Revision all imports after change in main (#53)

* Revision all imports after change in main

* Minor fix

Author: jorgensd

.github/workflows/build-publish.yml

@@ -20,7 +20,7 @@ jobs:
   build:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: dokken92/dolfinx_custom:10092021
+    container: dokken92/dolfinx_custom:28112021
 
     env:
       HDF5_MPI: "ON"

.github/workflows/docker-image.yml

@@ -37,4 +37,4 @@ jobs:
         run: echo ${{ secrets.DOCKERHUB_TOKEN }} | docker login -u ${{ secrets.DOCKERHUB_USERNAME }} --password-stdin
       - name: Push to the DockerHub registry
         run: |
-          docker push dokken92/dolfinx_custom:10092021
+          docker push dokken92/dolfinx_custom:28112021

.github/workflows/main-test.yml

@@ -27,9 +27,6 @@ jobs:
 
     env:
       HDF5_MPI: "ON"
-      CC: mpicc
-      HDF5_DIR: "/usr/lib/x86_64-linux-gnu/hdf5/mpich/"
-      DISPLAY: ":99.0"
       PYVISTA_OFF_SCREEN: true
 
     # Steps represent a sequence of tasks that will be executed as part of the job
@@ -39,12 +36,12 @@ jobs:
 
       - name: Install dependencies
         run: |
-          wget -qO - https://deb.nodesource.com/setup_16.x | bash
+          wget -qO - https://deb.nodesource.com/setup_17.x | bash
           apt-get -qq update
           apt-get install -y libgl1-mesa-dev xvfb nodejs
           apt-get clean
           rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-          pip3 install --no-cache-dir --no-binary=h5py h5py meshio
+          CC=mpicc HDF_MPI="ON" HDF5_DIR="/usr/lib/x86_64-linux-gnu/hdf5/mpich/" pip3 install --no-cache-dir --no-binary=h5py h5py meshio
           pip3 install --no-cache-dir tqdm pandas seaborn
           pip3 install notebook nbconvert jupyter-book myst_parser pyvista jupyterlab
           pip3 install --no-cache-dir matplotlib itkwidgets ipywidgets setuptools --upgrade

Changelog.md

@@ -1,6 +1,9 @@
 # Changelog
 
-## Dev
+## Dev 
+- Various API changes relating to the import structure of DOLFINx
+
+## 0.3.0 (09.09.2021)
 - Major improvements in [Form compiler parameters](chapter4/compiler_parameters), using pandas and seaborn for visualization of speed-ups gained using form compiler parameters.
 - API change: `dolfinx.cpp.la.scatter_forward(u.x)` -> `u.x.scatter_forward`
 - Various plotting updates due to new version of pyvista.

Dockerfile

@@ -1,4 +1,4 @@
-FROM dokken92/dolfinx_custom:03112021
+FROM dokken92/dolfinx_custom:28112021
 
