Merge remote-tracking branch 'upstream/main' into ruff2

* upstream/main:
  ruff NPY rule compliance (SciTools#5653)
  ruff ICN rule compliance (SciTools#5652)
  ruff EXE rule compliance (SciTools#5651)
  ruff com rule compliance (SciTools#5650)
  Remove compliant ignored ruff rules (SciTools#5649)
  fix for ruff rule D301 (SciTools#5646)
  Updated environment lockfiles (SciTools#5645)
  Bump scitools/workflows from 2023.10.0 to 2023.12.1 (SciTools#5648)

.github/workflows/ci-manifest.yml

@@ -23,4 +23,4 @@ concurrency:
 jobs:
   manifest:
     name: "check-manifest"
-    uses: scitools/workflows/.github/workflows/ci-manifest.yml@2023.10.0
+    uses: scitools/workflows/.github/workflows/ci-manifest.yml@2023.12.1

.github/workflows/refresh-lockfiles.yml

@@ -14,5 +14,5 @@ on:
 
 jobs:
   refresh_lockfiles:
-    uses: scitools/workflows/.github/workflows/refresh-lockfiles.yml@2023.10.0
+    uses: scitools/workflows/.github/workflows/refresh-lockfiles.yml@2023.12.1
     secrets: inherit

.ruff.toml

@@ -42,7 +42,7 @@ lint.ignore = [
     "D211",  # No blank lines allowed before class docstring
     "D214",  # Section is over-indented
     "D300",  # triple double quotes `""" / Use triple single quotes `'''`
-    "D301",  # Use `r"""` if any backslashes in a docstring
+    "D400",  # First line should end with a period
     "D401",  # First line of docstring should be in imperative mood: ...
     "D403",  # First word of the first line should be capitalized
     "D404",  # First word of the docstring should not be "This"
@@ -58,22 +58,10 @@ lint.ignore = [
     # https://docs.astral.sh/ruff/rules/#pyupgrade-up
     "UP",
 
-    # flake8-2020 (YTT)
-    # https://docs.astral.sh/ruff/rules/#flake8-2020-ytt
-    "YTT",
-
     # flake8-annotations (ANN)
     # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
     "ANN",
 
-    # flake8-async (ASYNC)
-    # https://docs.astral.sh/ruff/rules/#flake8-async-async
-    "ASYNC",
-
-    # flake8-trio (TRIO)
-    # https://docs.astral.sh/ruff/rules/#flake8-trio-trio
-    "TRIO",
-
     # flake8-bandit (S)
     # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
     "S",
@@ -94,10 +82,6 @@ lint.ignore = [
     # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
     "A",
 
-    # flake8-commas (COM)
-    # https://docs.astral.sh/ruff/rules/#flake8-commas-com
-    "COM",
-
     # flake8-copyright (CPY)
     # https://docs.astral.sh/ruff/rules/#flake8-copyright-cpy
     "CPY",
@@ -110,22 +94,10 @@ lint.ignore = [
     # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
     "DTZ",
 
-    # flake8-debugger (T10)
-    # https://docs.astral.sh/ruff/rules/#flake8-debugger-t10
-    "T10",
-
-    # flake8-django (DJ)
-    # https://docs.astral.sh/ruff/rules/#flake8-django-dj
-    "DJ",
-
     # flake8-errmsg (EM)
     # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
     "EM",
 
-    # flake8-executable (EXE)
-    # https://docs.astral.sh/ruff/rules/#flake8-executable-exe
-    "EXE",
-
     # flake8-future-annotations (FA)
     # https://docs.astral.sh/ruff/rules/#flake8-future-annotations-fa
     "FA",
@@ -134,10 +106,6 @@ lint.ignore = [
     # https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc
     "ISC",
 
-    # flake8-import-conventions (ICN)
-    # https://docs.astral.sh/ruff/rules/#flake8-import-conventions-icn
-    "ICN",
-
     # flake8-logging-format (G)
     # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
     "G",
@@ -162,10 +130,6 @@ lint.ignore = [
     # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
     "PT",
 
-    # flake8-quotes (Q)
-    # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
-    "Q",
-
     # flake8-raise (RSE)
     # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
     "RSE",
@@ -194,10 +158,6 @@ lint.ignore = [
     # https://docs.astral.sh/ruff/rules/#flake8-type-checking-tch
     "TCH",
 
