Merge pull request #303 from boutproject/xarray-2024-07

Update to xarray 2023.1.0

Author: ZedThree

.github/workflows/master.yml

@@ -20,7 +20,7 @@ jobs:
     if: always()
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.x"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
       fail-fast: false
 
     steps:
@@ -61,7 +61,7 @@ jobs:
       run: |
         sudo apt-get update && sudo apt-get install libhdf5-dev libnetcdf-dev
         python -m pip install --upgrade pip
-        pip install xarray~=0.18.0 pandas~=1.4.0
+        pip install xarray~=2023.1.0 pandas~=1.4.0
     - name: Install package
       run: |
         pip install -e .[tests]

.github/workflows/pythonpackage.yml

@@ -31,7 +31,6 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        sudo apt-get update && sudo apt-get install libhdf5-dev libnetcdf-dev
         python -m pip install --upgrade pip
     - name: Install package
       run: |
@@ -59,9 +58,8 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        sudo apt-get update && sudo apt-get install libhdf5-dev libnetcdf-dev
         python -m pip install --upgrade pip
-        pip install xarray~=0.18.0 pandas~=1.4.0
+        pip install xarray~=2023.1.0 pandas~=1.4.0
     - name: Install package
       run: |
         pip install -e .[tests]

.github/workflows/ruff.yaml

@@ -5,11 +5,11 @@ jobs:
   dependency-review:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.x'
       - name: Install ruff
         run: pip install ruff
       - name: Run ruff
-        run: ruff xbout
+        run: ruff check xbout

pyproject.toml

@@ -33,7 +33,7 @@ classifiers = [
 ]
 requires-python = ">=3.8"
 dependencies = [
-    "xarray>=0.18.0,<2022.9.0",
+    "xarray>=2023.01.0",
     "boutdata>=0.1.4",
     "dask[array]>=2.10.0",
     "gelidum>=0.5.3",
@@ -82,5 +82,5 @@ write_to = "xbout/_version.py"
 [tool.setuptools]
 packages = ["xbout"]
 
-[tool.ruff]
+[tool.ruff.lint]
 ignore = ["E501"]

xbout/boutdataset.py

@@ -597,12 +597,12 @@ def interpolate_to_cartesian(
         n_toroidal = ds.sizes[zdim]
 
         # Create Cartesian grid to interpolate to
-        Xmin = ds["X_cartesian"].min()
-        Xmax = ds["X_cartesian"].max()
-        Ymin = ds["Y_cartesian"].min()
-        Ymax = ds["Y_cartesian"].max()
-        Zmin = ds["Z_cartesian"].min()
-        Zmax = ds["Z_cartesian"].max()
+        Xmin = ds["X_cartesian"].min().data[()]
+        Xmax = ds["X_cartesian"].max().data[()]
+        Ymin = ds["Y_cartesian"].min().data[()]
+        Ymax = ds["Y_cartesian"].max().data[()]
+        Zmin = ds["Z_cartesian"].min().data[()]
+        Zmax = ds["Z_cartesian"].max().data[()]
         newX_1d = xr.DataArray(np.linspace(Xmin, Xmax, nX), dims="X")
         newX = newX_1d.expand_dims({"Y": nY, "Z": nZ}, axis=[1, 2])
         newY_1d = xr.DataArray(np.linspace(Ymin, Ymax, nY), dims="Y")

xbout/geometries.py

@@ -10,6 +10,7 @@
     _set_attrs_on_all_vars,
     _set_as_coord,
     _1d_coord_from_spacing,
+    _maybe_rename_dimension,
 )
 
 REGISTERED_GEOMETRIES = {}
@@ -144,7 +145,7 @@ def apply_geometry(ds, geometry_name, *, coordinates=None, grid=None):
         # 'dx' may not be consistent between different regions (e.g. core and PFR).
         # For some geometries xcoord may have already been created by
         # add_geometry_coords, in which case we do not need this.
-        nx = updated_ds.dims[xcoord]
+        nx = updated_ds.sizes[xcoord]
 
         # can't use commented out version, uncommented one works around xarray bug
         # removing attrs
@@ -181,7 +182,7 @@ def apply_geometry(ds, geometry_name, *, coordinates=None, grid=None):
     if zcoord in updated_ds.dims and zcoord not in updated_ds.coords:
         # Generates a coordinate whose value is 0 on the first grid point, not dz/2, to
         # match how BOUT++ generates fields from input file expressions.
-        nz = updated_ds.dims[zcoord]
+        nz = updated_ds.sizes[zcoord]
 
         # In BOUT++ v5, dz is either a Field2D or Field3D.
         # We can use it as a 1D coordinate if it's a Field3D, _or_ if nz == 1
@@ -213,7 +214,7 @@ def apply_geometry(ds, geometry_name, *, coordinates=None, grid=None):
                 dz = updated_ds["dz"]
 
             z0 = 2 * np.pi * updated_ds.metadata["ZMIN"]
-            z1 = z0 + nz * dz
+            z1 = z0 + nz * dz.data[()]
             if not np.all(
                 np.isclose(
                     z1,
@@ -392,12 +393,12 @@ def add_toroidal_geometry_coords(ds, *, coordinates=None, grid=None):
         ],
     )
 
-    if "t" in ds.dims:
+    if coordinates["t"] != "t":
         # Rename 't' if user requested it
-        ds = ds.rename(t=coordinates["t"])
+        ds = _maybe_rename_dimension(ds, "t", coordinates["t"])
 
     # Change names of dimensions to Orthogonal Toroidal ones
-    ds = ds.rename(y=coordinates["y"])
+    ds = _maybe_rename_dimension(ds, "y", coordinates["y"])
 
     # TODO automatically make this coordinate 1D in simplified cases?
     ds = ds.rename(psixy=coordinates["x"])
@@ -413,7 +414,7 @@ def add_toroidal_geometry_coords(ds, *, coordinates=None, grid=None):
 
     # If full data (not just grid file) then toroidal dim will be present
     if "z" in ds.dims:
-        ds = ds.rename(z=coordinates["z"])
+        ds = _maybe_rename_dimension(ds, "z", coordinates["z"])
 
         # Record which dimension 'z' was renamed to.
         ds.metadata["bout_zdim"] = coordinates["z"]
@@ -505,7 +506,7 @@ def add_s_alpha_geometry_coords(ds, *, coordinates=None, grid=None):
     ds["r"] = ds["hthe"].isel({ycoord: 0}).squeeze(drop=True)
     ds["r"].attrs["units"] = "m"
     ds = ds.set_coords("r")
-    ds = ds.rename(x="r")
+    ds = ds.swap_dims(x="r")
     ds.metadata["bout_xdim"] = "r"
 
     if hthe_from_grid: