +407,10 @@
    "source": [
     "## Plotting the mesh using pyvista\n",
     "We will visualizing the mesh using [pyvista](https://docs.pyvista.org/), an interface to the VTK toolkit.\n",
-    "We start by converting the mesh to a format that can be used with `pyvista`.\n",
-    "To do this we use the function `dolfinx.plot.vtk_mesh`. The first step is to create an unstructured grid that can be used by `pyvista`.\n",
-    "We need to start a virtual framebuffer for plotting through docker containers. You can print the current backend and change it with `pyvista.set_jupyter_backend(backend)`"
+    "We start by converting the mesh to a format that can be used with {py:mod}`pyvista`.\n",
+    "To do this we use the function {py:func}`dolfinx.plot.vtk_mesh`.\n",
+    "It creates the data required to create a {py:class}`pyvista.UnstructuredGrid`.\n",
+    "You can print the current backend and change it with {py:func}`pyvista.set_jupyter_backend`."
    ]
   },
   {
@@ -420,6 +421,7 @@
    "outputs": [],
    "source": [
     "import pyvista\n",
+    "\n",
     "print(pyvista.global_theme.jupyter_backend)"
    ]
   },

chapter1/fundamentals_code.py

@@ -222,9 +222,10 @@
 
 # ## Plotting the mesh using pyvista
 # We will visualizing the mesh using [pyvista](https://docs.pyvista.org/), an interface to the VTK toolkit.
-# We start by converting the mesh to a format that can be used with `pyvista`.
-# To do this we use the function `dolfinx.plot.vtk_mesh`. The first step is to create an unstructured grid that can be used by `pyvista`.
-# We need to start a virtual framebuffer for plotting through docker containers. You can print the current backend and change it with `pyvista.set_jupyter_backend(backend)`
+# We start by converting the mesh to a format that can be used with {py:mod}`pyvista`.
+# To do this we use the function {py:func}`dolfinx.plot.vtk_mesh`.
+# It creates the data required to create a {py:class}`pyvista.UnstructuredGrid`.
+# You can print the current backend and change it with {py:func}`pyvista.set_jupyter_backend`.
 
 import pyvista
 print(pyvista.global_theme.jupyter_backend)

chapter1/membrane_code.ipynb

@@ -244,10 +244,24 @@
    "outputs": [],
    "source": [
     "from dolfinx.plot import vtk_mesh\n",
-    "import pyvista\n",
-    "pyvista.start_xvfb()\n",
-    "\n",
-    "# Extract topology from mesh and create pyvista mesh\n",
+    "import pyvista\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "25",
+   "metadata": {},
+   "source": [
+    "Extract topology from mesh and create pyvista mesh"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "26",
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "topology, cell_types, x = vtk_mesh(V)\n",
     "grid = pyvista.UnstructuredGrid(topology, cell_types, x)\n",
     "\n",