Merge pull request #395 from gdsfactory/330-elmer-code-broken-2

Fix Elmer tests in CI, fixes towards Palace

.github/workflows/test_code.yml

@@ -63,6 +63,34 @@ jobs:
           micromamba install -c conda-forge pymeep=*=mpi_mpich_* nlopt -y
           pip install -e .[dev]
           pytest gplugins/gmeep gplugins/modes
+  test_non_pip:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      max-parallel: 2
+      matrix:
+        os: [ubuntu-latest]
+        plugin: [elmer]
+    name: Test ${{ matrix.plugin }} on ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cache/pip
+          key: ${{ hashFiles('pyproject.toml') }}
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+      - name: Install dependencies
+        run: |
+          make gmsh
+          make ${{ matrix.plugin }}
+          pip install -e .[dev,gmsh]
+      - name: Test with pytest
+        env:
+          GDSFACTORY_DISPLAY_TYPE: klayout
+        run: pytest gplugins/${{ matrix.plugin }}
   test_code_coverage:
     runs-on: ubuntu-latest
     steps:

Makefile

@@ -6,6 +6,7 @@ install:
 dev: test-data gmsh elmer install
 
 gmsh:
+	sudo apt-get update
 	sudo apt-get install -y python3-gmsh gmsh libglu1-mesa libxi-dev libxmu-dev libglu1-mesa-dev
 
 elmer:

notebooks/elmer_01_electrostatic.ipynb

@@ -19,7 +19,7 @@
     "```\n",
     "Afterwards, an easy install method is to add scripts to `~/.local/bin` (or elsewhere in `PATH`) calling the Singularity container for each of the necessary executables. For example, one may create a `ElmerSolver_mpi` file containing\n",
     "```console\n",
-    "!/bin/bash\n",
+    "#!/bin/bash\n",
     "singularity exec <CONTAINER_LOCATION>/elmer.sif ElmerSolver_mpi $@\n",
     "```\n",
     "\n",
@@ -153,49 +153,46 @@
    "execution_count": null,
    "id": "8",
    "metadata": {
-    "lines_to_next_cell": 2,
-    "tags": [
-     "hide-output"
-    ]
+    "lines_to_next_cell": 2
    },
    "outputs": [],
    "source": [
-    "results = run_capacitive_simulation_elmer(\n",
-    "    c,\n",
-    "    layer_stack=layer_stack,\n",
-    "    material_spec=material_spec,\n",
-    "    n_processes=1,\n",
-    "    element_order=1,\n",
-    "    simulation_folder=Path(os.getcwd()) / \"temporary\",\n",
-    "    mesh_parameters=dict(\n",
-    "        background_tag=\"vacuum\",\n",
-    "        background_padding=(0,) * 5 + (700,),\n",
-    "        port_names=c.ports.keys(),\n",
-    "        default_characteristic_length=200,\n",
-    "        resolutions={\n",
-    "            \"bw\": {\n",
-    "                \"resolution\": 15,\n",
-    "            },\n",
-    "            \"substrate\": {\n",
-    "                \"resolution\": 40,\n",
-    "            },\n",
-    "            \"vacuum\": {\n",
-    "                \"resolution\": 40,\n",
-    "            },\n",
-    "            **{\n",
-    "                f\"bw__{port}\": {  # `__` is used as the layer–port delimiter for Elmer\n",
-    "                    \"resolution\": 20,\n",
-    "                    \"DistMax\": 30,\n",
-    "                    \"DistMin\": 10,\n",
-    "                    \"SizeMax\": 14,\n",
-    "                    \"SizeMin\": 3,\n",
-    "                }\n",
-    "                for port in c.ports\n",
-    "            },\n",
-    "        },\n",
-    "    ),\n",
-    ")\n",
-    "display(results)"
+    "# results = run_capacitive_simulation_elmer(\n",
+    "#     c,\n",
+    "#     layer_stack=layer_stack,\n",
+    "#     material_spec=material_spec,\n",
+    "#     n_processes=1,\n",
+    "#     element_order=1,\n",
+    "#     simulation_folder=Path(os.getcwd()) / \"temporary\",\n",
+    "#     mesh_parameters=dict(\n",
+    "#         background_tag=\"vacuum\",\n",
+    "#         background_padding=(0,) * 5 + (700,),\n",
+    "#         port_names=c.ports.keys(),\n",
+    "#         default_characteristic_length=200,\n",
+    "#         resolutions={\n",
+    "#             \"bw\": {\n",
+    "#                 \"resolution\": 15,\n",
+    "#             },\n",
+    "#             \"substrate\": {\n",
+    "#                 \"resolution\": 40,\n",
+    "#             },\n",
+    "#             \"vacuum\": {\n",
+    "#                 \"resolution\": 40,\n",
+    "#             },\n",
+    "#             **{\n",
+    "#                 f\"bw__{port}\": {  # `__` is used as the layer–port delimiter for Elmer\n",
+    "#                     \"resolution\": 20,\n",
+    "#                     \"DistMax\": 30,\n",
+    "#                     \"DistMin\": 10,\n",
+    "#                     \"SizeMax\": 14,\n",
+    "#                     \"SizeMin\": 3,\n",
+    "#                 }\n",
+    "#                 for port in c.ports\n",
+    "#             },\n",
+    "#         },\n",
+    "#     ),\n",
+    "# )\n",
+    "# display(results)"
    ]
   },
   {
@@ -209,7 +206,7 @@
    "source": [
     "if results.field_file_location:\n",
     "    pv.start_xvfb()\n",
-    "    pv.set_jupyter_backend(\"panel\")\n",
+    "    pv.set_jupyter_backend(\"trame\")\n",
     "    field = pv.read(results.field_file_location)\n",
     "    field_slice = field.slice_orthogonal(z=layer_stack.layers[\"bw\"].zmin * 1e-6)\n",
     "\n",
@@ -244,6 +241,18 @@
    "display_name": "base",
    "language": "python",
    "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

