Fix legacy code, typos, suppress run_time warnings, added further support for PyVista visualisations, flagged all kernel killing code raised in Issue #46

notebooks/Exercise_01.ipynb

@@ -49,8 +49,7 @@
     "import iris\n",
     "from geovista import GeoPlotter\n",
     "from esmf_regrid.experimental.unstructured_scheme import MeshToGridESMFRegridder, GridToMeshESMFRegridder\n",
-    "from iris.experimental.ugrid.load import PARSE_UGRID_ON_LOAD\n",
-    "pv.rcParams[\"use_ipyvtk\"] = True\n",
+    "# pv.rcParams[\"use_ipyvtk\"] = True\n",
     "iris.FUTURE.datum_support = True  # avoids some warnings"
    ]
   },

notebooks/Sec_01_Load_and_Examine.ipynb

@@ -20,17 +20,7 @@
    "source": [
     "## Iris unstructured loading\n",
     "\n",
-    "\"Unstructured\" data can be loaded from UGRID files (i.e. netCDF files containing a UGRID-style mesh). This is just like normal [Iris](https://scitools-iris.readthedocs.io/en/latest) loading, except that we must *enable* the interpretion of UGRID content like this:\n",
-    "\n",
-    "```python\n",
-    "with PARSE_UGRID_ON_LOAD.context():\n",
-    "    cube_list = iris.load(path [, constraints])\n",
-    "    # ..and/or..\n",
-    "    single_cube = iris.load_cube(path [, constraints])\n",
-    "    # ..and/or..\n",
-    "    selected_cubes = iris.load_cubes(path, cube_constraints)\n",
-    "\n",
-    "```"
+    "\"Unstructured\" data can be loaded from UGRID files (i.e. netCDF files containing a UGRID-style mesh). This is just like normal [Iris](https://scitools-iris.readthedocs.io/en/latest) loading."
    ]
   },
   {
@@ -40,7 +30,7 @@
    "source": [
     "### Enable UGRID loading\n",
     "\n",
-    "To test loading of UGRID files, like demonstrated above, we need to import `iris`, and the `PARSE_UGRID_ON_LOAD` object from [iris.experimental.ugrid.load](https://scitools-iris.readthedocs.io/en/latest/generated/api/iris/experimental/ugrid/load.html#)\n"
+    "To test loading of UGRID files, like demonstrated above, we need to import `iris`."
    ]
   },
   {
@@ -52,9 +42,11 @@
    },
    "outputs": [],
    "source": [
-    "import iris \n",
+    "import iris\n",
     "\n",
-    "from iris.experimental.ugrid.load import PARSE_UGRID_ON_LOAD"
+    "# This will suppress RuntimeWarning flags\n",
+    "import warnings\n",
+    "warnings.filterwarnings(\"ignore\")"
    ]
   },
   {
@@ -103,20 +95,25 @@
    "outputs": [],
    "source": [
     "print('loading...')\n",
-    "with PARSE_UGRID_ON_LOAD.context():\n",
-    "    cubes = iris.load(lfric_filepth)\n",
+    "\n",
+    "iris.FUTURE.date_microseconds = True\n",
+    "\n",
+    "cubes = iris.load(lfric_filepth)\n",
     "\n",
     "print(f'\\n... Loaded {len(cubes)} cubes.')\n",
-    "print('Showing first 6:')\n",
-    "cubes[:6]"
+    "print('Showing them all:')\n",
+    "cubes"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "604a48f9-8275-40e9-9d97-9294ce4e8ad7",
    "metadata": {},
    "source": [
-    "Putting just `cubes` at the end of the code above triggers noteboook printing output. You can click on each cube to expand it into detail view. Try this. Try also to use `print(cubes)` instead. To spot some structual differences between LFRic and UM data also load some cubes from `um_filepath` above. "
+    "Putting just `cubes` at the end of the code above triggers notebook printing output. You can click on each cube to expand it into detail view. Try this. <span style=\"color:red; font-weight:bold;\">Currently does not show any data, just empty table</span>\n",
+    "\n",
+    "\n",
+    "Try also to use `print(cubes)` instead. To spot some structual differences between LFRic and UM data also load some cubes from `um_filepath` above. "
    ]
   },
   {
@@ -151,22 +148,21 @@
    },
    "outputs": [],
    "source": [
-    "with PARSE_UGRID_ON_LOAD.context():\n",
-    "    lfric_rh = iris.load_cube(lfric_filepth,'relative_humidity_wrt_water')\n",
+    "lfric_rh = iris.load_cube(lfric_filepth,'relative_humidity_wrt_water')\n",
     "\n",
     "# just uncomment to explore: \n",
-    "#print(lfric_rh)\n",
-    "#print(lfric_rh.mesh)\n",
-    "#print(lfric_rh.location)\n",
-    "#print(lfric_rh.mesh_dim)\n"
+    "# print(lfric_rh)\n",
+    "# print(lfric_rh.mesh)\n",
+    "# print(lfric_rh.location)\n",
+    "# print(lfric_rh.mesh_dim)\n"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "ee291cd1-7009-43e1-b62a-2ab615d458f0",
    "metadata": {},
    "source": [
-    "If the cube is not a mesh cube these propertise are  `None`, which we can demonstrate with a cube from the \"UM file\":   "
+    "If the cube is not a mesh cube these properties are `None`, which we can demonstrate with a cube from the \"UM file\":   "
    ]
   },
   {
@@ -179,8 +175,27 @@
    "outputs": [],
    "source": [
     "um_cube = iris.load_cube(um_filepth,'air_temperature')\n",
-    "#print(um_cube)\n",
-    "print(um_cube.mesh)\n"
+    "print('You can see the data here: \\n \\n', um_cube)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3b558541",
+   "metadata": {},
+   "source": [
+    "It is clearly not a mesh.\n",
+    "\n",
+    "If we try to print the mesh property, then the output is as follows:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9cdbd267",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print(um_cube.mesh)"
    ]
   },
   {

