[StepSecurity] Apply security best practices

.pre-commit-config.yaml

@@ -27,11 +27,6 @@ repos:
     hooks:
       - id: toml-sort-fix
         exclude: '.pylintrc.toml'
-  - repo: https://github.com/pylint-dev/pylint
-    rev: v3.0.3
-    hooks:
-      - id: pylint
-        args: [ '--rcfile=.pylintrc.toml', '--errors-only', '--jobs=0', '--disable=import-error' ]
   - repo: https://github.com/adrienverge/yamllint.git
     rev: v1.33.0
     hooks:
@@ -49,6 +44,11 @@ repos:
     rev: v0.1.13
     hooks:
       - id: ruff
+  - repo: https://github.com/pylint-dev/pylint
+    rev: v3.0.3
+    hooks:
+      - id: pylint
+        args: [ '--rcfile=.pylintrc.toml', '--errors-only', '--jobs=0', '--disable=import-error' ]
   - repo: https://github.com/pycqa/flake8
     rev: 7.0.0
     hooks:

.pylintrc.toml

@@ -374,6 +374,7 @@ disable = [
     "invalid-unary-operand-type",
     "locally-disabled",
     "missing-module-docstring",
+    "no-member",
     "protected-access",
     "raw-checker-failed",
     "redefined-outer-name",
@@ -521,7 +522,7 @@ missing-member-max-choices = 1
 mixin-class-rgx = ".*[Mm]ixin"
 
 # List of decorators that change the signature of a decorated function.
-# signature-mutators =
+signature-mutators = ["xclim.sdba.base.map_groups"]
 
 [tool.pylint.variables]
 # List of additional names supposed to be defined in builtins. Remember that you

pyproject.toml

@@ -292,7 +292,7 @@ lines-after-imports = 1
 no-lines-before = ["future", "standard-library"]
 
 [tool.ruff.mccabe]
-max-complexity = 15
+max-complexity = 20
 
 [tool.ruff.per-file-ignores]
 "docs/*.py" = ["D100", "D101", "D102", "D103"]

tests/test_indicators.py

@@ -159,11 +159,10 @@ def test_attrs(tas_series):
     assert f"xclim version: {__version__}" in txm.attrs["history"]
     assert txm.name == "tmin5 degC"
     assert uniIndTemp.standard_name == "{freq} mean temperature"
-    # fmt: off
     assert (
-        uniIndTemp.cf_attrs[0]["another_attr"] == "With a value."  # pylint: disable=unsubscriptable-object
+        uniIndTemp.cf_attrs[0]["another_attr"]  # pylint: disable=unsubscriptable-object
+        == "With a value."
     )
-    # fmt: on
 
     thresh = xr.DataArray(
         [1],
@@ -247,14 +246,8 @@ 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
-    # fmt: off
-    assert (
-        xclim.indicators.cf.fg.__module__ == "xclim.indicators.cf"  # pylint: disable=no-member
-    )
-    assert (
-        xclim.indicators.icclim.GD4.__module__ == "xclim.indicators.icclim"  # pylint: disable=no-member
-    )
-    # fmt: on
+    assert xclim.indicators.cf.fg.__module__ == "xclim.indicators.cf"
+    assert xclim.indicators.icclim.GD4.__module__ == "xclim.indicators.icclim"
 
 
 def test_temp_unit_conversion(tas_series):
@@ -267,9 +260,7 @@ def test_temp_unit_conversion(tas_series):
     with pytest.raises(AssertionError):
         np.testing.assert_array_almost_equal(txk, txc + 273.15)
 
-    uniIndTemp.cf_attrs[0][  # noqa; # pylint: disable=unsubscriptable-object
-        "units"
-    ] = "degC"
+    uniIndTemp.cf_attrs[0]["units"] = "degC"  # pylint: disable=unsubscriptable-object
     txc = uniIndTemp(a, freq="YS")
     np.testing.assert_array_almost_equal(txk, txc + 273.15)
 

tests/test_locales.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+# pylint: disable=unsubscriptable-object
 # Tests for `xclim.locales`
 from __future__ import annotations
 
@@ -159,13 +159,11 @@ def test_xclim_translations(locale, official_indicators):
 
 
 @pytest.mark.parametrize(
-    # fmt: off
     "initeng,expected",
     [
         (False, ""),
-        (True, atmos.tg_mean.cf_attrs[0]["long_name"]),  # pylint: disable=unsubscriptable-object
+        (True, atmos.tg_mean.cf_attrs[0]["long_name"]),
     ],
-    # fmt: on
 )
 def test_local_dict_generation(initeng, expected):
     dic = generate_local_dict("tlh", init_english=initeng)

tests/test_sdba/test_base.py

@@ -1,3 +1,4 @@
+# pylint: disable=missing-kwoa
 from __future__ import annotations
 
 import jsonpickle
@@ -193,7 +194,7 @@ def func(ds, *, dim):
             d = ds.tas.mean(dim)
             return d.rename("data").to_dataset()
 
