updates:

kthyng · kthyng · commit 562eff88749a · 2025-08-27T15:45:56.000-07:00
* update Python test versions
* update dependencies
* some fixes in `extract_model` to keep things working with `ocean-model-skill-assessor`
diff --git a/ci/environment-py3.11-win.yml b/ci/environment-py3.11-win.yml
@@ -1,22 +1,21 @@
-name: test-env-win
+name: test-env-extract-model
 channels:
   - conda-forge
 dependencies:
   - python=3.11
-  - cf_xarray>=0.6
+  - cf_xarray
   - dask
   - netcdf4
-  - numpy #<1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
+  - numpy
   - pip
   - requests
-  - scikit-learn  # used by xoak for tree
+  - scikit-learn
   - xarray
   - xoak
-  # - xroms
   - pytest
   - pytest-benchmark
   - pip:
-    - xroms >=0.5.3
+    - xroms >=0.6.2
     - codecov
     - pytest-cov
     - coverage[toml]
diff --git a/ci/environment-py3.11.yml b/ci/environment-py3.11.yml
@@ -1,4 +1,4 @@
-name: test-env-mac-unix
+name: test-env-extract-model
 channels:
   - conda-forge
 dependencies:
@@ -9,15 +9,15 @@ dependencies:
   - numpy #<1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
   - pip
   - requests
-  - scikit-learn  # used by xoak for tree
+  - scikit-learn
   - xarray
   - xesmf
   - xoak
   # - xroms
   - pytest
   - pytest-benchmark
   - pip:
-    - xroms >=0.5.3
+    - xroms >=0.6.2
     - codecov
     - pytest-cov
     - coverage[toml]
diff --git a/ci/environment-py3.12-win.yml b/ci/environment-py3.12-win.yml
@@ -1,4 +1,4 @@
-name: test-env-win
+name: test-env-extract-model
 channels:
   - conda-forge
 dependencies:
@@ -9,14 +9,14 @@ dependencies:
   - numpy #<1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
   - pip
   - requests
-  - scikit-learn  # used by xoak for tree
+  - scikit-learn
   - xarray
   - xoak
   # - xroms
   - pytest
   - pytest-benchmark
   - pip:
-    - xroms >=0.5.3
+    - xroms >=0.6.2
     - codecov
     - pytest-cov
     - coverage[toml]
diff --git a/ci/environment-py3.12.yml b/ci/environment-py3.12.yml
@@ -1,23 +1,23 @@
-name: test-env-mac-unix
+name: test-env-extract-model
 channels:
   - conda-forge
 dependencies:
   - python=3.12
-  - cf_xarray>=0.6
+  - cf_xarray
   - dask
   - netcdf4
-  - numpy #<1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
+  - numpy 
   - pip
   - requests
-  - scikit-learn  # used by xoak for tree
+  - scikit-learn
   - xarray
   - xesmf
   - xoak
   # - xroms
   - pytest
   - pytest-benchmark
   - pip:
-    - xroms >=0.5.3
+    - xroms >=0.6.2
     - codecov
     - pytest-cov
     - coverage[toml]
diff --git a/ci/environment-py3.13-win.yml b/ci/environment-py3.13-win.yml
@@ -1,22 +1,22 @@
-name: test-env-win
+name: test-env-extract-model
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python=3.13
   - cf_xarray>=0.6
   - dask
   - netcdf4
   - numpy #<1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
   - pip
   - requests
-  - scikit-learn  # used by xoak for tree
+  - scikit-learn
   - xarray
   - xoak
   # - xroms
   - pytest
   - pytest-benchmark
   - pip:
-    - xroms >=0.5.3
+    - xroms >=0.6.2
     - codecov
     - pytest-cov
     - coverage[toml]
diff --git a/ci/environment-py3.13.yml b/ci/environment-py3.13.yml
@@ -1,23 +1,23 @@
-name: test-env-mac-unix
+name: test-env-extract-model
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python=3.13
   - cf_xarray>=0.6
   - dask
   - netcdf4
   - numpy #<1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
   - pip
   - requests
-  - scikit-learn  # used by xoak for tree
+  - scikit-learn
   - xarray
   - xesmf
   - xoak
   # - xroms
   - pytest
   - pytest-benchmark
   - pip:
-    - xroms >=0.5.3
+    - xroms >=0.6.2
     - codecov
     - pytest-cov
     - coverage[toml]
diff --git a/docs/environment.yml b/docs/environment.yml
@@ -3,14 +3,14 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-   - python=3.8
+   - python=3.12
    # If your docs code examples depend on other packages add them here
    - cf_xarray
    - cmocean
-   - dask <=2022.05.0 # for xESMF, https://github.com/axiom-data-science/extract_model/issues/49
+   - dask
    - matplotlib-base
    - netcdf4
-   - numpy <1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
+   - numpy
    - numba  # required by xesmf
    - pip
    - pooch
diff --git a/docs/whats_new.rst b/docs/whats_new.rst
@@ -1,6 +1,12 @@
 :mod:`What's New`
 -----------------
 
