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

* upstream/main: Make further topics obviously different (SciTools#5684) [pre-commit.ci] pre-commit autoupdate (SciTools#5682) ruff complliance for D100. (SciTools#5678) move tests.pp to tests.__init__ (SciTools#5679) ruff compliance for D417, D106 (SciTools#5677) ruff compliance for D200. (SciTools#5675)
tkknight · Jan 10, 2024 · b1fd68b · b1fd68b
2 parents 2a60b7c + d528fce
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -29,7 +29,7 @@ repos:
     -   id: no-commit-to-branch
 
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.1.9"
+    rev: "v0.1.11"
     hooks:
     -   id: ruff
         types: [file, python]
@@ -45,7 +45,7 @@ repos:
         additional_dependencies: [tomli]
 
 -   repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
     -   id: flake8
         types: [file, python]

diff --git a/.ruff.toml b/.ruff.toml
@@ -25,14 +25,10 @@ lint.ignore = [
     # (D-1) Permanent
     "D105",  # Missing docstring in magic method
     # (D-2) Temporary, to be removed when we are more compliant. Rare cases mmove  to (1).
-    "D417",  # Missing argument descriptions in the docstring
     "D101",  # Missing docstring in public class
     "D102",  # Missing docstring in public method
-    "D104",  # Missing docstring in public package
     # (D-3) Temporary, before an initial review, either fix ocurrences or move to (2).
-    "D100",  # Missing docstring in public module
     "D103",  # Missing docstring in public function
-    "D200",  # One-line docstring should fit on one line
     "D205",  # 1 blank line required between summary line and description
     "D401",  # First line of docstring should be in imperative mood: ...
 

diff --git a/benchmarks/benchmarks/aux_factory.py b/benchmarks/benchmarks/aux_factory.py
@@ -2,9 +2,7 @@
 #
 # 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.
-"""AuxFactory benchmark tests.
-
-"""
+"""AuxFactory benchmark tests."""
 
 import numpy as np
 

diff --git a/benchmarks/benchmarks/coords.py b/benchmarks/benchmarks/coords.py
@@ -2,9 +2,7 @@
 #
 # 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.
-"""Coord benchmark tests.
-
-"""
+"""Coord benchmark tests."""
 
 import numpy as np
 

diff --git a/benchmarks/benchmarks/cperf/equality.py b/benchmarks/benchmarks/cperf/equality.py
@@ -2,8 +2,7 @@
 #
 # 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.
-"""Equality benchmarks for the CPerf scheme of the UK Met Office's NG-VAT project.
-"""
+"""Equality benchmarks for the CPerf scheme of the UK Met Office's NG-VAT project."""
 from .. import on_demand_benchmark
 from . import SingleDiagnosticMixin
 

diff --git a/benchmarks/benchmarks/cperf/load.py b/benchmarks/benchmarks/cperf/load.py
@@ -2,8 +2,7 @@
 #
 # 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.
-"""File loading benchmarks for the CPerf scheme of the UK Met Office's NG-VAT project.
-"""
+"""File loading benchmarks for the CPerf scheme of the UK Met Office's NG-VAT project."""
 from .. import on_demand_benchmark
 from . import SingleDiagnosticMixin
 

diff --git a/benchmarks/benchmarks/cperf/save.py b/benchmarks/benchmarks/cperf/save.py
@@ -2,8 +2,7 @@
 #
 # 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.
-"""File saving benchmarks for the CPerf scheme of the UK Met Office's NG-VAT project.
-"""
+"""File saving benchmarks for the CPerf scheme of the UK Met Office's NG-VAT project."""
 
 from iris import save
 

diff --git a/benchmarks/benchmarks/cube.py b/benchmarks/benchmarks/cube.py
@@ -2,9 +2,7 @@
 #
 # 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.
-"""Cube benchmark tests.
-
-"""
+"""Cube benchmark tests."""
 
 import numpy as np
 

diff --git a/benchmarks/benchmarks/experimental/__init__.py b/benchmarks/benchmarks/experimental/__init__.py
@@ -2,6 +2,4 @@
 #
 # 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.
-"""Benchmark tests for the experimental module.
-
-"""
+"""Benchmark tests for the experimental module."""
diff --git a/benchmarks/benchmarks/experimental/ugrid/__init__.py b/benchmarks/benchmarks/experimental/ugrid/__init__.py
@@ -2,9 +2,7 @@
 #
 # 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.
-"""Benchmark tests for the experimental.ugrid module.
-
-"""
+"""Benchmark tests for the experimental.ugrid module."""
 
