Merge branch 'SciTools:main' into shapefile_masking

.pre-commit-config.yaml

@@ -29,7 +29,7 @@ repos:
     -   id: no-commit-to-branch
 
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.1.14"
+    rev: "v0.2.1"
     hooks:
     -   id: ruff
         types: [file, python]

docs/src/whatsnew/latest.rst

@@ -97,7 +97,10 @@ This document explains the changes made to Iris for this release
 💣 Incompatible Changes
 =======================
 
-#. N/A
+#. `@bouweandela`_ and  `@trexfeathers`_ (reviewer) updated :class:`~iris.cube.Cube`
+   comparison so equality is now possible between cubes with data containing a
+   :obj:`numpy.nan`. e.g. ``Cube([np.nan, 1.0]) == Cube([np.nan, 1.0])`` will now
+   evaluate to :obj:`True`, while previously this would have been :obj:`False`. (:pull:`5713`)
 
 
 🚀 Performance Enhancements
@@ -119,6 +122,9 @@ This document explains the changes made to Iris for this release
 
 #. `@bouweandela`_ made comparing coordinates and arrays to themselves faster. (:pull:`5691`)
 
+#. `@bouweandela`_ and  `@trexfeathers`_ (reviewer) made comparing cubes to
+   themselves faster. (:pull:`5713`)
+
 
 🔥 Deprecations
 ===============
@@ -227,6 +233,13 @@ This document explains the changes made to Iris for this release
 
 #. `@bjlittle`_ replaced `black`_ with `ruff`_. (:pull:`5634`)
 
+#. `@tkknight`_ and `@bjlittle`_ (reviewer) updated codebase to be compliant with
+   almost all of the rules for `ruff pydocstyle`_. 
+   (https://github.com/SciTools/iris/issues/5625#issuecomment-1859159734)
+
+#. `@tkknight`_ and `@bjlittle`_ (reviewer) updated codebase to ensure docstrings
+   that are not covered by the ruff checks, are consistent with numpydocstyle.
+   (:issue:`4721`)
 
 .. comment
     Whatsnew author names (@github name) in alphabetical order. Note that,
@@ -247,3 +260,4 @@ This document explains the changes made to Iris for this release
 .. _NEP29 Drop Schedule: https://numpy.org/neps/nep-0029-deprecation_policy.html#drop-schedule
 .. _codespell: https://github.com/codespell-project/codespell
 .. _split attributes project: https://github.com/orgs/SciTools/projects/5?pane=info
+.. _ruff pydocstyle: https://docs.astral.sh/ruff/rules/#pydocstyle-d

lib/iris/analysis/__init__.py

@@ -1577,7 +1577,7 @@ def _lazy_max_run(array, axis=-1, **kwargs):
     stepped_run_lengths = da.reductions.cumreduction(
         np.maximum.accumulate,
         np.maximum,
-        np.NINF,
+        -np.inf,
         run_totals,
         axis=axis,
         dtype=cum_sum.dtype,

lib/iris/cube.py

@@ -3824,6 +3824,9 @@ def _deepcopy(self, memo, data=None):
 
     # START OPERATOR OVERLOADS
     def __eq__(self, other):
+        if other is self:
+            return True
+
         result = NotImplemented
 
         if isinstance(other, Cube):
@@ -3862,7 +3865,13 @@ def __eq__(self, other):
             if result:
                 # TODO: why do we use allclose() here, but strict equality in
                 #  _DimensionalMetadata (via util.array_equal())?
-                result = da.allclose(self.core_data(), other.core_data()).compute()
+                result = bool(
+                    np.allclose(
+                        self.core_data(),
+                        other.core_data(),
+                        equal_nan=True,
+                    )
+                )
         return result
 
     # Must supply __ne__, Python does not defer to __eq__ for negative equality

lib/iris/fileformats/netcdf/loader.py

@@ -708,7 +708,7 @@ def set(
             apply the `dimension_chunksizes` controls only to these variables,
             or when building :class:`~iris.cube.Cube` from these data variables.
             If ``None``, settings apply to all loaded variables.
-        dimension_chunksizes : dict of {str: int}
+        **dimension_chunksizes : dict of {str: int}
             Kwargs specifying chunksizes for dimensions of file variables.
             Each key-value pair defines a chunk size for a named file
             dimension, e.g. ``{'time': 10, 'model_levels':1}``.

lib/iris/tests/test_cell.py

@@ -131,7 +131,7 @@ def test_numpy_int_equality(self):
 
     def test_numpy_float_equality(self):
         dtypes = (
-            np.float_,
+            np.float64,
             np.float16,
             np.float32,
             np.float64,

lib/iris/tests/unit/cube/test_Cube.py

@@ -2841,11 +2841,20 @@ def test_unit_multiply(self):
 class Test__eq__data(tests.IrisTest):
     """Partial cube equality testing, for data type only."""
 
