Fix bounding boxes and more (#135)

* Start fixing code for nightly build

* rerun all files

* Try fixing subdomains

* Fix meshio

Author: jorgensd

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

@@ -1,17 +1,10 @@
 name: Install dependencies
 
-
 runs:
   using: composite
   steps:
       - name: Install apt dependencies and upgrade pip
         shell: bash -el {0}
         run: |
           apt-get update && apt-get install -y libgl1-mesa-glx libxrender1 xvfb
-          python3 -m pip install -U pip
-      # Install `h5py` master branch
-      # https://github.com/hl5py/h5py/issues/2222
-      - name: Install h5py and pip requirements
-        shell: bash -el {0}
-        run: |
-          python3 -m pip install --no-binary=h5py git+https://github.com/h5py/h5py@master
+          python3 -m pip install -U pip

chapter1/complex_mode.ipynb

@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.14.4
+#       jupytext_version: 1.14.6
 #   kernelspec:
 #     display_name: Python 3 (DOLFINx complex)
 #     language: python

chapter1/complex_mode.py

@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.14.5
+#       jupytext_version: 1.14.6
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python

chapter1/fundamentals_code.ipynb

@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.14.5
+#       jupytext_version: 1.14.6
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python
@@ -167,9 +167,9 @@ def on_boundary(x):
 # This is efficiently done by creating a bounding box tree of the cells of the mesh, allowing a quick recursive search through the mesh entities.
 
 from dolfinx import geometry
-bb_tree = geometry.BoundingBoxTree(domain, domain.topology.dim)
+bb_tree = geometry.bb_tree(domain, domain.topology.dim)
 
-# Now we can compute which cells the bounding box tree collides with using `dolfinx.geometry.compute_collisions_point`. This function returns a list of cells whose bounding box collide for each input point. As different points might have different number of cells, the data is stored in `dolfinx.cpp.graph.AdjacencyList_int32`, where one can access the cells for the `i`th point by calling `links(i)`.
+# Now we can compute which cells the bounding box tree collides with using `dolfinx.geometry.compute_collisions_points`. This function returns a list of cells whose bounding box collide for each input point. As different points might have different number of cells, the data is stored in `dolfinx.cpp.graph.AdjacencyList_int32`, where one can access the cells for the `i`th point by calling `links(i)`.
 #  However, as the bounding box of a cell spans more of $\mathbb{R}^n$ than the actual cell, we check that the actual cell collides with cell 
 #  using `dolfinx.geometry.select_colliding_cells`, who measures the exact distance between the point and the cell (approximated as a convex hull for higher order geometries).
 # This function also returns an adjacency-list, as the point might align with a facet, edge or vertex that is shared between multiple cells in the mesh.
@@ -179,7 +179,7 @@ def on_boundary(x):
 cells = []
 points_on_proc = []
 # Find cells whose bounding-box collide with the the points
-cell_candidates = geometry.compute_collisions(bb_tree, points.T)
+cell_candidates = geometry.compute_collisions_points(bb_tree, points.T)
 # Choose one of the cells that contains the point
 colliding_cells = geometry.compute_colliding_cells(domain, cell_candidates, points.T)
 for i, point in enumerate(points.T):

chapter1/fundamentals_code.py

@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.14.5
+#       jupytext_version: 1.14.6
 #   kernelspec:
 #     display_name: Python 3 (ipykernel)
 #     language: python

chapter1/membrane_code.ipynb

@@ -134,22 +134,7 @@
    "cell_type": "code",
    "execution_count": 5,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "INFO:root:running build_ext\n",
-      "INFO:root:building 'libffcx_forms_442e05267a595f45eac6a101af56222e5c3d2bb0' extension\n",
-      "INFO:root:x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/local/lib/python3.10/dist-packages/ffcx/codegeneration -I/usr/include/python3.10 -c libffcx_forms_442e05267a595f45eac6a101af56222e5c3d2bb0.c -o ./libffcx_forms_442e05267a595f45eac6a101af56222e5c3d2bb0.o -O2\n",
-      "INFO:root:x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 ./libffcx_forms_442e05267a595f45eac6a101af56222e5c3d2bb0.o -L/usr/lib/x86_64-linux-gnu -o ./libffcx_forms_442e05267a595f45eac6a101af56222e5c3d2bb0.cpython-310-x86_64-linux-gnu.so\n",
-      "INFO:root:running build_ext\n",
-      "INFO:root:building 'libffcx_forms_0a9ce6478cf28d3c30ef59bb7181b230b125b637' extension\n",
-      "INFO:root:x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/local/lib/python3.10/dist-packages/ffcx/codegeneration -I/usr/include/python3.10 -c libffcx_forms_0a9ce6478cf28d3c30ef59bb7181b230b125b637.c -o ./libffcx_forms_0a9ce6478cf28d3c30ef59bb7181b230b125b637.o -O2\n",
-      "INFO:root:x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 ./libffcx_forms_0a9ce6478cf28d3c30ef59bb7181b230b125b637.o -L/usr/lib/x86_64-linux-gnu -o ./libffcx_forms_0a9ce6478cf28d3c30ef59bb7181b230b125b637.cpython-310-x86_64-linux-gnu.so\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "bilinear_form = fem.form(a)\n",
     "linear_form = fem.form(L)"
@@ -209,17 +194,18 @@
    },
    "outputs": [],
    "source": [
+    "import matplotlib as mpl\n",
     "pyvista.start_xvfb()\n",
     "\n",
     "grid = pyvista.UnstructuredGrid(*plot.create_vtk_mesh(V))\n",
     "\n",
     "plotter = pyvista.Plotter()\n",
-    "plotter.open_gif(\"u_time.gif\")\n",
+    "plotter.open_gif(\"u_time.gif\", fps=10)\n",
     "\n",
     "grid.point_data[\"uh\"] = uh.x.array\n",
     "warped = grid.warp_by_scalar(\"uh\", factor=1)\n",
     "\n",
-    "viridis = plt.cm.get_cmap(\"viridis\", 25)\n",
+    "viridis = mpl.colormaps.get_cmap(\"viridis\").resampled(25)\n",
     "sargs = dict(title_font_size=25, label_font_size=20, fmt=\"%.2e\", color=\"black\",\n",
     "             position_x=0.1, position_y=0.8, width=0.8, height=0.1)\n",
     "\n",