Merge pull request #94 from COSIMA/separate-ic-and-boundary

Separate ic and boundary
COSIMA · Feb 16, 2024 · 3e98442 · 3e98442
2 parents 2904cb2 + 3f8f0ed
commit 3e98442
Show file tree

Hide file tree

Showing 10 changed files with 653 additions and 309 deletions.
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -17,6 +17,7 @@ jobs:
   testing:
     needs: formatting
     runs-on: ubuntu-latest
+    container: ghcr.io/cosima/regional-test-env:updated
     defaults:
       run:
         shell: bash -el {0}
@@ -29,6 +30,7 @@ jobs:
       - name: Set up Python ${{ matrix.python-version }}
         uses: conda-incubator/setup-miniconda@v2
         with:
+          miniconda-version: "latest"
           auto-update-conda: true
           auto-activate-base: false
           environment-file: environment-ci.yml
@@ -38,14 +40,22 @@ jobs:
           python -m pip install .
       - name: Install pytest
         run: |
-          python -m pip install pytest pytest-cov
+          python -m pip install pytest pytest-cov nbval
       - name: Test with pytest
         run: |
           if [[ "${{ matrix.python-version }}" == "3.10" ]]; then
             python -m pytest --cov=regional_mom6 --cov-report=xml tests/
           else
             python -m pytest tests/
           fi
+      - name: Test the example notebook
+        run: |
+          ln -s /data demos/PATH_TO_GLORYS_DATA
+          ln -s /data demos/PATH_TO_GEBCO_FILE
+          ln -s /build/FRE-NCtools/tools demos/PATH_TO_FRE_TOOLS
+          ln -s ../ demos/PATH_TO_REGIONAL_MOM6_CODE
+          python -m pytest --nbval demos/reanalysis-forced.ipynb --nbval-current-env --cov=regional_mom6 --cov-report=xml tests/
+
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3
         if: ${{ matrix.python-version == '3.10' }}

diff --git a/.gitignore b/.gitignore
@@ -7,3 +7,4 @@ regional_mom6.egg-info
 .pytest_cache
 .env
 env
+docker
diff --git a/README.md b/README.md
@@ -39,6 +39,15 @@ Source](https://earthsystemmodeling.org/esmpy_doc/release/latest/html/install.ht
 instructions to do this in a Conda-free way. With `esmpy` available, you can then install
 `regional_mom6` via pip. If your environment doesn't yet have pip, then `conda install pip` should do the job.
 
+It's recommended that you get started with the example notebooks. In this case you'll want to clone this entire repo so that you have access to the `demo` folder. This contains some template configuration files for MOM6, and example notebooks that walk you through the package. 
+
+```bash 
+git clone git@github.com:COSIMA/regional-mom6.git
+pip install .
+```
+
+Alternatively you can install the python package only. Some functionality will be missing in this case, namely the `setup_run_directory` function as it relies on copying across and modifying the template files. 
+
 ```bash
 pip install git+https://github.com/COSIMA/regional-mom6.git
 ```

diff --git a/demos/README.md b/demos/README.md
diff --git a/demos/access_om2-forced.ipynb b/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.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",
+    "        )"
    ]
   },
   {
@@ -802,7 +815,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "expt.FRE_tools((10,10))\n"
+    "expt.FRE_tools(layout = (10,10))\n"
    ]
   },
   {

diff --git a/demos/premade_run_directories/common_files/MOM_override b/demos/premade_run_directories/common_files/MOM_override
@@ -1,9 +1,4 @@
 ## Add override files here
 