+v1.4.2 (August 27, 2025)
+========================
+* update Python test versions
+* update dependencies
+* some fixes in `extract_model` to keep things working with `ocean-model-skill-assessor`
+
 v1.4.1 (October 25, 2024)
 =========================
 * Small changes so horizontal coordinate search works more consistently with past.
diff --git a/environment.yml b/environment.yml
@@ -2,26 +2,24 @@ name: extract_model
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python=3.12
   # Required for full project functionality (dont remove)
   - pytest
   - pytest-benchmark
   # Examples (remove and add as needed)
   - cf_xarray
   - cmocean
-  - dask #<=2022.05.0 # for xESMF, https://github.com/axiom-data-science/extract_model/issues/49
+  - dask
   - extract_model
   - matplotlib
   - netcdf4
-  - numpy #<1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
+  - numpy
   - numba  # required by xesmf
   - pip
   - pooch
   - requests
-  - scikit-learn  # used by xoak for tree
   - xarray
   - xcmocean
   - xesmf  # don't install if on windows
-  - xoak
   # - pip:  # install from github to get recent PRs I contributed
   #   - git@github.com:xarray-contrib/cf-xarray.git
diff --git a/extract_model/extract_model.py b/extract_model/extract_model.py
@@ -613,11 +613,34 @@ def pt_in_itriangle_proj(ix, iy):
                 z_attrs = da.cf["vertical"].attrs
                 z_attrs.update({"axis": "Z"})
                 zkey = da.cf["vertical"].name
-                da = xgcm_grid.transform(
-                    da, "Z", np.array(Z), target_data=da.cf["vertical"], method="linear"
-                )
-                da[zkey].attrs = z_attrs
-                da = order(da)  # reorder dimensions to convention
+                if isinstance(da, xr.DataArray):
+                    with warnings.catch_warnings():
+                        warnings.simplefilter("ignore")
+                        da = xgcm_grid.transform(
+                            da, "Z", np.array(Z), target_data=da.cf["vertical"], method="linear"
+                        )
+                    da[zkey].attrs = z_attrs
+                    da = order(da)  # reorder dimensions to convention
+                elif isinstance(da, xr.Dataset):
+                    da_calcs = {}
+                    for data_var in da.data_vars:
+                        if "s_rho" in da.dims:
+                            dause = da[data_var].chunk({"s_rho": -1})#.copy()
+                        else:
+                            dause = da[data_var]
+                        with warnings.catch_warnings():
+                            warnings.simplefilter("ignore")
+                            da_calcs[data_var] = xgcm_grid.transform(
+                                dause,
+                                "Z",
+                                np.array(Z),
+                                target_data=dause.cf["vertical"],
+                                method="linear",
+                            )
+                        da_calcs[data_var][zkey].attrs = z_attrs
+                    for data_var in da_calcs.keys():
+                        da[data_var] = da_calcs[data_var]
+                    da = order(da)  # reorder dimensions to convention
 
             # # if the vertical coord is greater than 1D, can only do restricted interpolation
             # # at the moment
@@ -902,11 +925,10 @@ def sel2d(
                 return output
 
     else:
-
         # make sure the mask matches
         if mask is not None:
-            # import pdb; pdb.set_trace()
-            msg = f"Mask {mask.name} dimensions do not match horizontal var {var.name} dimensions. mask dims: {mask.dims}, var dims: {var.dims}"
+            msg = f"Mask {mask.name} dimensions do not match horizontal Dataset/DataArray dimensions. mask dims: {mask.dims}, var dims: {var.dims}"
+            # msg = f"Mask {mask.name} dimensions do not match horizontal var {var.name} dimensions. mask dims: {mask.dims}, var dims: {var.dims}"
             assert len(set(mask.dims) - set(var.dims)) == 0, msg
 
