Expand documentation, remove redundant README file and dependencies f…

…rom .toml file, update tests and demos to reflect the structural changes (ocean_forcing method replaced with separate initial condition and boundary forcing functions)

demos/access_om2-forced.ipynb

@@ -770,9 +770,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "expt.ocean_forcing(\n",
-    "    tmpdir,  ## Path to ocean foring files\n",
-    "    {\"time\":\"time\",\n",
+    "# Define a mapping from the MOM5 B grid variables and dimensions to the MOM6 C grid ones\n",
+    "ocean_varnames =     {\"time\":\"time\",\n",
     "     \"yh\":\"yt_ocean\",\n",
     "     \"xh\":\"xt_ocean\",\n",
     "     \"xq\":\"xu_ocean\",\n",
@@ -781,10 +780,24 @@
     "     \"eta\":\"eta_t\",\n",
     "     \"u\":\"u\",\n",
     "     \"v\":\"v\",\n",
-    "     \"tracers\":{\"salt\":\"salt\",\"temp\":\"temp\"}},\n",
-    "    boundaries = [\"south\",\"north\",\"west\",\"east\"],\n",
+    "     \"tracers\":{\"salt\":\"salt\",\"temp\":\"temp\"}}\n",
+    "\n",
+    "# Set up the initial condition\n",
+    "expt.initial_condition(\n",
+    "    tmpdir,     # The directory where the unprocessed initial condition is stored, as definied earlier\n",
+    "    ocean_varnames,\n",
     "    gridtype=\"B\"\n",
-    "    )"
+    "    )\n",
+    "\n",
+    "# Now iterate through our four boundaries \n",
+    "for i,orientation in enumerate([\"south\",\"north\",\"west\",\"east\"]):\n",
+    "    expt.setup_rectangular_boundary(\n",
+    "        tmpdir / (orientation + \"_unprocessed.nc\"),\n",
+    "        ocean_varnames,\n",
+    "        orientation,    # Needs to know the cardinal direction of the boundary\n",
+    "        i + 1,          # Just a number to identify the boundary. Indexes from 1 \n",
+    "        gridtype=\"B\"\n",
+    "        )"
    ]
   },
   {

demos/reanalysis-forced.ipynb

@@ -222,9 +222,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "expt.ocean_forcing(\n",
-    "    glorys_path,  ## Path to ocean foring files\n",
-    "    {\"time\":\"time\",\n",
+    "# Define a mapping from the GLORYS variables and dimensions to the MOM6 ones\n",
+    "ocean_varnames =     {\"time\":\"time\",\n",
     "     \"y\":\"latitude\",\n",
     "     \"x\":\"longitude\",\n",
     "     \"zl\":\"depth\",\n",
@@ -234,10 +233,24 @@
     "     \"tracers\":{\"salt\":\"so\",\n",
     "                \"temp\":\"thetao\"\n",
     "                }\n",
-    "    },\n",
-    "    boundaries = [\"south\",\"north\",\"west\",\"east\"],\n",
-    "    gridtype=\"A\"  ## Grid type. This is an Arakawa A grid sice velocities and tracers are all on the same points\n",
-    ")"
+    "    }\n",
+    "\n",
+    "# Set up the initial condition\n",
+    "expt.initial_condition(\n",
+    "    glorys_path,     # The directory where the unprocessed initial condition is stored, as definied earlier\n",
+    "    ocean_varnames,\n",
+    "    gridtype=\"A\"\n",
+    "    )\n",
+    "\n",
+    "# Now iterate through our four boundaries \n",
+    "for i,orientation in enumerate([\"south\",\"north\",\"west\",\"east\"]):\n",
+    "    expt.setup_rectangular_boundary(\n",
+    "        glorys_path / (orientation + \"_unprocessed.nc\"),\n",
+    "        ocean_varnames,\n",
+    "        orientation,    # Needs to know the cardinal direction of the boundary\n",
+    "        i + 1,          # Just a number to identify the boundary. Indexes from 1 \n",
+    "        gridtype=\"A\"\n",
+    "        )"
    ]
   },
   {

pyproject.toml

@@ -15,7 +15,6 @@ dependencies = [
   "scipy>=1.2.0",
   "xarray",
   "xesmf>=0.8",
-  "ruamel.yaml>=0.18.0",
   "f90nml>=1.4.1",
 ]