Merge branch 'main' into joss-paper

.github/workflows/package.yml

@@ -0,0 +1,24 @@
+name: Packaging
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build_and_upload:
+    name: Build sdist and wheels
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - run: pipx run build
+      - name: Publish package to TestPyPI
+        if: github.event_name == 'release' && github.event.release.prerelease
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+      - name: Publish package to PyPI
+        if: github.event_name == 'release' && ! github.event.release.prerelease
+        uses: pypa/gh-action-pypi-publish@release/v1

README.md

@@ -92,7 +92,7 @@ The above installs the version of `regional-mom6` (plus any required dependencie
 
 #### "*I want to live on the edge! I want the latest developments*"
 
-To install `regional-mom6` directly via GitHub using `pip`, first install `esmpy` as described above. Then:
+To install `regional-mom6` directly from the [GitHub repository](https://github.com/COSIMA/regional-mom6/) using `pip`, first install `esmpy` as described above. Then:
 
 ```bash
 pip install git+https://github.com/COSIMA/regional-mom6.git

docs/demos.rst

@@ -6,4 +6,4 @@ Demos
    :name: demo-gallery
 
    demo_notebooks/reanalysis-forced.ipynb
-   demo_notebooks/access_om2-forced.ipynb
+

docs/index.rst

@@ -1,8 +1,7 @@
 Regional MOM6 Documentation
 ===========================
 
-Python package for automatic generation of regional configurations for the `Modular Ocean Model version 6`_ (MOM6).
-
+[regional-mom6](https://github.com/COSIMA/regional-mom6/) is a Python package for automatic generation of regional configurations for the `Modular Ocean Model version 6`_ (MOM6).
 
 In brief...
 -----------

docs/installation.md

@@ -39,7 +39,7 @@ The above installs the version of `regional-mom6` (plus any required dependencie
 
 ## "*I want to live on the edge! I want the latest developments*"
 
-To install `regional-mom6` directly via GitHub using `pip`, first install `esmpy` as described above. Then:
+To install `regional-mom6` directly from the [GitHub repository](https://github.com/COSIMA/regional-mom6/) using `pip`, first install `esmpy` as described above. Then:
 
 ```bash
 pip install git+https://github.com/COSIMA/regional-mom6.git

pyproject.toml

@@ -6,6 +6,7 @@ authors = [
   {name = "Ashley Barnes, COSIMA community, and contributors"},
 ]
 dynamic = ["version"]
+readme = "README.md"
 dependencies = [
   "bottleneck",
   "dask[array]",

regional_mom6/regional_mom6.py

@@ -296,7 +296,7 @@ def rectangular_hgrid(λ, φ):
         np.diff(λ), dλ * np.ones(np.size(λ) - 1)
     ), "provided array of longitudes must be uniformly spaced"
 
-    # dx = R * cos(φ) * np.deg2rad(dλ) / 2
+    # dx = R * cos(np.deg2rad(φ)) * np.deg2rad(dλ) / 2
     # Note: division by 2 because we're on the supergrid
     dx = np.broadcast_to(
         R * np.cos(np.deg2rad(φ)) * np.deg2rad(dλ) / 2,
@@ -364,7 +364,7 @@ class experiment:
 
     Methods in this class generate the various input files needed for a MOM6
     experiment forced with open boundary conditions (OBCs). The code is agnostic
-    to the user's choice of boundary forcing, bathymetry and surface forcing;
+    to the user's choice of boundary forcing, bathymetry, and surface forcing;
     users need to prescribe what variables are all called via mapping dictionaries
     from MOM6 variable/coordinate name to the name in the input dataset.
 
@@ -825,7 +825,8 @@ def initial_condition(
         eta_out.yh.attrs = ic_raw_tracers.lat.attrs
         eta_out.attrs = ic_raw_eta.attrs
 
-        # if temp units are K, convert to C
+        ## if min(temp) > 100 then assume that units must be degrees K
+        ## (otherwise we can't be on Earth) and convert to degrees C
         if np.min(tracers_out["temp"].isel({"zl": 0})) > 100:
             tracers_out["temp"] -= 273.15
 
@@ -898,8 +899,8 @@ def rectangular_boundary(
                 ``'north'``, or ``'south'``.
             segment_number (int): Number the segments according to how they'll be specified in
                 the ``MOM_input``.
-            arakawa_grid (Optional[str]): Arakawa grid staggering of input; either ``'A'``, ``'B'``,
-                or ``'C'``.
+            arakawa_grid (Optional[str]): Arakawa grid staggering type of the boundary forcing.
+                Either ``'A'`` (default), ``'B'``, or ``'C'``.
         """
 
         print("Processing {} boundary...".format(orientation), end="")
@@ -924,8 +925,8 @@ def setup_bathymetry(
         self,
         *,
         bathymetry_path,
-        longitude_coordinate_name="lat",
-        latitude_coordinate_name="lon",
+        longitude_coordinate_name="lon",
+        latitude_coordinate_name="lat",
         vertical_coordinate_name="elevation",
         fill_channels=False,
         minimum_layers=3,
@@ -1167,7 +1168,7 @@ def tidy_bathymetry(
             {"depth": (["ny", "nx"], bathymetry["elevation"].values)}
         )
         bathymetry.attrs["depth"] = "meters"
-        bathymetry.attrs["standard_name"] = "bathymetryraphic depth at T-cell centers"
+        bathymetry.attrs["standard_name"] = "bathymetric depth at T-cell centers"
         bathymetry.attrs["coordinates"] = "zi"
 
         bathymetry.expand_dims("tiles", 0)
@@ -1339,7 +1340,7 @@ def FRE_tools(self, layout=None):
             "Running GFDL's FRE Tools. The following information is all printed by the FRE tools themselves"
         )
         if not (self.mom_input_dir / "bathymetry.nc").exists():
-            print("No bathymetry file! Need to run .setup_bathymetry method first")
+            print("No bathymetry file! Need to run setup_bathymetry method first")
             return
 
         for p in self.mom_input_dir.glob("mask_table*"):
@@ -1399,8 +1400,6 @@ def setup_run_directory(
         existing files in the 'rundir' directory for the experiment.
 
         Args:
-            regional_mom6_path (str): Path to the regional MOM6 source code that was cloned
-                from GitHub. Default is current path, ``'.'``.
             surface_forcing (Optional[str]): Specify the choice of surface forcing, one
                 of: ``'jra'`` or ``'era5'``. If not prescribed then constant fluxes are used.
             using_payu (Optional[bool]): Whether or not to use payu (https://github.com/payu-org/payu)
@@ -1755,7 +1754,7 @@ def __init__(
 
     def rectangular_brushcut(self):
         """
-        Cut out and interpolate tracers. This method assumes that the boundary
+        Cut out and interpolate tracers. ``rectangular_brushcut`` assumes that the boundary
         is a simple Northern, Southern, Eastern, or Western boundary.
         """
         if self.orientation == "north":
@@ -1949,7 +1948,7 @@ def rectangular_brushcut(self):
             },
         }
 
-        ### Generate our dz variable. This needs to be in layer thicknesses
+        ### Generate the dz variable; needs to be in layer thicknesses
         dz = segment_out[self.z].diff(self.z)
         dz.name = "dz"
         dz = xr.concat([dz, dz[-1]], dim=self.z)