 from copy import deepcopy
 

diff --git a/benchmarks/benchmarks/generate_data/ugrid.py b/benchmarks/benchmarks/generate_data/ugrid.py
@@ -2,8 +2,7 @@
 #
 # 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.
-"""Scripts for generating supporting data for UGRID-related benchmarking.
-"""
+"""Scripts for generating supporting data for UGRID-related benchmarking."""
 from iris import load_cube as iris_loadcube
 from iris.experimental.ugrid import PARSE_UGRID_ON_LOAD
 

diff --git a/benchmarks/benchmarks/import_iris.py b/benchmarks/benchmarks/import_iris.py
@@ -2,6 +2,9 @@
 #
 # 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.
+
+"""import iris benchmarking."""
+
 from importlib import import_module, reload
 
 ################

diff --git a/benchmarks/benchmarks/iterate.py b/benchmarks/benchmarks/iterate.py
@@ -2,9 +2,7 @@
 #
 # 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.
-"""Iterate benchmark tests.
-
-"""
+"""Iterate benchmark tests."""
 import numpy as np
 
 from iris import coords, cube, iterate

diff --git a/benchmarks/benchmarks/metadata_manager_factory.py b/benchmarks/benchmarks/metadata_manager_factory.py
@@ -2,9 +2,7 @@
 #
 # 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.
-"""metadata_manager_factory benchmark tests.
-
-"""
+"""metadata_manager_factory benchmark tests."""
 
 from iris.common import (
     AncillaryVariableMetadata,

diff --git a/benchmarks/benchmarks/mixin.py b/benchmarks/benchmarks/mixin.py
@@ -2,9 +2,7 @@
 #
 # 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.
-"""Mixin benchmark tests.
-
-"""
+"""Mixin benchmark tests."""
 
 import numpy as np
 

diff --git a/benchmarks/benchmarks/plot.py b/benchmarks/benchmarks/plot.py
@@ -2,9 +2,7 @@
 #
 # 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.
-"""Plot benchmark tests.
-
-"""
+"""Plot benchmark tests."""
 import matplotlib as mpl
 import numpy as np
 

diff --git a/benchmarks/benchmarks/regridding.py b/benchmarks/benchmarks/regridding.py
@@ -2,9 +2,7 @@
 #
 # 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.
-"""Regridding benchmark test.
-
-"""
+"""Regridding benchmark test."""
 
 # import iris tests first so that some things can be initialised before
 # importing anything else

diff --git a/benchmarks/benchmarks/sperf/combine_regions.py b/benchmarks/benchmarks/sperf/combine_regions.py
@@ -2,8 +2,7 @@
 #
 # 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.
-"""Region combine benchmarks for the SPerf scheme of the UK Met Office's NG-VAT project.
-"""
+"""Region combine benchmarks for the SPerf scheme of the UK Met Office's NG-VAT project."""
 import os.path
 
 from dask import array as da

diff --git a/benchmarks/benchmarks/sperf/equality.py b/benchmarks/benchmarks/sperf/equality.py
@@ -2,8 +2,7 @@
 #
 # 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.
-"""Equality benchmarks for the SPerf scheme of the UK Met Office's NG-VAT project.
-"""
+"""Equality benchmarks for the SPerf scheme of the UK Met Office's NG-VAT project."""
 from .. import on_demand_benchmark
 from . import FileMixin
 

diff --git a/benchmarks/benchmarks/sperf/load.py b/benchmarks/benchmarks/sperf/load.py
@@ -2,8 +2,7 @@
 #
 # 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.
-"""File loading benchmarks for the SPerf scheme of the UK Met Office's NG-VAT project.
-"""
+"""File loading benchmarks for the SPerf scheme of the UK Met Office's NG-VAT project."""
 from .. import on_demand_benchmark
 from . import FileMixin
 

diff --git a/benchmarks/benchmarks/sperf/save.py b/benchmarks/benchmarks/sperf/save.py
@@ -2,8 +2,7 @@
 #
 # 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.
-"""File saving benchmarks for the SPerf scheme of the UK Met Office's NG-VAT project.
-"""
+"""File saving benchmarks for the SPerf scheme of the UK Met Office's NG-VAT project."""
 import os.path
 
 from iris import save

diff --git a/benchmarks/benchmarks/trajectory.py b/benchmarks/benchmarks/trajectory.py
@@ -2,9 +2,7 @@
 #
 # 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.
-"""Trajectory benchmark test.
-
-"""
+"""Trajectory benchmark test."""
 
