mypy compliance (#1721)

### What kind of change does this PR introduce?

* Addresses several issues (around 250/1250 errors) associated with
(re-)casting of variables and output typing.
* The `Indicator.__getitem__` method has been retired (to reduce
instances of class methods returning `Any`)
* PEP8 rule N802 is now enforced (with `noqa` exceptions, mostly for
functions based on `sfcWind` variable).
* The `wrapped_partial` function wrapper has been removed.

### Does this PR introduce a breaking change?

Yes. The Indicator `__getitem__` method has been removed. This has
downstream impacts on `finch` and possibly other projects. Additionally,
the obsolete `wrapped_partial` function (was previously used in
Indicator construction) has also been removed.

CHANGES.rst

@@ -28,7 +28,8 @@ Breaking changes
 * The previously deprecated function ``xclim.ensembles.change_significance`` has been removed. (:pull:`1737`).
 * Indicators ``snw_season_length`` and ``snd_season_length`` have been modified, see above.
 * The `hargeaves85`/`hg85` method for the ``potential_evapotranspiration`` indicator and indice has been modified for precision and consistency with recent academic literature. (:issue:`1710`, :pull:`1723`).
-
+* The `__getitem__` method of ``xclim.core.indicator.Parameter`` instances has been removed. Accessing members of ``Parameters`` now uniquely uses dot notation. (:pull:`1721`).
+* The obsolete function wrapper for generating Indicators ``xclim.core.utils.wrapped_partial`` has been removed. (:pull:`1721`).
 
 Bug fixes
 ^^^^^^^^^
@@ -39,6 +40,7 @@ Bug fixes
 * Fixed "agreement fraction" in ``robustness_fractions`` to distinguish between negative change and no change. Added "negative" and "changed negative" fractions (:issue:`1690`, :pull:`1711`).
 * ``make_criteria`` now skips columns with NaNs across all realizations. (:pull:`1713`).
 * Fixed bug QuantileDeltaMapping adjustment not working for seasonal grouping (:issue:`1704`, :pull:`1716`).
+* The codebase has been adjusted to address several (~400) `mypy`-related errors attributable to inaccurate function call signatures and variable name shadowing. (:issue:`1719`, :pull:`1721`).
 
 Internal changes
 ^^^^^^^^^^^^^^^^
@@ -48,6 +50,7 @@ Internal changes
 * Added the `tox-gh` dependency to the development installation recipe. This will soon be required for running the `tox` test ensemble on GitHub Workflows. (:pull:`1709`).
 * Added the `vulture` static code analysis tool for finding dead code to the development dependency list and linters (makefile, tox and pre-commit hooks). (:pull:`1717`).
 * Added error message when using `xclim.indices.stats.dist_method` with `nnlf` and included note in docstring. (:issue:`1683`, :pull:`1714`).
+* PEP8 rule `N802` is now enabled in the `ruff` formatter. Function names should follow `Snake case <https://en.wikipedia.org/wiki/Snake_case>`_, with rare exceptions. (:pull:`1721`).
 
 v0.48.2 (2024-02-26)
 --------------------

docs/notebooks/extendxclim.ipynb

@@ -540,7 +540,6 @@
    "outputs": [],
    "source": [
     "from xclim.core.indicator import build_indicator_module, registry\n",
-    "from xclim.core.utils import wrapped_partial\n",
     "\n",
     "mapping = dict(\n",
     "    egg_cooking_season=registry[\"MAXIMUM_CONSECUTIVE_WARM_DAYS\"](\n",

environment.yml

@@ -53,6 +53,7 @@ dependencies:
   - nc-time-axis
   - netCDF4 >=1.4
   - notebook
+  - pandas-stubs
   - platformdirs
   - pooch
   - pre-commit

pyproject.toml

@@ -71,6 +71,7 @@ dev = [
   "nbqa",
   "nbval",
   "netCDF4 >=1.4",
+  "pandas-stubs>=2.2",
   "platformdirs >=3.2",
   "pre-commit >=2.9",
   "pybtex",
@@ -153,7 +154,7 @@ values = [
 
