Merge branch 'main' into add_full_land_var

Author: chengzhuzhang

.github/workflows/build_workflow.yml

@@ -29,17 +29,17 @@ jobs:
         uses: actions/checkout@v3
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
-        name: Set up Python 3.11
+        name: Set up Python 3.13
         uses: actions/setup-python@v3
         with:
-          python-version: "3.11"
+          python-version: "3.13"
 
       - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
         # Run all pre-commit hooks on all the files.
         # Getting only staged files can be tricky in case a new PR is opened
         # since the action is run on a branch in detached head state
         name: Install and Run Pre-commit
-        uses: pre-commit/[email protected].0
+        uses: pre-commit/[email protected].1
 
   build:
     name: Build (Python ${{ matrix.python-version }})
@@ -50,7 +50,7 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13"]
     container:
       image: ghcr.io/e3sm-project/containers-e3sm-diags-test-data:e3sm-diags-test-data-0.0.2
     steps:

conda-env/ci.yml

@@ -7,7 +7,7 @@ channels:
 dependencies:
   # Base
   # =================
-  - python >=3.10
+  - python >=3.11,<3.14
   - pip
   - setuptools
   - beautifulsoup4

conda-env/dev.yml

@@ -5,7 +5,7 @@ channels:
 dependencies:
   # Base
   # =======================
-  - python >=3.10
+  - python >=3.11,<3.14
   - pip
   - setuptools
   - beautifulsoup4

e3sm_diags/derivations/formulas.py

@@ -75,7 +75,8 @@ def qsat(temp: xr.DataArray, surfp: xr.DataArray) -> xr.DataArray:
 
     # Calculation of saturation water vapour pressure (sat_wvp) from Teten's
     # formula/
-    sat_wvp: xr.DataArray = a1 * np.exp(a3 * (temp - T0) / (temp - a4))
+    # FIXME: error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[float64]]", variable has type "DataArray")  [assignment]
+    sat_wvp: xr.DataArray = a1 * np.exp(a3 * (temp - T0) / (temp - a4))  # type: ignore
 
     # Calculation of saturation specific humidity at 2m qsat  (equal to huss)
     # with units g/kg.

e3sm_diags/driver/tc_analysis_driver.py

@@ -88,8 +88,10 @@ def run_diag(parameter: TCAnalysisParameter) -> TCAnalysisParameter:
     ref_data = collections.OrderedDict()
 
     test_data["metrics"] = generate_tc_metrics_from_te_stitch_file(test_te_file)
-    test_data["cyclone_density"] = test_cyclones_hist
-    test_data["aew_density"] = test_aew_hist
+    # FIXME: mypy error: Incompatible types in assignment (expression has type "DataArray", target has type "dict[str, Any]")  [assignment]
+    test_data["cyclone_density"] = test_cyclones_hist  # type: ignore
+    # FIXME: mypy error: Incompatible types in assignment (expression has type "DataArray", target has type "dict[str, Any]")  [assignment]
+    test_data["aew_density"] = test_aew_hist  # type: ignore
     test_num_years = int(test_end_yr) - int(test_start_yr) + 1
     test_data["aew_num_years"] = test_num_years  # type: ignore
     test_data["cyclone_num_years"] = test_num_years  # type: ignore
@@ -121,8 +123,10 @@ def run_diag(parameter: TCAnalysisParameter) -> TCAnalysisParameter:
         # Note the refactor included subset that was missed in original implementation
         ref_aew_hist = xr.open_dataset(ref_aew_file).sel()["density"]
         ref_data["metrics"] = generate_tc_metrics_from_te_stitch_file(ref_te_file)
-        ref_data["cyclone_density"] = ref_cyclones_hist
-        ref_data["aew_density"] = ref_aew_hist
+        # FIXME: mypy error: Incompatible types in assignment (expression has type "DataArray", target has type "dict[str, Any]")  [assignment]
+        ref_data["cyclone_density"] = ref_cyclones_hist  # type: ignore
+        # FIXME: mypy error: Incompatible types in assignment (expression has type "DataArray", target has type "dict[str, Any]")  [assignment]
+        ref_data["aew_density"] = ref_aew_hist  # type: ignore
         ref_num_years = int(ref_end_yr) - int(ref_start_yr) + 1
         ref_data["aew_num_years"] = ref_num_years  # type: ignore
         ref_data["cyclone_num_years"] = ref_num_years  # type: ignore
@@ -142,9 +146,11 @@ def run_diag(parameter: TCAnalysisParameter) -> TCAnalysisParameter:
         ref_aew_hist = xr.open_dataset(ref_aew_file).sel(
             lat=slice(0, 35), lon=slice(180, 360)
         )["density"]
-        ref_data["cyclone_density"] = ref_cyclones_hist
+        # FIXME: mypy error: Incompatible types in assignment (expression has type "DataArray", target has type "dict[str, Any]")  [assignment]
+        ref_data["cyclone_density"] = ref_cyclones_hist  # type: ignore
         ref_data["cyclone_num_years"] = 40  # type: ignore
-        ref_data["aew_density"] = ref_aew_hist
+        # FIXME: mypy error: Incompatible types in assignment (expression has type "DataArray", target has type "dict[str, Any]")  [assignment]
+        ref_data["aew_density"] = ref_aew_hist  # type: ignore
         # Question, should the num_years = 5?
         ref_data["aew_num_years"] = 1  # type: ignore
         parameter.ref_name = "Observation"