-!#override OBC_SEGMENT_001 = "J=0,I=0:N,ORLANSKI" !
-!#override OBC_SEGMENT_002 = "J=0,I=0:N,ORLANSKI" !
-!#override OBC_SEGMENT_003 = "J=0,I=0:N,ORLANSKI" !
-!#override OBC_SEGMENT_004 = "J=0,I=0:N,ORLANSKI" !
-
 #override DT=50
 #override DT_THERM=300
diff --git a/demos/reanalysis-forced.ipynb b/demos/reanalysis-forced.ipynb
@@ -37,8 +37,7 @@
     "import regional_mom6 as rm\n",
     "from pathlib import Path\n",
     "from dask.distributed import Client\n",
-    "client = Client()\n",
-    "client"
+    "client = Client() # Start a dask cluster"
    ]
   },
   {
@@ -67,13 +66,13 @@
     "daterange = [\"2003-01-01 00:00:00\", \"2003-01-05 00:00:00\"] ## 2003 is a good compimise for GLORYs and JRA forcing as they overlap. JRA ends in 2012, GLORYS starts in 1993\n",
     "\n",
     "## Place where all your input files go \n",
-    "inputdir = Path(f\"YOUR_PATH/mom6_inputdirs/{expt_name}/\")\n",
+    "inputdir = Path(f\"mom6_input_directories/{expt_name}/\")\n",
     "\n",
     "## Directory where you'll run the experiment from\n",
-    "rundir = Path(f\"YOUR_PATH/mom6_rundirs/{expt_name}/\")\n",
+    "rundir = Path(f\"mom6_run_directories/{expt_name}/\")\n",
     "\n",
     "## Directory where fre tools are stored \n",
-    "toolpath = Path(\"PATH_TO_COMPILED_FRE_TOOLS\") ## Compiled tools needed for construction of mask tables\n",
+    "toolpath = Path(\"PATH_TO_FRE_TOOLS\") ## Compiled tools needed for construction of mask tables\n",
     "\n",
     "## Path to where your raw ocean forcing files are stored\n",
     "glorys_path = Path(\"PATH_TO_GLORYS_DATA\" )\n",
@@ -197,7 +196,12 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "nbval-ignore-output",
+     "nbval-skip"
+    ]
+   },
    "outputs": [],
    "source": [
     "expt.topog.depth.plot()"
@@ -222,9 +226,8 @@
    "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 +237,24 @@
     "     \"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 / \"ic_unprocessed.nc\",     # 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.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",
+    "        )"
    ]
   },
   {
@@ -255,7 +272,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "expt.FRE_tools((10,10)) ## Here the tuple defines the processor layout\n"
+    "expt.FRE_tools(layout=(10,10)) ## Here the tuple defines the processor layout\n"
    ]
   },
   {
@@ -289,7 +306,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "nbval-skip"
+    ]
+   },
    "outputs": [],
    "source": [
     "expt.setup_era5(\"PATH_TO_ERA5_DATA/era5/single-levels/reanalysis\")"
@@ -301,7 +322,9 @@
    "source": [
     "## Step 8: Modify the default input directory to make a (hopefully) runnable configuration out of the box\n",
     "\n",
-    "This step copies the default directory, and modifies the `MOM_layout` files to match your experiment by inserting the right number of x,y points and cpu layout. If you use Payu to run mom6, set the `using_payu` flag to `True` and an example `config.yaml` file will be copied to your run directory. This still needs to be modified manually to work with your projects, executable etc."
+    "This step copies the default directory, and modifies the `MOM_layout` files to match your experiment by inserting the right number of x,y points and cpu layout. If you use Payu to run mom6, set the `using_payu` flag to `True` and an example `config.yaml` file will be copied to your run directory. This still needs to be modified manually to work with your projects, executable etc.\n",
+    "\n",
+    "You also need to pass the path to where you git cloned the mom6-regional code. This just ensures that the funciton can find the premade run directories."
    ]
   },
   {
@@ -310,7 +333,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "expt.setup_run_directory(surface_forcing = \"era5\",using_payu = False)"
+    "expt.setup_run_directory(\"PATH_TO_REGIONAL_MOM6_CODE\",surface_forcing = \"era5\",using_payu = False)"
    ]
   },
   {
@@ -331,9 +354,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python [conda env:analysis3-unstable]",
+   "display_name": "Python [conda env:analysis3-23.10] *",
    "language": "python",
-   "name": "conda-env-analysis3-unstable-py"
+   "name": "conda-env-analysis3-23.10-py"
   },
   "language_info": {
    "codemirror_mode": {

diff --git a/pyproject.toml b/pyproject.toml
@@ -15,7 +15,6 @@ dependencies = [
   "scipy>=1.2.0",
   "xarray",
   "xesmf>=0.8",
-  "PyYAML>=6.0.1",
   "f90nml>=1.4.1",
 ]
-Original file line number
+Diff line change
@@ Expand Up / @@ -7,3 +7,4 @@ regional_mom6.egg-info @@
     .pytest_cache
     .env
     env
+    docker