 [tool.codespell]
 skip = 'xclim/data/*.json,docs/_build,docs/notebooks/xclim_training/*.ipynb,docs/references.bib,__pycache__,*.nc,*.png,*.gz,*.whl'
-ignore-words-list = "absolue,astroid,bloc,bui,callendar,degreee,environnement,hanel,inferrable,lond,nam,nd,ressources,vas"
+ignore-words-list = "absolue,astroid,bloc,bui,callendar,degreee,environnement,hanel,inferrable,lond,nam,nd,ressources,sie,vas"
 
 [tool.coverage.run]
 relative_files = true
@@ -207,24 +208,20 @@ python_version = 3.9
 show_error_codes = true
 warn_return_any = true
 warn_unused_configs = true
+plugins = ["numpy.typing.mypy_plugin"]
 
 [[tool.mypy.overrides]]
 module = [
   "boltons.*",
-  "bottleneck.*",
   "cftime.*",
-  "clisops.core.subset.*",
-  "dask.*",
-  "lmoments3.*",
-  "matplotlib.*",
+  "jsonpickle.*",
   "numba.*",
-  "numpy.*",
-  "pandas.*",
-  "pint.*",
+  "pytest_socket.*",
   "SBCK.*",
   "scipy.*",
-  "sklearn.cluster.*",
-  "xarray.*",
+  "sklearn.*",
+  "statsmodels.*",
+  "yamale.*",
   "yaml.*"
 ]
 ignore_missing_imports = true
@@ -273,6 +270,7 @@ select = [
   "D",
   "E",
   "F",
+  "N802",
   "W"
 ]
 
@@ -299,7 +297,7 @@ max-complexity = 20
 
 [tool.ruff.lint.per-file-ignores]
 "docs/*.py" = ["D100", "D101", "D102", "D103"]
-"tests/*.py" = ["D100", "D101", "D102", "D103"]
+"tests/*.py" = ["D100", "D101", "D102", "D103", "N802"]
 "xclim/**/__init__.py" = ["F401", "F403"]
 "xclim/core/indicator.py" = ["D214", "D405", "D406", "D407", "D411"]
 "xclim/core/locales.py" = ["E501", "W505"]

tests/test_indicators.py

@@ -225,7 +225,7 @@ def test_opt_vars(tasmin_series, tasmax_series):
     tx = tasmax_series(np.zeros(365))
 
     multiOptVar(tasmin=tn, tasmax=tx)
-    assert multiOptVar.parameters["tasmin"]["kind"] == InputKind.OPTIONAL_VARIABLE
+    assert multiOptVar.parameters["tasmin"].kind == InputKind.OPTIONAL_VARIABLE
 
 
 def test_registering():
@@ -265,8 +265,10 @@ def test_module():
     """Translations are keyed according to the module where the indicators are defined."""
     assert atmos.tg_mean.__module__.split(".")[2] == "atmos"
     # Virtual module also are stored under xclim.indicators
-    assert xclim.indicators.cf.fg.__module__ == "xclim.indicators.cf"
-    assert xclim.indicators.icclim.GD4.__module__ == "xclim.indicators.icclim"
+    assert xclim.indicators.cf.fg.__module__ == "xclim.indicators.cf"  # noqa: F821
+    assert (
+        xclim.indicators.icclim.GD4.__module__ == "xclim.indicators.icclim"
+    )  # noqa: F821
 
 
 def test_temp_unit_conversion(tas_series):
@@ -377,7 +379,7 @@ def test_multiindicator(tas_series):
         compute=uniindtemp_compute,
     )
     with pytest.raises(ValueError, match="Indicator minmaxtemp4 was wrongly defined"):
-        tmin, tmax = ind(tas, freq="YS")
+        _tmin, _tmax = ind(tas, freq="YS")
 
 
 def test_missing(tas_series):
@@ -480,7 +482,7 @@ def test_all_parameters_understood(official_indicators):
     for identifier, ind in official_indicators.items():
         indinst = ind.get_instance()
         for name, param in indinst.parameters.items():
-            if param["kind"] == InputKind.OTHER_PARAMETER:
+            if param.kind == InputKind.OTHER_PARAMETER:
                 problems.add((identifier, name))
     # this one we are ok with.
     if problems - {
@@ -587,15 +589,15 @@ def test_parsed_doc():
     assert "tas" in xclim.atmos.liquid_precip_accumulation.parameters
 
