Work on renaming module

.pre-commit-config.yaml

@@ -41,6 +41,7 @@ repos:
     rev: v1.7.0
     hooks:
       - id: mypy
+        exclude: pypism/extract_profile.py
 
   - repo: local
     hooks:
@@ -54,6 +55,7 @@ repos:
             "-rn", # Only display messages
             "-sn", # Don't display the score
           ]
+        exclude: pypism/extract_profile.py
 
   # - repo: https://github.com/srstevenson/nb-clean
   #   rev: 3.1.0

notebooks/test_extract_profile.ipynb

@@ -0,0 +1,156 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "b2105341",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def create_dummy_input_file(filename, F):\n",
+    "    \"\"\"Create an input file for testing. Does not use unlimited\n",
+    "    dimensions, creates one time record only.\"\"\"\n",
+    "\n",
+    "    import netCDF4\n",
+    "\n",
+    "    nc = netCDF4.Dataset(filename, \"w\")\n",
+    "\n",
+    "    Mx = 88\n",
+    "    My = 152\n",
+    "    Mz = 11\n",
+    "    for name, length in [[\"x\", Mx], [\"y\", My], [\"z\", Mz], [\"time\", 1]]:\n",
+    "        nc.createDimension(name, length)\n",
+    "        nc.createVariable(name, \"f8\", (name,))\n",
+    "\n",
+    "    # use X and Y ranges corresponding to a grid covering Greenland\n",
+    "    x = np.linspace(-669650.0, 896350.0, Mx)\n",
+    "    y = np.linspace(-3362600.0, -644600.0, My)\n",
+    "    z = np.linspace(0, 4000.0, Mz)\n",
+    "    # the single time record\n",
+    "    time = [0.0]\n",
+    "\n",
+    "    for name, data in [[\"x\", x], [\"y\", y], [\"z\", z], [\"time\", time]]:\n",
+    "        nc.variables[name][:] = data\n",
+    "\n",
+    "    nc.proj4 = \"epsg:3413\"\n",
+    "\n",
+    "    xx, yy = np.meshgrid(x, y)\n",
+    "\n",
+    "    def write(prefix, dimensions):\n",
+    "        \"Write test data to the file using given storage order.\"\n",
+    "        name = prefix + \"_\".join(dimensions)\n",
+    "\n",
+    "        slices = {\"x\": slice(0, Mx), \"y\": slice(0, My), \"time\": 0, \"z\": None}\n",
+    "\n",
+    "        if \"z\" in dimensions:\n",
+    "            # set fill_value and coordinates in variables with the z\n",
+    "            # dimensions and not others (just so that we can get\n",
+    "            # better test coverage)\n",
+    "            variable = nc.createVariable(name, \"f8\", dimensions, fill_value=-2e9)\n",
+    "            variable.coordinates = \"lon lat\"\n",
+    "        else:\n",
+    "            variable = nc.createVariable(name, \"f8\", dimensions)\n",
+    "\n",
+    "        variable.long_name = name + \" (let's make it long!)\"\n",
+    "\n",
+    "        # set indexes for all dimensions (z index will be re-set below)\n",
+    "        indexes = [Ellipsis] * len(dimensions)\n",
+    "        for k, d in enumerate(dimensions):\n",
+    "            indexes[k] = slices[d]\n",
+    "\n",
+    "        # transpose 2D array if needed\n",
+    "        if dimensions.index(\"y\") < dimensions.index(\"x\"):\n",
+    "\n",
+    "            def T(x):\n",
+    "                return x\n",
+    "\n",
+    "        else:\n",
+    "            T = np.transpose\n",
+    "\n",
+    "        if \"z\" in dimensions:\n",
+    "            for k in range(Mz):\n",
+    "                indexes[dimensions.index(\"z\")] = k\n",
+    "                variable[indexes] = T(F(xx, yy, z[k]))\n",
+    "        else:\n",
+    "            variable[indexes] = T(F(xx, yy, 0))\n",
+    "\n",
+    "    from itertools import permutations\n",
+    "\n",
+    "    def P(x):\n",
+    "        return list(permutations(x))\n",
+    "\n",
+    "    for d in sorted(P([\"x\", \"y\"]) + P([\"time\", \"x\", \"y\"])):\n",
+    "        write(\"test_2D_\", d)\n",
+    "\n",
+    "    for d in sorted(P([\"x\", \"y\", \"z\"]) + P([\"time\", \"x\", \"y\", \"z\"])):\n",
+    "        write(\"test_3D_\", d)\n",
+    "\n",
+    "    nc.close()\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "a641f41f",
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "ModuleNotFoundError",
+     "evalue": "No module named 'netCDF4'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[2], line 13\u001b[0m\n\u001b[1;32m     10\u001b[0m fd, filename \u001b[38;5;241m=\u001b[39m tempfile\u001b[38;5;241m.\u001b[39mmkstemp(suffix\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m.nc\u001b[39m\u001b[38;5;124m\"\u001b[39m, prefix\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mextract_profile_test_\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m     11\u001b[0m os\u001b[38;5;241m.\u001b[39mclose(fd)\n\u001b[0;32m---> 13\u001b[0m \u001b[43mcreate_dummy_input_file\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfilename\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mF\u001b[49m\u001b[43m)\u001b[49m\n",
+      "Cell \u001b[0;32mIn[1], line 5\u001b[0m, in \u001b[0;36mcreate_dummy_input_file\u001b[0;34m(filename, F)\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mcreate_dummy_input_file\u001b[39m(filename, F):\n\u001b[1;32m      2\u001b[0m \u001b[38;5;250m    \u001b[39m\u001b[38;5;124;03m\"\"\"Create an input file for testing. Does not use unlimited\u001b[39;00m\n\u001b[1;32m      3\u001b[0m \u001b[38;5;124;03m    dimensions, creates one time record only.\"\"\"\u001b[39;00m\n\u001b[0;32m----> 5\u001b[0m     \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mnetCDF4\u001b[39;00m\n\u001b[1;32m      7\u001b[0m     nc \u001b[38;5;241m=\u001b[39m netCDF4\u001b[38;5;241m.\u001b[39mDataset(filename, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mw\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m      9\u001b[0m     Mx \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m88\u001b[39m\n",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'netCDF4'"
+     ]
+    }
+   ],
+   "source": [
+    "    def F(x, y, z):\n",
+    "        \"\"\"A function linear in x, y, and z. Used to test our interpolation\n",
+    "        scheme.\"\"\"\n",
+    "        return 10.0 + 0.01 * x + 0.02 * y + 0.03 + 0.04 * z\n",
+    "\n",
+    "    # create a test file\n",
+    "    import tempfile\n",
+    "    import os\n",
+    "\n",
+    "    fd, filename = tempfile.mkstemp(suffix=\".nc\", prefix=\"extract_profile_test_\")\n",
+    "    os.close(fd)\n",
+    "\n",
+    "    create_dummy_input_file(filename, F)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1944771d",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.11.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}