 # import iris tests first so that some things can be initialised before
 # importing anything else

diff --git a/benchmarks/bm_runner.py b/benchmarks/bm_runner.py
@@ -2,8 +2,7 @@
 #
 # 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.
-"""Argparse conveniences for executing common types of benchmark runs.
-"""
+"""Argparse conveniences for executing common types of benchmark runs."""
 
 from abc import ABC, abstractmethod
 import argparse

diff --git a/docs/gallery_tests/__init__.py b/docs/gallery_tests/__init__.py
@@ -2,3 +2,5 @@
 #
 # 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.
+
+"""Gallery Tests."""
diff --git a/docs/gallery_tests/test_gallery_examples.py b/docs/gallery_tests/test_gallery_examples.py
@@ -3,6 +3,8 @@
 # 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.
 
+"""Test all the gallery examples."""
+
 import importlib
 
 import matplotlib.pyplot as plt

diff --git a/docs/src/conf.py b/docs/src/conf.py
@@ -17,6 +17,8 @@
 # serve to show the default.
 # ----------------------------------------------------------------------------
 
+"""sphinx config."""
+
 import datetime
 from importlib.metadata import version as get_version
 import ntpath
@@ -298,7 +300,6 @@ def _dotv(version):
 html_theme_options = {
     "footer_start": ["copyright", "sphinx-version"],
     "footer_end": ["custom_footer"],
-    "collapse_navigation": True,
     "navigation_depth": 3,
     "show_toc_level": 4,
     "show_prev_next": True,

diff --git a/docs/src/developers_guide/documenting/__init__.py b/docs/src/developers_guide/documenting/__init__.py
@@ -0,0 +1 @@
+# noqa: D104
diff --git a/docs/src/developers_guide/documenting/docstrings_attribute.py b/docs/src/developers_guide/documenting/docstrings_attribute.py
@@ -1,3 +1,6 @@
+"""docstring attribute example."""
+
+
 class ExampleClass:
     """Class Summary."""
 

diff --git a/docs/src/developers_guide/documenting/docstrings_sample_routine.py b/docs/src/developers_guide/documenting/docstrings_sample_routine.py
@@ -1,3 +1,6 @@
+"""docstring routine example."""
+
+
 def sample_routine(arg1, arg2, kwarg1="foo", kwarg2=None):
     """Purpose section text goes here.
 

diff --git a/docs/src/further_topics/filtering_warnings.rst b/docs/src/further_topics/filtering_warnings.rst
@@ -47,9 +47,9 @@ Warnings:
 
     >>> my_operation()
     ...
-    iris/coord_systems.py:434: IrisUserWarning: Setting inverse_flattening does not affect other properties of the GeogCS object. To change other properties set them explicitly or create a new GeogCS instance.
+    iris/coord_systems.py:432: IrisUserWarning: Setting inverse_flattening does not affect other properties of the GeogCS object. To change other properties set them explicitly or create a new GeogCS instance.
       warnings.warn(wmsg, category=iris.exceptions.IrisUserWarning)
-    iris/coord_systems.py:772: IrisDefaultingWarning: Discarding false_easting and false_northing that are not used by Cartopy.
+    iris/coord_systems.py:770: IrisDefaultingWarning: Discarding false_easting and false_northing that are not used by Cartopy.
       warnings.warn(
 
 Warnings can be suppressed using the Python warnings filter with the ``ignore``
@@ -110,7 +110,7 @@ You can target specific Warning messages, e.g.
     ...     warnings.filterwarnings("ignore", message="Discarding false_easting")
     ...     my_operation()
     ...
-    iris/coord_systems.py:434: IrisUserWarning: Setting inverse_flattening does not affect other properties of the GeogCS object. To change other properties set them explicitly or create a new GeogCS instance.
+    iris/coord_systems.py:432: IrisUserWarning: Setting inverse_flattening does not affect other properties of the GeogCS object. To change other properties set them explicitly or create a new GeogCS instance.
       warnings.warn(wmsg, category=iris.exceptions.IrisUserWarning)
 