notebooks/Sec_02_Meshes.ipynb

@@ -100,14 +100,6 @@
     "## Next notebook\n",
     "See the next section: [03 - Plotting and Visualisation](./Sec_03_Plotting.ipynb)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "12005e21-9a61-44a2-85c1-01d11da5ade3",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

notebooks/Sec_03_Plotting.ipynb

@@ -39,10 +39,18 @@
    "outputs": [],
    "source": [
     "import geovista as gv\n",
-    "from geovista.pantry import um_orca2\n",
+    "from geovista.pantry.data import nemo_orca2\n",
     "from display_demo_routines import popup_2d_data_xx_yy\n",
     "\n",
-    "example_data = um_orca2()\n",
+    "# This will suppress RuntimeWarning flags\n",
+    "import warnings\n",
+    "warnings.filterwarnings(\"ignore\")\n",
+    "\n",
+    "# This is needed to run in a Jupyter notebook\n",
+    "import pyvista\n",
+    "pyvista.set_jupyter_backend('trame') # make sure trame, trame-vtk, and trame-vuetify are installed in conda env\n",
+    "\n",
+    "example_data = nemo_orca2()\n",
     "popup_2d_data_xx_yy(example_data, \"ORCA test data\")"
    ]
   },
@@ -99,8 +107,8 @@
     "from pv_conversions import pv_from_lfric_cube\n",
     "\n",
     "pv = pv_from_lfric_cube(lfric_rh)\n",
-    "#print(pv)\n",
-    "#pv"
+    "print(pv)\n",
+    "pv"
    ]
   },
   {
@@ -246,7 +254,7 @@
    "outputs": [],
    "source": [
     "viewpoint = plotter.camera_position\n",
-    "#print(viewpoint)"
+    "print(viewpoint)"
    ]
   },
   {