 # create user with a home directory
 ARG NB_USER

chapter1/fundamentals_code.ipynb

@@ -51,7 +51,7 @@
     "However, in cases where we have a solution we know that should have no approximation error, we know that the solution should\n",
     "be produced to machine precision by the program.\n",
     "\n",
-    "The first eight lines of the program are importing the different modules required for solving the problem."
+    "We start by importing external modules used alongside `dolfinx`."
    ]
   },
   {
@@ -60,7 +60,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import dolfinx\n",
     "import numpy\n",
     "import ufl\n",
     "from mpi4py import MPI"
@@ -70,9 +69,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "A major difference between a traditional FEniCS code and a FEniCSx code, is that one is not advised to use the wildcard import.\n",
+    "A major difference between a traditional FEniCS code and a FEniCSx code, is that one is not advised to use the wildcard import. We will see this throughout this first example.\n",
     "## Generating  simple meshes\n",
-    "The next step is to define the discrete domain, _the mesh_\n"
+    "The next step is to define the discrete domain, _the mesh_. We do this by importing the built-in `dolfinx.generation.UnitSquareMesh` function, that can build a $[0,1]\\times[0,1]$ mesh, consisting of either triangles or quadrilaterals."
    ]
   },
   {
@@ -81,7 +80,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mesh = dolfinx.UnitSquareMesh(MPI.COMM_WORLD, 8, 8, dolfinx.cpp.mesh.CellType.quadrilateral)"
+    "from dolfinx.generation import UnitSquareMesh\n",
+    "from dolfinx.mesh import CellType\n",
+    "mesh = UnitSquareMesh(MPI.COMM_WORLD, 8, 8, CellType.quadrilateral)"
    ]
   },
   {
@@ -111,7 +112,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    " V = dolfinx.FunctionSpace(mesh, (\"CG\", 1))"
+    "from dolfinx.fem import FunctionSpace\n",
+    "V = FunctionSpace(mesh, (\"CG\", 1))"
    ]
   },
   {
@@ -124,12 +126,15 @@
     "and hexahedra). For an overview, see:\n",
     "*FIXME: Add link to all the elements we support*\n",
     "\n",
-    "The element degree in the code is 1. This means that we are choosing the standard $P_1$ linear Lagrange element, which has degrees of freedom at the vertices. The computed solution will be continuous across elements and linearly varying in $x$ and $y$ inside each element. Higher degree polynomial approximations are obtained by increasing the degree argument. \n",
+    "The element degree in the code is 1. This means that we are choosing the standard $P_1$ linear Lagrange element, which has degrees of freedom at the vertices. \n",
+    "The computed solution will be continuous across elements and linearly varying in $x$ and $y$ inside each element. Higher degree polynomial approximations are obtained by increasing the degree argument. \n",
     "\n",
     "## Defining the boundary conditions\n",
     "\n",
-    "The next step is to specify the boundary condition $u=u_D$ on $\\partial\\Omega_D$, which is done by over several steps. The first step is to define the function $u_D$. Into this function, we would like to interpolate the boundary condition $1 + x^2+2y^2$. We do this by first defining a `dolfinx.Function`, and then using a [lambda-function](https://docs.python.org/3/tutorial/controlflow.html#lambda-expressions) in Python to define the \n",
-    "spatially varying function. As we would like this program to work on one or multiple processors, we have to update the coefficients of $u_D$ that data shared between the processors. We do this by sending (scattering) the ghost values in the underlying data structure of `uD`.\n"
+    "The next step is to specify the boundary condition $u=u_D$ on $\\partial\\Omega_D$, which is done by over several steps. \n",
+    "The first step is to define the function $u_D$. Into this function, we would like to interpolate the boundary condition $1 + x^2+2y^2$.\n",
+    "We do this by first defining a `dolfinx.Function`, and then using a [lambda-function](https://docs.python.org/3/tutorial/controlflow.html#lambda-expressions) in Python to define the \n",
+    "spatially varying function.\n"
    ]
   },
   {
@@ -138,9 +143,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "uD = dolfinx.Function(V)\n",
-    "uD.interpolate(lambda x: 1 + x[0]**2 + 2 * x[1]**2)\n",
-    "uD.x.scatter_forward()"
+    "from dolfinx.fem import Function\n",
+    "uD = Function(V)\n",
+    "uD.interpolate(lambda x: 1 + x[0]**2 + 2 * x[1]**2)"
    ]
   },
   {
@@ -150,7 +155,7 @@
     "We now have the boundary data (and in this case the solution of \n",
     "the finite element problem) represented in the discrete function space.\n",
     "Next we would like to apply the boundary values to all degrees of freedom that are on the boundary of the discrete domain. We start by identifying the facets (line-segments) representing the outer boundary, using `dolfinx.cpp.mesh.compute_boundary_facets`.\n",
-    "This function returns an array of booleans of the same size as the number of facets on this processor, where `True` indicates that the local facet $i$ is on the boundary. To reduce this to only the indices that are `True`, we use `numpy.where`.\n"