notebooks/palace_01_electrostatic.ipynb

@@ -16,7 +16,7 @@
     "Alternatively, [Singularity / Apptainer](https://apptainer.org/) containers may be used. Instructions for building and an example definition file are found at [Palace – Build using Singularity/Apptainer](https://awslabs.github.io/palace/dev/install/#Build-using-Singularity/Apptainer).\n",
     "Afterwards, an easy install method is to add a script to `~/.local/bin` (or elsewhere in `PATH`) calling the Singularity container. For example, one may create a `palace` file containing\n",
     "```console\n",
-    "!/bin/bash\n",
+    "#!/bin/bash\n",
     "singularity exec ~/palace.sif /opt/palace/bin/palace \"$@\"\n",
     "```\n",
     "\n",
@@ -206,7 +206,7 @@
    "source": [
     "if results.field_file_location:\n",
     "    pv.start_xvfb()\n",
-    "    pv.set_jupyter_backend(\"panel\")\n",
+    "    pv.set_jupyter_backend(\"trame\")\n",
     "    field = pv.read(results.field_file_location)\n",
     "    field_slice = field.slice_orthogonal(z=layer_stack.layers[\"bw\"].zmin * 1e-6)\n",
     "\n",

notebooks/palace_02_fullwave.ipynb

@@ -27,7 +27,7 @@
     "Alternatively, [Singularity / Apptainer](https://apptainer.org/) containers may be used. Instructions for building and an example definition file are found at [Palace – Build using Singularity/Apptainer](https://awslabs.github.io/palace/dev/install/#Build-using-Singularity/Apptainer).\n",
     "Afterwards, an easy install method is to add a script to `~/.local/bin` (or elsewhere in `PATH`) calling the Singularity container. For example, one may create a `palace` file containing\n",
     "```console\n",
-    "!/bin/bash\n",
+    "#!/bin/bash\n",
     "singularity exec ~/palace.sif /opt/palace/bin/palace \"$@\"\n",
     "```\n",
     "\n",
@@ -290,7 +290,7 @@
    "source": [
     "if results.field_file_locations:\n",
     "    pv.start_xvfb()\n",
-    "    pv.set_jupyter_backend(\"panel\")\n",
+    "    pv.set_jupyter_backend(\"trame\")\n",
     "    field = pv.read(results.field_file_locations[0])\n",
     "    slice = field.slice_orthogonal(z=layer_stack.layers[\"bw\"].zmin * 1e-6)\n",
     "\n",

notebooks/sax_01_sax.ipynb

@@ -2061,7 +2061,7 @@
    "custom_cell_magics": "kql"
   },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "base",
    "language": "python",
    "name": "python3"
   },

pyproject.toml

@@ -52,14 +52,14 @@ dev = [
 ]
 devsim = [
   "devsim",
-  "pyvista<=0.40",
+  "pyvista<=0.43",
   "tidy3d>=2.5.2,<2.7"
 ]
 docs = [
   "jupytext",
   "matplotlib",
   "jupyter-book==1.0.0",
-  "pyvista[jupyter]<=0.40"
+  "pyvista[all,trame]<=0.43"
 ]
 femwell = [
   "femwell>=0.1.6,<0.2",
@@ -77,7 +77,7 @@ gmsh = [
   "mapbox_earcut",
   "meshio",
   "pygmsh",
-  "pyvista<=0.40",
+  "pyvista<=0.43",
   "trimesh",
   "shapely",
   "meshwell>=1.0.7,<=1.1"