e3sm_diags/driver/utils/dataset_xr.py

@@ -920,7 +920,8 @@ def _get_dataset_with_derivation_func(
         func_args = [ds[var].copy() for var in src_var_keys]
 
         if func in FUNC_NEEDS_TARGET_VAR:
-            func_args = [target_var_key] + func_args  # pragma: nocover
+            # FIXME: error: Incompatible types in assignment (expression has type "list[DataArray | str]", variable has type "list[DataArray]")  [assignment]
+            func_args = [target_var_key] + func_args  # type: ignore  # pragma: no cover
 
         # If the target variable key contains a wildcard, there are can be
         # N number of function arguments. For the cases, we need to pass the

e3sm_diags/driver/utils/zwf_functions.py

@@ -374,9 +374,11 @@ def resolveWavesHayashi(varfft: xr.DataArray, nDayWin: int, spd: int) -> xr.Data
         if (c != "wavenumber") and (c != "frequency"):
             ocoords[c] = varfft[c]
         elif c == "wavenumber":
-            ocoords["wavenumber"] = wave
+            # FIXME: mypy error: Incompatible types in assignment (expression has type "ndarray[tuple[int], dtype[Any]]", target has type "DataArray")  [assignment]
+            ocoords["wavenumber"] = wave  # type: ignore
         elif c == "frequency":
-            ocoords["frequency"] = freq
+            # FIXME: mypy error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[float64]]", target has type "DataArray")  [assignment]
+            ocoords["frequency"] = freq  # type: ignore
     pee = xr.DataArray(pee, dims=odims, coords=ocoords)
     return pee
 

e3sm_diags/plot/tropical_subseasonal_plot.py

@@ -339,10 +339,12 @@ def _wave_frequency_plot(  # noqa: C901
         print("west_power: %12.5f" % west_power)
         print("ew_ratio: %12.5f\n" % ew_ratio)
 
-        z = np.log10(z)
+        # FIXME: mypy error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "DataArray")  [assignment]
+        z = np.log10(z)  # type: ignore
 
     if "spec_background" in var_name and subplot_num < 2:
-        z = np.log10(z)
+        # FIXME: mypy error: Incompatible types in assignment (expression has type "ndarray[tuple[Any, ...], dtype[Any]]", variable has type "DataArray")  [assignment]
+        z = np.log10(z)  # type: ignore
 
     z.attrs["long_name"] = PlotDesc[var_name]["long_name_desc"]
     z.attrs["method"] = (

pyproject.toml

@@ -15,14 +15,13 @@ authors = [
 ]
 license = { text = "BSD 3-Clause" }
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 classifiers = [
   "Development Status :: 5 - Production/Stable",
   "Intended Audience :: Developers",
   "License :: OSI Approved :: BSD 3-Clause License",
   "Natural Language :: English",
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
@@ -215,7 +214,7 @@ testpaths = "tests/e3sm_diags"
 
 [tool.mypy]
 # Docs: https://mypy.readthedocs.io/en/stable/config_file.html
-python_version = "3.10"
+python_version = "3.13"
 check_untyped_defs = true
 ignore_missing_imports = true
 warn_unused_ignores = true

tests/e3sm_diags/driver/utils/test_dataset_xr.py

@@ -875,7 +875,8 @@ def test_returns_climo_dataset_using_climo_of_time_series_files(self):
             name="ts", data=np.array([[1.0, 1.0], [1.0, 1.0]]), dims=["lat", "lon"]
         )
         # Set all of the correct attributes.
-        expected = expected.assign(**spatial_coords)
+        # FIXME: mypy error: Argument 1 to "assign" of "Dataset" has incompatible type "**dict[str, DataArray]"; expected "Mapping[Any, Any] | None"  [arg-type]
+        expected = expected.assign(**spatial_coords)  # type: ignore
         expected = expected.drop_dims("time")
         expected = expected.bounds.add_missing_bounds(axes=["X", "Y"])