-    # flake8-gettext (INT)
-    # https://docs.astral.sh/ruff/rules/#flake8-gettext-int
-    "INT",
-
     # flake8-unused-arguments (ARG)
     # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
     "ARG",
@@ -238,10 +198,6 @@ lint.ignore = [
     # https://docs.astral.sh/ruff/rules/#flynt-fly
     "FLY",
 
-    # NumPy-specific rules (NPY)
-    # https://docs.astral.sh/ruff/rules/#numpy-specific-rules-npy
-    "NPY",
-
     # Airflow (AIR)
     # https://docs.astral.sh/ruff/rules/#airflow-air
     "AIR",
@@ -250,14 +206,6 @@ lint.ignore = [
     # https://docs.astral.sh/ruff/rules/#perflint-perf
     "PERF",
 
-    # refurb (FURB)
-    # https://docs.astral.sh/ruff/rules/#refurb-furb
-    "FURB",
-
-    # flake8-logging (LOG)
-    # https://docs.astral.sh/ruff/rules/#flake8-logging-log
-    "LOG",
-
     # Ruff-specific rules (RUF)
     # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
     "RUF",

benchmarks/benchmarks/cperf/equality.py

@@ -9,7 +9,7 @@
 
 
 class EqualityMixin(SingleDiagnosticMixin):
-    """Uses :class:`SingleDiagnosticMixin` as the realistic case will be comparing
+    r"""Uses :class:`SingleDiagnosticMixin` as the realistic case will be comparing
     :class:`~iris.cube.Cube`\\ s that have been loaded from file.
     """
 
@@ -24,7 +24,7 @@ def setup(self, file_type, three_d=False, three_times=False):
 
 @on_demand_benchmark
 class CubeEquality(EqualityMixin):
-    """Benchmark time and memory costs of comparing LFRic and UM
+    r"""Benchmark time and memory costs of comparing LFRic and UM
     :class:`~iris.cube.Cube`\\ s.
     """
 

benchmarks/benchmarks/plot.py

@@ -5,14 +5,14 @@
 """Plot benchmark tests.
 
 """
-import matplotlib
+import matplotlib as mpl
 import numpy as np
 
 from iris import coords, cube, plot
 
 from . import ARTIFICIAL_DIM_SIZE
 
-matplotlib.use("agg")
+mpl.use("agg")
 
 
 class AuxSort:

benchmarks/benchmarks/sperf/equality.py

@@ -10,7 +10,7 @@
 
 @on_demand_benchmark
 class CubeEquality(FileMixin):
-    """Benchmark time and memory costs of comparing :class:`~iris.cube.Cube`\\ s
+    r"""Benchmark time and memory costs of comparing :class:`~iris.cube.Cube`\\ s
      with attached :class:`~iris.experimental.ugrid.mesh.Mesh`\\ es.
 
     Uses :class:`FileMixin` as the realistic case will be comparing

lib/iris/_constraints.py

@@ -33,7 +33,7 @@ def __init__(self, name=None, cube_func=None, coord_values=None, **kwargs):
         ----------
         name : str or None, optional
             If a string, it is used as the name to match against the
-            :attr:`iris.cube.Cube.names` property. TREMTEST
+            :attr:`iris.cube.Cube.names` property.
         cube_func : callable or None, optional
             If a callable, it must accept a Cube as its first and only argument
             and return either True or False.

lib/iris/_merge.py

@@ -525,7 +525,7 @@ def _is_combination(name):
 
 
 def build_indexes(positions):
-    """Construct a mapping for each candidate dimension that maps for each
+    r"""Construct a mapping for each candidate dimension that maps for each
     of its scalar values the set of values for each of the other candidate
     dimensions.
 

lib/iris/cube.py

@@ -752,7 +752,7 @@ def _is_single_item(testee):
 
 
 class CubeAttrsDict(MutableMapping):
-    """A :class:`dict`\\-like object for :attr:`iris.cube.Cube.attributes`,
+    r"""A :class:`dict`\\-like object for :attr:`iris.cube.Cube.attributes`,
     providing unified user access to combined cube "local" and "global" attributes
     dictionaries, with the access behaviour of an ordinary (single) dictionary.
 
@@ -2018,7 +2018,7 @@ def coords(
         dim_coords=None,
         mesh_coords=None,
     ):
-        """Return a list of coordinates from the :class:`Cube` that match the
+        r"""Return a list of coordinates from the :class:`Cube` that match the
         provided criteria.
 