+    "This function returns an array of booleans of the same size as the number of facets on this processor, where `True` indicates that the local facet $i$ is on the boundary. To reduce this to only the indices that are `True`, we use `numpy.where`."
    ]
   },
   {
@@ -161,8 +166,9 @@
    "source": [
     "fdim = mesh.topology.dim - 1\n",
     "# Create facet to cell connectivity required to determine boundary facets\n",
+    "from dolfinx.cpp.mesh import compute_boundary_facets\n",
     "mesh.topology.create_connectivity(fdim, mesh.topology.dim)\n",
-    "boundary_facets = numpy.where(numpy.array(dolfinx.cpp.mesh.compute_boundary_facets(mesh.topology)) == 1)[0]"
+    "boundary_facets = numpy.where(numpy.array(compute_boundary_facets(mesh.topology)) == 1)[0]"
    ]
   },
   {
@@ -185,8 +191,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "boundary_dofs = dolfinx.fem.locate_dofs_topological(V, fdim, boundary_facets)\n",
-    "bc = dolfinx.DirichletBC(uD, boundary_dofs)"
+    "from dolfinx.fem import locate_dofs_topological, DirichletBC\n",
+    "boundary_dofs = locate_dofs_topological(V, fdim, boundary_facets)\n",
+    "bc = DirichletBC(uD, boundary_dofs)"
    ]
   },
   {
@@ -223,7 +230,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "f = dolfinx.Constant(mesh, -6)"
+    "from dolfinx.fem import Constant\n",
+    "f = Constant(mesh, -6)"
    ]
   },
   {
@@ -273,7 +281,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "problem = dolfinx.fem.LinearProblem(a, L, bcs=[bc], petsc_options={\"ksp_type\": \"preonly\", \"pc_type\": \"lu\"})\n",
+    "from dolfinx.fem import LinearProblem\n",
+    "problem = LinearProblem(a, L, bcs=[bc], petsc_options={\"ksp_type\": \"preonly\", \"pc_type\": \"lu\"})\n",
     "uh = problem.solve()"
    ]
   },
@@ -292,27 +301,27 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "V2 = dolfinx.FunctionSpace(mesh, (\"CG\", 2))\n",
-    "uex = dolfinx.Function(V2)\n",
-    "uex.interpolate(lambda x: 1 + x[0]**2 + 2 * x[1]**2)\n",
-    "uex.x.scatter_forward()"
+    "V2 = FunctionSpace(mesh, (\"CG\", 2))\n",
+    "uex = Function(V2)\n",
+    "uex.interpolate(lambda x: 1 + x[0]**2 + 2 * x[1]**2)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We compute the error in two different ways. First, we compute the $L^2$-norm of the error, defined by $E=\\sqrt{\\int_\\Omega (u_D-u_h)^2\\mathrm{d} x}$. We use UFL to express the $L^2$-error:"
+    "We compute the error in two different ways. First, we compute the $L^2$-norm of the error, defined by $E=\\sqrt{\\int_\\Omega (u_D-u_h)^2\\mathrm{d} x}$. We use UFL to express the $L^2$-error, and use `dolfinx.fem.assemble_scalar` to compute the scalar value."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [],
    "source": [
+    "from dolfinx.fem import assemble_scalar\n",
     "L2_error = ufl.inner(uh - uex, uh - uex) * ufl.dx\n",
-    "error_L2 = numpy.sqrt(dolfinx.fem.assemble_scalar(L2_error))"
+    "error_L2 = numpy.sqrt(assemble_scalar(L2_error))"
    ]
   },
   {
@@ -329,15 +338,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
       "Error_L2 : 8.24e-03\n",
-      "Error_max : 2.22e-15\n"
+      "Error_max : 3.11e-15\n"
      ]
     }
    ],
@@ -361,7 +370,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -371,7 +380,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 18,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -388,7 +397,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 19,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -409,13 +418,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 20,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "e67d55e5b10847bc8134ae036945a0bf",
+       "model_id": "c8d829e8954c46699aca8c42cd8b5b12",
        "version_major": 2,
        "version_minor": 0
       },
@@ -442,19 +451,19 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Interactive plotting in notebooks\n",
-    "To create an interactive plot using pyvista in a Jupyter notebook we us `pyvista.ITKPlotter` which uses `itkwidgets`. To modify the visualization, click on the three bars in the top left corner."
+    "## Alternative plotting\n",
+    "To create a more interactive plot using pyvista in a Jupyter notebook we us `pyvista.ITKPlotter` which uses `itkwidgets`. To modify the visualization, click on the three bars in the top left corner."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 21,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "f352aee90a2c403cadaa4c4885907023",
+       "model_id": "5a5bdbffdc324a548691f67bb09a5a4c",
        "version_major": 2,
        "version_minor": 0
       },
@@ -484,17 +493,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 22,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "2021-09-10 08:49:40.089 (   4.500s) [main            ]            VTKFile.cpp:617   WARN| Output data is interpolated into a first order Lagrange space.\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import dolfinx.io\n",
     "with dolfinx.io.VTKFile(MPI.COMM_WORLD, \"output.pvd\", \"w\") as vtk:\n",
@@ -537,7 +538,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.5"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,