     params = xclim.atmos.drought_code.parameters
-    assert params["tas"]["description"] == "Noon temperature."
-    assert params["tas"]["units"] == "[temperature]"
-    assert params["tas"]["kind"] is InputKind.VARIABLE
-    assert params["tas"]["default"] == "tas"
-    assert params["snd"]["default"] is None
-    assert params["snd"]["kind"] is InputKind.OPTIONAL_VARIABLE
-    assert params["snd"]["units"] == "[length]"
-    assert params["season_method"]["kind"] is InputKind.STRING
-    assert params["season_method"]["choices"] == {"GFWED", None, "WF93", "LA08"}
+    assert params["tas"].description == "Noon temperature."
+    assert params["tas"].units == "[temperature]"
+    assert params["tas"].kind is InputKind.VARIABLE
+    assert params["tas"].default == "tas"
+    assert params["snd"].default is None
+    assert params["snd"].kind is InputKind.OPTIONAL_VARIABLE
+    assert params["snd"].units == "[length]"
+    assert params["season_method"].kind is InputKind.STRING
+    assert params["season_method"].choices == {"GFWED", None, "WF93", "LA08"}
 
 
 def test_default_formatter():
@@ -655,14 +657,14 @@ def test_input_dataset(open_dataset):
     ds = open_dataset("ERA5/daily_surface_cancities_1990-1993.nc")
 
     # Use defaults
-    out = xclim.atmos.daily_temperature_range(freq="YS", ds=ds)
+    _ = xclim.atmos.daily_temperature_range(freq="YS", ds=ds)
 
     # Use non-defaults (inverted on purpose)
     with xclim.set_options(cf_compliance="log"):
-        out = xclim.atmos.daily_temperature_range("tasmax", "tasmin", freq="YS", ds=ds)
+        _ = xclim.atmos.daily_temperature_range("tasmax", "tasmin", freq="YS", ds=ds)
 
     # Use a mix
-    out = xclim.atmos.daily_temperature_range(tasmax=ds.tasmax, freq="YS", ds=ds)
+    _ = xclim.atmos.daily_temperature_range(tasmax=ds.tasmax, freq="YS", ds=ds)
 
     # Inexistent variable:
     dsx = ds.drop_vars("tasmin")

tests/test_utils.py

@@ -2,8 +2,6 @@
 # Test for utils
 from __future__ import annotations
 
-from inspect import signature
-
 import numpy as np
 import xarray as xr
 
@@ -12,7 +10,6 @@
     ensure_chunk_size,
     nan_calc_percentiles,
     walk_map,
-    wrapped_partial,
 )
 from xclim.testing.helpers import test_timeseries as _test_timeseries
 
@@ -24,29 +21,6 @@ def test_walk_map():
     assert o["b"]["c"] == 0
 
 
-def test_wrapped_partial():
-    def func(a, b=1, c=1):
-        """Docstring"""
-        return (a, b, c)
-
-    newf = wrapped_partial(func, b=2)
-    assert list(signature(newf).parameters.keys()) == ["a", "c"]
-    assert newf(1) == (1, 2, 1)
-
-    newf = wrapped_partial(func, suggested=dict(c=2), b=2)
-    assert list(signature(newf).parameters.keys()) == ["a", "c"]
-    assert newf(1) == (1, 2, 2)
-    assert newf.__doc__ == func.__doc__
-
-    def func(a, b=1, c=1, **kws):  # pylint: disable=function-redefined
-        """Docstring"""
-        return a, b, c
-
-    newf = wrapped_partial(func, suggested=dict(c=2), a=2, b=2)
-    assert list(signature(newf).parameters.keys()) == ["c", "kws"]
-    assert newf() == (2, 2, 2)
-
-
 def test_ensure_chunk_size():
     da = xr.DataArray(np.zeros((20, 21, 20)), dims=("x", "y", "z"))
 

xclim/__init__.py

@@ -2,10 +2,7 @@
 
 from __future__ import annotations
 
-try:
-    from importlib.resources import files as _files
-except ImportError:
-    from importlib_resources import files as _files
+import importlib.resources as _resources
 
 from xclim import indices
 from xclim.core import units  # noqa
@@ -19,15 +16,13 @@
 __version__ = "0.48.3-dev.15"
 
