Pylint fixes, remove deprecated functions

.pylintrc.toml

@@ -15,7 +15,7 @@
 # A comma-separated list of package or module names from where C extensions may
 # be loaded. Extensions are loading into the active Python interpreter and may
 # run arbitrary code.
-# extension-pkg-allow-list =
+extension-pkg-allow-list = ["cftime"]
 
 # A comma-separated list of package or module names from where C extensions may
 # be loaded. Extensions are loading into the active Python interpreter and may
@@ -36,7 +36,7 @@ fail-under = 10
 # from-stdin =
 
 # Files or directories to be skipped. They should be base names, not paths.
-ignore = ["CVS"]
+ignore = ["CVS", "conftest.py"]
 
 # Add files or directories matching the regular expressions patterns to the
 # ignore-list. The regex matches against paths and can be in Posix or Windows
@@ -62,7 +62,7 @@ ignored-modules = ["xclim.indicators"]
 # Use multiple processes to speed up Pylint. Specifying 0 will auto-detect the
 # number of processors available to use, and will cap the count on Windows to
 # avoid hangs.
-jobs = 1
+jobs = 4
 
 # Control the amount of potential inferred values when inferring a single object.
 # This can help the performance when dealing with large functions or complex,
@@ -78,7 +78,7 @@ persistent = true
 
 # Minimum Python version to use for version dependent checks. Will default to the
 # version used to run pylint.
-py-version = "3.8"
+py-version = "3.9"
 
 # Discover python modules and packages in the file system subtree.
 # recursive =
@@ -253,13 +253,13 @@ max-args = 15
 max-attributes = 7
 
 # Maximum number of boolean expressions in an if statement (see R0916).
-max-bool-expr = 5
+max-bool-expr = 10
 
 # Maximum number of branch for function / method body.
 max-branches = 30
 
 # Maximum number of locals for function / method body.
-max-locals = 50
+max-locals = 75
 
 # Maximum number of parents for a class (see R0901).
 max-parents = 7
@@ -268,7 +268,7 @@ max-parents = 7
 max-public-methods = 20
 
 # Maximum number of return / yield for function / method body.
-max-returns = 13
+max-returns = 15
 
 # Maximum number of statements in function / method body.
 max-statements = 100
@@ -295,10 +295,10 @@ indent-after-paren = 4
 indent-string = "    "
 
 # Maximum number of characters on a single line.
-max-line-length = 150
+max-line-length = 200
 
 # Maximum number of lines in a module.
-max-module-lines = 1500
+max-module-lines = 2000
 
 # Allow the body of a class to be on the same line as the declaration if body
 # contains single statement.
@@ -373,6 +373,7 @@ disable = [
     "invalid-name",
     "invalid-unary-operand-type",
     "locally-disabled",
+    "missing-function-docstring",
     "missing-module-docstring",
     "no-member",
     "protected-access",

CHANGELOG.rst

@@ -23,6 +23,7 @@ Breaking changes
 * As of ``cf_xarray>=0.9.3``, dimensionless quantities now use the ``"1"`` units attribute as specified by the CF conventions, previously an empty string was returned. (:pull:`1814`).
 * The definitions of the ``frost_free_season_start`` and ``frost_free_season_end`` have been slightly changed to be coherent with the ``frost_free_season_length`` and `xclim`'s notion of ``season`` in general. Indicator and indices signature have been adapted to the new conventions. (:pull:`1845`).
 * Season length indicators have been modified to return ``0`` for all cases where a proper season was not found, but the data is valid. Previously, a ``nan`` was given if neither a start nor an end were found, even if the data was valid, and a ``0`` was given if an end was found but without a valid start. (:pull:`1845`).
+* The following previously-deprecated functions have now been removed from `xclim`: ``xclim.core.calendar.convert_calendar``, ``xclim.core.calendar.date_range``, ``xclim.core.calendar.date_range_like``, ``xclim.core.calendar.interp_calendar``, ``xclim.core.calendar.days_in_year``, ``xclim.core.calendar.datetime_to_decimal_year``. For guidance on how to migrate to alternatives, see the `version 0.50.0 Breaking changes <#v0-50-0-2024-06-17>`_. (:issue:`1010`, :pull:`1845`).
 