+    def test_cube_identical_to_itself(self):
+        cube = Cube([1.0])
+        self.assertTrue(cube == cube)
+
     def test_data_float_eq(self):
         cube1 = Cube([1.0])
         cube2 = Cube([1.0])
         self.assertTrue(cube1 == cube2)
 
+    def test_data_float_nan_eq(self):
+        cube1 = Cube([np.nan, 1.0])
+        cube2 = Cube([np.nan, 1.0])
+        self.assertTrue(cube1 == cube2)
+
     def test_data_float_eqtol(self):
         val1 = np.array(1.0, dtype=np.float32)
         # NOTE: Since v2.3, Iris uses "allclose".  Prior to that we used

lib/iris/tests/unit/plot/test_contourf.py

@@ -93,7 +93,7 @@ def test_skip_contour(self):
     def test_apply_contour_nans(self):
         # Presence of nans should not prevent contours being added.
         cube = simple_2d()
-        cube.data = cube.data.astype(np.float_)
+        cube.data = cube.data.astype(np.float64)
         cube.data[0, 0] = np.nan
 
         levels = [2, 4, 6, 8]

requirements/locks/py310-linux-64.lock

@@ -66,11 +66,11 @@ https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.
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-https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.44.2-h2797004_0.conda#3b6a9f225c3dbe0d24f4fedd4625c5bf
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.45.1-h2797004_0.conda#fc4ccadfbf6d4784de88c41704792562
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 https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.15-h0b41bf4_0.conda#33277193f5b92bad9fdd230eb700929c
-https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.4-h232c23b_1.conda#53e951fab78d7e3bab40745f7b3d1620
+https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.5-h232c23b_0.conda#c442ebfda7a475f5e78f1c8e45f1e919
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@@ -86,7 +86,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libglib-2.78.3-h783c2da_0.conda#
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-https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.44.2-h2c6b66d_0.conda#4f2892c672829693fd978d065db4e8be
+https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.45.1-h2c6b66d_0.conda#93acf31b379acebada263b9bce3dc6ed
 https://conda.anaconda.org/conda-forge/linux-64/udunits2-2.2.28-h40f5838_3.conda#6bb8deb138f87c9d48320ac21b87e7a1
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@@ -95,7 +95,7 @@ https://conda.anaconda.org/conda-forge/noarch/asv_runner-0.1.0-pyhd8ed1ab_0.cond
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-https://conda.anaconda.org/conda-forge/noarch/certifi-2023.11.17-pyhd8ed1ab_0.conda#2011bcf45376341dd1d690263fdbc789
+https://conda.anaconda.org/conda-forge/noarch/certifi-2024.2.2-pyhd8ed1ab_0.conda#0876280e409658fc6f9e75d035960333
 https://conda.anaconda.org/conda-forge/noarch/cfgv-3.3.1-pyhd8ed1ab_0.tar.bz2#ebb5f5f7dc4f1a3780ef7ea7738db08c
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 https://conda.anaconda.org/conda-forge/noarch/click-8.1.7-unix_pyh707e725_0.conda#f3ad426304898027fc619827ff428eca
@@ -109,7 +109,7 @@ https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.2.0-pyhd8ed1ab_2.
 https://conda.anaconda.org/conda-forge/noarch/execnet-2.0.2-pyhd8ed1ab_0.conda#67de0d8241e1060a479e3c37793e26f9
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-https://conda.anaconda.org/conda-forge/noarch/fsspec-2023.12.2-pyhca7485f_0.conda#bf40f2a8835b78b1f91083d306b493d2
+https://conda.anaconda.org/conda-forge/noarch/fsspec-2024.2.0-pyhca7485f_0.conda#fad86b90138cf5d82c6f5a2ed6e683d9
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@@ -164,7 +164,7 @@ https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-h3faef2a_0.conda#f9
 https://conda.anaconda.org/conda-forge/linux-64/cffi-1.16.0-py310h2fee648_0.conda#45846a970e71ac98fd327da5d40a0a2c
 https://conda.anaconda.org/conda-forge/linux-64/coverage-7.4.1-py310h2372a71_0.conda#b2de1af90e44849451c9808312f964ae
 https://conda.anaconda.org/conda-forge/linux-64/cytoolz-0.12.3-py310h2372a71_0.conda#21362970a6fea90ca507c253c20465f2
-https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.47.2-py310h2372a71_0.conda#0688fca50c84de6ff0df1c6440941e0e
+https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.48.1-py310h2372a71_0.conda#480ff621e839c5f80a52975b167500d2
 https://conda.anaconda.org/conda-forge/linux-64/hdf5-1.14.3-nompi_h4f84152_100.conda#d471a5c3abc984b662d9bae3bb7fd8a5
 https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-7.0.1-pyha770c72_0.conda#746623a787e06191d80a2133e5daff17
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@@ -174,7 +174,7 @@ https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-21_linux64_openb
 https://conda.anaconda.org/conda-forge/noarch/nodeenv-1.8.0-pyhd8ed1ab_0.conda#2a75b296096adabbabadd5e9782e5fcc
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 https://conda.anaconda.org/conda-forge/linux-64/pillow-10.2.0-py310h01dd4db_0.conda#9ec32d0d90f7670eb29bbba18299cf29
-https://conda.anaconda.org/conda-forge/noarch/pip-23.3.2-pyhd8ed1ab_0.conda#8591c748f98dcc02253003533bc2e4b1
+https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67
 https://conda.anaconda.org/conda-forge/linux-64/proj-9.3.1-h1d62c97_0.conda#44ec51d0857d9be26158bb85caa74fdb
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@@ -184,7 +184,7 @@ https://conda.anaconda.org/conda-forge/noarch/virtualenv-20.25.0-pyhd8ed1ab_0.co
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-https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.3-py310hb13e2d6_0.conda#e5e9c6f112d581cdf465b8ca861cb14f
+https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.4-py310hb13e2d6_0.conda#6593de64c935768b6bad3e19b3e978be
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