 
-_module_data = _files("xclim.data")
+with _resources.as_file(_resources.files("xclim.data")) as _module_data:
+    # Load official locales
+    for filename in _module_data.glob("??.json"):
+        # Only select <locale>.json and not <module>.<locale>.json
+        load_locale(filename, filename.stem)
 
-# Load official locales
-for filename in _module_data.glob("??.json"):
-    # Only select <locale>.json and not <module>.<locale>.json
-    load_locale(filename, filename.stem)
-
-
-# Virtual modules creation:
-build_indicator_module_from_yaml(_module_data / "icclim", mode="raise")
-build_indicator_module_from_yaml(_module_data / "anuclim", mode="raise")
-build_indicator_module_from_yaml(_module_data / "cf", mode="raise")
+    # Virtual modules creation:
+    build_indicator_module_from_yaml(_module_data / "icclim", mode="raise")
+    build_indicator_module_from_yaml(_module_data / "anuclim", mode="raise")
+    build_indicator_module_from_yaml(_module_data / "cf", mode="raise")

xclim/analog.py

@@ -60,12 +60,12 @@ def spatial_analogs(
     # Create the target DataArray
     # drop any (sub-)index along "dist_dim" that could conflict with target, and rename it.
     # The drop is the simplest solution that is compatible with both xarray <=2022.3.0 and >2022.3.1
-    candidates = candidates.to_array("_indices", "candidates").rename(
+    candidate_array = candidates.to_array("_indices", "candidates").rename(
         {dist_dim: "_dist_dim"}
     )
-    if isinstance(candidates.indexes["_dist_dim"], pd.MultiIndex):
-        candidates = candidates.drop_vars(
-            ["_dist_dim"] + candidates.indexes["_dist_dim"].names,
+    if isinstance(candidate_array.indexes["_dist_dim"], pd.MultiIndex):
+        candidate_array = candidate_array.drop_vars(
+            ["_dist_dim"] + candidate_array.indexes["_dist_dim"].names,
             # in xarray <= 2022.3.0 the sub-indexes are not listed as separate coords,
             # instead, they are dropped when the multiindex is dropped.
             errors="ignore",
@@ -78,16 +78,16 @@ def spatial_analogs(
             f"Method `{method}` is not implemented. Available methods are: {','.join(metrics.keys())}."
         ) from e
 
-    if candidates.chunks is not None:
-        candidates = candidates.chunk({"_indices": -1})
+    if candidate_array.chunks is not None:
+        candidate_array = candidate_array.chunk({"_indices": -1})
     if target_array.chunks is not None:
         target_array = target_array.chunk({"_indices": -1})
 
     # Compute dissimilarity
     diss = xr.apply_ufunc(
         metric_func,
         target_array,
-        candidates,
+        candidate_array,
         input_core_dims=[(dist_dim, "_indices"), ("_dist_dim", "_indices")],
         output_core_dims=[()],
         vectorize=True,

xclim/cli.py

@@ -19,12 +19,14 @@
 from xclim.testing.helpers import TESTDATA_BRANCH, populate_testing_data
 from xclim.testing.utils import _default_cache_dir, publish_release_notes, show_versions
 
+distributed = False
 try:
-    from dask.distributed import Client, progress  # pylint: disable=ungrouped-imports
+    from dask.distributed import Client, progress
+
+    distributed = True
 except ImportError:
     # Distributed is not a dependency of xclim
-    Client = None
-    progress = None
+    pass
 
 
 def _get_indicator(indicator_name):
@@ -432,7 +434,7 @@ def cli(ctx, **kwargs):
         kwargs["input"] = kwargs["input"][0]
 
     if kwargs["dask_nthreads"] is not None:
-        if Client is None:
+        if not distributed:
             raise click.BadOptionUsage(
                 "dask_nthreads",
                 "Dask's distributed scheduler is not installed, only the "