 ::
@@ -128,9 +128,9 @@ Or you can target Warnings raised by specific lines of specific modules, e.g.
     ...     warnings.filterwarnings("ignore", module="iris.coord_systems", lineno=449)
     ...     my_operation()
     ...
-    iris/coord_systems.py:434: IrisUserWarning: Setting inverse_flattening does not affect other properties of the GeogCS object. To change other properties set them explicitly or create a new GeogCS instance.
+    iris/coord_systems.py:432: IrisUserWarning: Setting inverse_flattening does not affect other properties of the GeogCS object. To change other properties set them explicitly or create a new GeogCS instance.
       warnings.warn(wmsg, category=iris.exceptions.IrisUserWarning)
-    iris/coord_systems.py:772: IrisDefaultingWarning: Discarding false_easting and false_northing that are not used by Cartopy.
+    iris/coord_systems.py:770: IrisDefaultingWarning: Discarding false_easting and false_northing that are not used by Cartopy.
       warnings.warn(
 
 ::
@@ -190,7 +190,7 @@ module during execution:
     ...     )
     ...     my_operation()
     ...
-    iris/coord_systems.py:434: IrisUserWarning: Setting inverse_flattening does not affect other properties of the GeogCS object. To change other properties set them explicitly or create a new GeogCS instance.
+    iris/coord_systems.py:432: IrisUserWarning: Setting inverse_flattening does not affect other properties of the GeogCS object. To change other properties set them explicitly or create a new GeogCS instance.
       warnings.warn(wmsg, category=iris.exceptions.IrisUserWarning)
 
 ----

diff --git a/docs/src/userguide/plotting_examples/1d_quickplot_simple.py b/docs/src/userguide/plotting_examples/1d_quickplot_simple.py
@@ -1,3 +1,5 @@
+"""Simple 1D plot using iris.quickplot.plot()."""
+
 import matplotlib.pyplot as plt
 
 import iris

diff --git a/docs/src/userguide/plotting_examples/1d_simple.py b/docs/src/userguide/plotting_examples/1d_simple.py
@@ -1,3 +1,5 @@
+"""Simple 1D plot using iris.plot.plot()."""
+
 import matplotlib.pyplot as plt
 
 import iris

diff --git a/docs/src/userguide/plotting_examples/1d_with_legend.py b/docs/src/userguide/plotting_examples/1d_with_legend.py
@@ -1,3 +1,5 @@
+"""Simple 1D plot using iris.plot.plot() with a legend."""
+
 import matplotlib.pyplot as plt
 
 import iris

diff --git a/docs/src/userguide/plotting_examples/brewer.py b/docs/src/userguide/plotting_examples/brewer.py
@@ -1,3 +1,5 @@
+"""Plot a chart of all Brewer colour schemes."""
+
 import matplotlib.pyplot as plt
 import numpy as np
 

diff --git a/docs/src/userguide/plotting_examples/cube_blockplot.py b/docs/src/userguide/plotting_examples/cube_blockplot.py
@@ -1,3 +1,5 @@
+"""Cube block plot using using iris.plot.pcolormesh()."""
+
 import matplotlib.pyplot as plt
 
 import iris

diff --git a/docs/src/userguide/plotting_examples/cube_brewer_cite_contourf.py b/docs/src/userguide/plotting_examples/cube_brewer_cite_contourf.py
@@ -1,3 +1,5 @@
+"""Addind a citation for a plot using iris.plot.citation()."""
+
 import matplotlib.pyplot as plt
 
 import iris

diff --git a/docs/src/userguide/plotting_examples/cube_brewer_contourf.py b/docs/src/userguide/plotting_examples/cube_brewer_contourf.py
@@ -1,3 +1,5 @@
+"""Plot a cube with a Brewer colour palette using iris.quickplot.contourf()."""
+
 import matplotlib.cm as mpl_cm
 import matplotlib.pyplot as plt
 

diff --git a/docs/src/userguide/plotting_examples/cube_contour.py b/docs/src/userguide/plotting_examples/cube_contour.py
@@ -1,3 +1,8 @@
+"""Simple contour plot of a cube.
+
+Can use iris.plot.contour() or iris.quicplot.contour().
+
+"""
 import matplotlib.pyplot as plt
 
 import iris