-        data = func(  # pylint: disable=missing-kwoa
+        data = func(
             xr.Dataset(dict(tas=tas)),
             group="time.dayofyear",
             window=5,
@@ -212,7 +213,7 @@ def func(ds, *, dim):
             return data.rename("data").to_dataset()
 
         # with a scalar aux coord
-        data = func(  # pylint: disable=missing-kwoa
+        data = func(
             xr.Dataset(dict(tas=tas.isel(lat=0, drop=True)), coords=dict(leftover=1)),
             group="time.dayofyear",
         ).load()

xclim/cli.py

@@ -464,9 +464,9 @@ def cli(ctx, **kwargs):
     ctx.obj = kwargs
 
 
-@cli.result_callback()  # noqa
+@cli.result_callback()
 @click.pass_context
-def write_file(ctx, *args, **kwargs):  # noqa: W0613
+def write_file(ctx, *args, **kwargs):
     """Write the output dataset to file."""
     if ctx.obj["output"] is not None:
         if ctx.obj["verbose"]:

xclim/core/options.py

@@ -137,7 +137,7 @@ def run_check(*args, **kwargs):
     return run_check
 
 
-class set_options:  # noqa: C0103
+class set_options:
     """Set options for xclim in a controlled context.
 
     Attributes

xclim/indices/fire/_ffdi.py

@@ -1,3 +1,4 @@
+# pylint: disable=no-value-for-parameter
 r"""
 McArthur Forest Fire Danger (Mark 5) System
 ===========================================
@@ -97,7 +98,7 @@ def _keetch_byram_drought_index(p, t, pa, kbdi0, kbdi: float):  # pragma: no cov
     nopython=True,
     cache=True,
 )
-def _griffiths_drought_factor(p, smd, lim, df):  # pragma: no cover  # noqa: C901
+def _griffiths_drought_factor(p, smd, lim, df):
     """Compute the Griffiths drought factor.
 
     Parameters
@@ -248,11 +249,7 @@ def _keetch_byram_drought_index_pass(pr, tasmax, pr_annual, kbdi0):
         --------
         DO NOT CALL DIRECTLY, use `keetch_byram_drought_index` instead.
         """
-        # fmt: off
-        return _keetch_byram_drought_index(  # pylint: disable=no-value-for-parameter
-            pr, tasmax, pr_annual, kbdi0
-        )
-        # fmt: on
+        return _keetch_byram_drought_index(pr, tasmax, pr_annual, kbdi0)
 
     pr = convert_units_to(pr, "mm/day", context="hydro")
     tasmax = convert_units_to(tasmax, "C")
@@ -330,11 +327,7 @@ def _griffiths_drought_factor_pass(pr, smd, lim):
         --------
         DO NOT CALL DIRECTLY, use `griffiths_drought_factor` instead.
         """
-        # fmt: off
-        return _griffiths_drought_factor(  # pylint: disable=no-value-for-parameter
-            pr, smd, lim
-        )
-        # fmt: on
+        return _griffiths_drought_factor(pr, smd, lim)
 
     pr = convert_units_to(pr, "mm/day", context="hydro")
     smd = convert_units_to(smd, "mm/day")

xclim/sdba/nbutils.py

@@ -1,3 +1,4 @@
+# pylint: disable=no-value-for-parameter
 """
 Numba-accelerated Utilities
 ===========================
@@ -34,7 +35,7 @@ def vecquantiles(da: DataArray, rnk: DataArray, dim: str | DataArray.dims) -> Da
     da = da.transpose(*rnk.dims, tem)
 
     res = DataArray(
-        _vecquantiles(da.values, rnk.values),  # pylint: disable=no-value-for-parameter
+        _vecquantiles(da.values, rnk.values),
         dims=rnk.dims,
         coords=rnk.coords,
         attrs=da.attrs,
@@ -184,12 +185,7 @@ def _first_and_last_nonnull(arr):
 
 
 @njit
-def _extrapolate_on_quantiles(
-    # fmt: off
-    interp, oldx, oldg, oldy, newx, newg, method="constant"
-    # noqa
-    # fmt: on
-):
+def _extrapolate_on_quantiles(interp, oldx, oldg, oldy, newx, newg, method="constant"):
     """Apply extrapolation to the output of interpolation on quantiles with a given grouping.
 
     Arguments are the same as _interp_on_quantiles_2D.

xclim/testing/diagnostics.py

@@ -1,3 +1,4 @@
+# pylint: disable=no-member,missing-kwoa
 """
 SDBA Diagnostic Testing Module
 ==============================
@@ -128,7 +129,7 @@ def adapt_freq_graph():
     x = series(synth_rainfall(2, 2, wet_freq=0.25, size=n), "pr")  # sim
     y = series(synth_rainfall(2, 2, wet_freq=0.5, size=n), "pr")  # ref
 
-    xp = adapt_freq(x, y, thresh=0).sim_ad  # pylint: disable=no-member,missing-kwoa
+    xp = adapt_freq(x, y, thresh=0).sim_ad  # noqa
 
     fig, (ax1, ax2) = plt.subplots(2, 1)
     sx = x.sortby(x)