         .. seealso::
@@ -2184,7 +2184,7 @@ def coord(
         dim_coords=None,
         mesh_coords=None,
     ):
-        """Return a single coordinate from the :class:`Cube` that matches the
+        r"""Return a single coordinate from the :class:`Cube` that matches the
         provided criteria.
 
         .. note::
@@ -2359,7 +2359,7 @@ def _any_meshcoord(self):
 
     @property
     def mesh(self):
-        """Return the unstructured :class:`~iris.experimental.ugrid.Mesh`
+        r"""Return the unstructured :class:`~iris.experimental.ugrid.Mesh`
         associated with the cube, if the cube has any
         :class:`~iris.experimental.ugrid.MeshCoord`\\ s,
         or ``None`` if it has none.
@@ -2379,7 +2379,7 @@ def mesh(self):
 
     @property
     def location(self):
-        """Return the mesh "location" of the cube data, if the cube has any
+        r"""Return the mesh "location" of the cube data, if the cube has any
         :class:`~iris.experimental.ugrid.MeshCoord`\\ s,
         or ``None`` if it has none.
 
@@ -2398,7 +2398,7 @@ def location(self):
         return result
 
     def mesh_dim(self):
-        """Return the cube dimension of the mesh, if the cube has any
+        r"""Return the cube dimension of the mesh, if the cube has any
         :class:`~iris.experimental.ugrid.MeshCoord`\\ s,
         or ``None`` if it has none.
 

lib/iris/exceptions.py

@@ -176,7 +176,7 @@ class CannotAddError(ValueError):
 
 
 class IrisUserWarning(UserWarning):
-    """Base class for :class:`UserWarning`\\ s generated by Iris."""
+    r"""Base class for :class:`UserWarning`\\ s generated by Iris."""
 
     pass
 

lib/iris/experimental/ugrid/load.py

@@ -3,7 +3,7 @@
 # This file is part of Iris and is released under the BSD license.
 # See LICENSE in the root of the repository for full licensing details.
 
-"""Extensions to Iris' NetCDF loading to allow the construction of
+r"""Extensions to Iris' NetCDF loading to allow the construction of
 :class:`~iris.experimental.ugrid.mesh.Mesh`\\ es from UGRID data in the file.
 
 Eventual destination: :mod:`iris.fileformats.netcdf`.
@@ -143,7 +143,7 @@ def load_mesh(uris, var_name=None):
 
 
 def load_meshes(uris, var_name=None):
-    """Load :class:`~iris.experimental.ugrid.mesh.Mesh` objects from one or more NetCDF files.
+    r"""Load :class:`~iris.experimental.ugrid.mesh.Mesh` objects from one or more NetCDF files.
 
     Parameters
     ----------

lib/iris/experimental/ugrid/mesh.py

@@ -659,7 +659,7 @@ def normalise(element, axis):
 
     @classmethod
     def from_coords(cls, *coords):
-        """Construct a :class:`Mesh` by derivation from one or more
+        r"""Construct a :class:`Mesh` by derivation from one or more
         :class:`~iris.coords.Coord`\\ s.
 
         The :attr:`~Mesh.topology_dimension`, :class:`~iris.coords.Coord`
@@ -1865,7 +1865,7 @@ def to_MeshCoord(self, location, axis):
         return MeshCoord(mesh=self, location=location, axis=axis)
 
     def to_MeshCoords(self, location):
-        """Generate a tuple of
+        r"""Generate a tuple of
         :class:`~iris.experimental.ugrid.mesh.MeshCoord`\\ s, each referencing
         the current :class:`Mesh`, one for each :attr:`AXES` value, passing
         through the ``location`` argument.

lib/iris/fileformats/_nc_load_rules/engine.py

@@ -20,7 +20,7 @@
 
 
 class FactEntity:
-    """An object with an 'entity_lists' property  which is a dict of 'FactList's.
+    r"""An object with an 'entity_lists' property  which is a dict of 'FactList's.
 
     A Factlist, in turn, is an object with property 'case_specific_facts',
     which is a list of tuples of strings

lib/iris/fileformats/pp.py

@@ -1218,7 +1218,7 @@ def save(self, file_handle):
                     ia //= PP_WORD_DEPTH
                 else:
                     # ia is the datalength in WORDS
-                    ia = np.product(extra_elem.shape)
+                    ia = np.prod(extra_elem.shape)
                     # flip the byteorder if the data is not big-endian
                     if extra_elem.dtype.newbyteorder(">") != extra_elem.dtype:
                         # take a copy of the extra data when byte swapping