 Bug fixes
 ^^^^^^^^^
@@ -37,6 +38,8 @@ Internal changes
 * In order to adapt to changes in `pytest`, the doctest fixtures have been split from the main testing suite and doctests are now run using ``$ python -c 'from xclim.testing.utils import run_doctests; run_doctests()'``. (:pull:`1632`).
 * `tox` has been reconfigured to run doctests in a separate environment (``tox -e doctests``). (:pull:`1632`).
 * Added ``xclim.indices.generic.season`` to make season start, end, and length indices. Added a ``stat`` argument to ``xclim.indices.run_length.season`` to avoid returning a dataset. (:pull:`1845`).
+* Many ``DeprecationWarning`` and ``FutureWarning`` messages emitted from `xarray` and `pint` have been addressed. (:issue:`1719`, :pull:`1881`).
+* The codebase has been adjusted to address many `pylint`-related warnings and errors. In some cases, `casting` was used to redefine some `numpy` and `xarray` objects. (:issue:`1719`, :pull:`1881`).
 
 CI changes
 ^^^^^^^^^^

docs/conf.py

@@ -30,6 +30,7 @@
 xarray.CFTimeIndex.__module__ = "xarray"
 
 import xclim  # noqa
+from xclim import indicators as _indicators  # noqa
 from xclim.core.indicator import registry  # noqa
 
 # If extensions (or modules to document with autodoc) are in another
@@ -45,7 +46,7 @@
 indicators = {}
 # FIXME: Include cf module when its indicators documentation is improved.
 for module in ("atmos", "generic", "land", "seaIce", "icclim", "anuclim"):
-    for key, ind in getattr(xclim.indicators, module).__dict__.items():
+    for key, ind in getattr(_indicators, module).__dict__.items():
         if hasattr(ind, "_registry_id") and ind._registry_id in registry:  # noqa
             indicators[ind._registry_id] = {  # noqa
                 "realm": ind.realm,

environment.yml

@@ -74,7 +74,7 @@ dependencies:
   - tokenize-rt >=5.2.0
   - tox >=4.16.0
   # - tox-conda  # Will be added when a [email protected]+ compatible plugin is released.
-  - vulture # ==2.11  # The conda-forge version is out of date.
+  - vulture ==2.11
   - xdoctest >=1.1.5
   - yamllint >=1.35.1
   - pip >=24.0

tests/test_units.py

@@ -358,6 +358,7 @@ def test_to_agg_units(in_u, opfunc, op, exp, exp_u):
         attrs={"units": in_u},
     )
 
+    # FIXME: This is emitting warnings from deprecated DataArray.argmax() usage.
     out = to_agg_units(getattr(da, opfunc)(), da, op)
     np.testing.assert_allclose(out, exp)
 

xclim/analog.py

@@ -458,7 +458,7 @@ def pivot(x, y):
 
         return np.max(np.abs(cx - cy))
 
-    return max(pivot(x, y), pivot(y, x))
+    return max(pivot(x, y), pivot(y, x))  # pylint: disable=arguments-out-of-order
 
 
 @metric

xclim/cli.py

@@ -21,7 +21,7 @@
 
 distributed = False
 try:
-    from dask.distributed import Client, progress
+    from dask.distributed import Client, progress  # pylint: disable=ungrouped-imports
 
     distributed = True
 except ImportError:  # noqa: S110
@@ -361,7 +361,7 @@ def list_commands(self, ctx):
             "show_version_info",
         )
 
-    def get_command(self, ctx, name):
+    def get_command(self, ctx, cmd_name):
         """Return the requested command."""
         command = {
             "dataflags": dataflags,
@@ -370,9 +370,9 @@ def get_command(self, ctx, name):
             "prefetch_testing_data": prefetch_testing_data,
             "release_notes": release_notes,
             "show_version_info": show_version_info,
-        }.get(name)
+        }.get(cmd_name)
         if command is None:
-            command = _create_command(name)
+            command = _create_command(cmd_name)
         return command
 
 

xclim/core/bootstrapping.py

@@ -153,12 +153,12 @@ def bootstrap_func(compute_index_func: Callable, **kwargs) -> xarray.DataArray:
             "`bootstrap` is unnecessary when no year overlap between reference "
             "(percentiles period) and studied (index period) periods."
         )
-    pdoy_args = dict(
-        window=per_da.attrs["window"],
-        alpha=per_da.attrs["alpha"],
-        beta=per_da.attrs["beta"],
-        per=per_da.percentiles.data[()],
-    )
+    pdoy_args = {
+        "window": per_da.attrs["window"],
+        "alpha": per_da.attrs["alpha"],
+        "beta": per_da.attrs["beta"],
+        "per": per_da.percentiles.data[()],
+    }
     bfreq = _get_bootstrap_freq(kwargs["freq"])
     # Group input array in years, with an offset matching freq
     overlap_years_groups = overlap_da.resample(time=bfreq).groups