         # currently lons, lats 1D only
diff --git a/extract_model/preprocessing.py b/extract_model/preprocessing.py
@@ -2,6 +2,7 @@
 
 
 from typing import Optional
+import warnings
 
 import numpy as np
 import xarray as xr
@@ -156,35 +157,37 @@ def preprocess_roms(
             # }
 
             ds.coords["z_rho"] = order(ds["z_rho"])
-            ds.coords["z_rho_u"] = grid.interp(
-                ds.z_rho.chunk({ds.z_rho.cf["X"].name: -1}), "X"
-            )
-            ds.coords["z_rho_u"].attrs = {
-                "long_name": "depth of U-points on vertical RHO grid",
-                "time": "ocean_time",
-                "field": "z_rho_u, scalar, series",
-                "units": "m",
-            }
-
-            ds.coords["z_rho_v"] = grid.interp(
-                ds.z_rho.chunk({ds.z_rho.cf["Y"].name: -1}), "Y"
-            )
-            ds.coords["z_rho_v"].attrs = {
-                "long_name": "depth of V-points on vertical RHO grid",
-                "time": "ocean_time",
-                "field": "z_rho_v, scalar, series",
-                "units": "m",
-            }
-
-            ds.coords["z_rho_psi"] = grid.interp(
-                ds.z_rho_u.chunk({ds.z_rho_u.cf["Y"].name: -1}), "Y"
-            )
-            ds.coords["z_rho_psi"].attrs = {
-                "long_name": "depth of PSI-points on vertical RHO grid",
-                "time": "ocean_time",
-                "field": "z_rho_psi, scalar, series",
-                "units": "m",
-            }
+            with warnings.catch_warnings():
+                warnings.simplefilter("ignore")
+                ds.coords["z_rho_u"] = grid.interp(
+                    ds.z_rho.chunk({ds.z_rho.cf["X"].name: -1}), "X"
+                )
+                ds.coords["z_rho_u"].attrs = {
+                    "long_name": "depth of U-points on vertical RHO grid",
+                    "time": "ocean_time",
+                    "field": "z_rho_u, scalar, series",
+                    "units": "m",
+                }
+
+                ds.coords["z_rho_v"] = grid.interp(
+                    ds.z_rho.chunk({ds.z_rho.cf["Y"].name: -1}), "Y"
+                )
+                ds.coords["z_rho_v"].attrs = {
+                    "long_name": "depth of V-points on vertical RHO grid",
+                    "time": "ocean_time",
+                    "field": "z_rho_v, scalar, series",
+                    "units": "m",
+                }
+
+                ds.coords["z_rho_psi"] = grid.interp(
+                    ds.z_rho_u.chunk({ds.z_rho_u.cf["Y"].name: -1}), "Y"
+                )
+                ds.coords["z_rho_psi"].attrs = {
+                    "long_name": "depth of PSI-points on vertical RHO grid",
+                    "time": "ocean_time",
+                    "field": "z_rho_psi, scalar, series",
+                    "units": "m",
+                }
 
             # will use this to update coordinate encoding
             name_dict.update(
@@ -330,7 +333,9 @@ def preprocess_roms_grid(ds):
         "Y": {"center": "eta_rho", "inner": "eta_v"},
         "Z": {"center": "s_rho", "outer": "s_w"},
     }
-    grid = Grid(ds, coords=coords, periodic=False)
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+        grid = Grid(ds, coords=coords, periodic=False)
     return grid
 
 
diff --git a/extract_model/utils.py b/extract_model/utils.py
@@ -140,7 +140,7 @@ def f_standard_names(value):
     to_merge.append(ds.filter_by_attrs(standard_name=f_standard_names))
 
     # Combine
-    return xr.merge(to_merge)
+    return xr.merge(to_merge, compat='no_conflicts')
 
 
 def naive_subbox(ds: xr.Dataset, bbox: BBoxType, dask_array_chunks: bool = False):
@@ -354,15 +354,15 @@ def sub_grid(
             subs = sub_bbox(ds[varname], bbox, other=-500, drop=False)
 
             # index
-            i_xi_rho = int((subs != -500).sum(dim="xi_rho").argmax())
+            i_xi_rho = int(np.argmax((subs != -500).sum(dim="xi_rho").values))
             xi_rho_bool = subs.isel(eta_rho=i_xi_rho) != -500
             if "T" in subs.cf.axes:
                 xi_rho_bool = xi_rho_bool.cf.isel(T=0)
             if "Z" in subs.cf.axes:
                 xi_rho_bool = xi_rho_bool.cf.isel(Z=0)
             xi_rho = np.arange(ds.lon_rho.shape[1])[xi_rho_bool]
 
-            i_eta_rho = int((subs != -500).sum(dim="eta_rho").argmax())
+            i_eta_rho = int(np.argmax((subs != -500).sum(dim="eta_rho").values))
             eta_rho_bool = subs.isel(xi_rho=i_eta_rho) != -500
             if "T" in subs.cf.axes:
                 eta_rho_bool = eta_rho_bool.cf.isel(T=0)
diff --git a/setup.cfg b/setup.cfg
