nep29: drop py39 and support py312 (#5894)

* nep29: drop py39 and support py312

* update lockfiles

* update benchmark config

* fix tests

* tmp benchmark workaround

* bm_runner workaround

* revert benchmark workaround + whatsnew entry

.github/workflows/ci-tests.yml

@@ -35,18 +35,18 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.11"]
+        python-version: ["3.12"]
         session: ["doctest", "gallery", "linkcheck"]
         include:
           - os: "ubuntu-latest"
-            python-version: "3.11"
+            python-version: "3.12"
             session: "tests"
             coverage: "--coverage"
           - os: "ubuntu-latest"
-            python-version: "3.10"
+            python-version: "3.11"
             session: "tests"
           - os: "ubuntu-latest"
-            python-version: "3.9"
+            python-version: "3.10"
             session: "tests"
 
     env:

.github/workflows/ci-wheels.yml

@@ -52,7 +52,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         session: ["wheel"]
     env:
       ENV_NAME: "ci-wheels"

benchmarks/asv.conf.json

@@ -23,7 +23,7 @@
     //  * No build-time environment variables.
     //  * Is run in the same environment as the ASV install itself.
     "delegated_env_commands": [
-        "PY_VER=3.11 nox --envdir={conf_dir}/.asv/env/nox01 --session=tests --install-only --no-error-on-external-run --verbose"
+        "PY_VER=3.12 nox --envdir={conf_dir}/.asv/env/nox01 --session=tests --install-only --no-error-on-external-run --verbose"
     ],
     // The parent directory of the above environment.
     //  The most recently modified environment in the directory will be used.

benchmarks/bm_runner.py

@@ -67,7 +67,7 @@ def _check_requirements(package: str) -> None:
 
 def _prep_data_gen_env() -> None:
     """Create or access a separate, unchanging environment for generating test data."""
-    python_version = "3.11"
+    python_version = "3.12"
     data_gen_var = "DATA_GEN_PYTHON"
     if data_gen_var in environ:
         echo("Using existing data generation environment.")

docs/src/whatsnew/latest.rst

@@ -79,7 +79,8 @@ This document explains the changes made to Iris for this release
 🔗 Dependencies
 ===============
 
-#. N/A
+#. `@bjlittle`_ dropped support for ``py39`` and adopted support for ``py312`` as per
+   the `NEP-29`_ schedule. (:pull:`5894`)
 
 
 📚 Documentation
@@ -105,6 +106,7 @@ This document explains the changes made to Iris for this release
 
 #. `@jfrost-mo`_ enabled colour output for pytest on GitHub Actions. (:pull:`5895`)
 
+
 .. comment
     Whatsnew author names (@github name) in alphabetical order. Note that,
     core dev names are automatically included by the common_links.inc:
@@ -120,3 +122,4 @@ This document explains the changes made to Iris for this release
 .. _NPY002: https://docs.astral.sh/ruff/rules/numpy-legacy-random/
 .. _numpydoc validation: https://numpydoc.readthedocs.io/en/latest/validation.html#
 .. _Dask version 2024.2.1: https://docs.dask.org/en/stable/changelog.html#v2024-2-1
+.. _NEP-29: https://numpy.org/neps/nep-0029-deprecation_policy.html#drop-schedule

lib/iris/tests/test_coding_standards.py

@@ -69,8 +69,8 @@ def test_python_versions():
     Test is designed to fail whenever Iris' supported Python versions are
     updated, insisting that versions are updated EVERYWHERE in-sync.
     """
-    latest_supported = "3.11"
-    all_supported = ["3.9", "3.10", latest_supported]
+    latest_supported = "3.12"
+    all_supported = ["3.10", "3.11", latest_supported]
 
     root_dir = Path(__file__).parents[3]
     workflows_dir = root_dir / ".github" / "workflows"

lib/iris/tests/unit/common/metadata/test__NamedTupleMeta.py

@@ -45,7 +45,7 @@ def _members(self):
         self.assertEqual(self.names(Metadata.__bases__), expected)
         expected = ["Metadata", "object"]
         self.assertEqual(self.names(Metadata.__mro__), expected)
-        emsg = "Can't instantiate abstract class .* with abstract method.* _members"
+        emsg = "Can't instantiate abstract class"
         with self.assertRaisesRegex(TypeError, emsg):
             _ = Metadata()
 

lib/iris/tests/unit/coords/test_Coord.py

@@ -1124,7 +1124,7 @@ def test_copy_coord(self, ignore_axis, copy_or_from, result, sample_coord):
 
 class Test___init____abstractmethod(tests.IrisTest):
     def test(self):
-        emsg = "Can't instantiate abstract class Coord with abstract method.* __init__"
+        emsg = "Can't instantiate abstract class Coord"
         with self.assertRaisesRegex(TypeError, emsg):
             _ = Coord(points=[0, 1])
 

lib/iris/tests/unit/coords/test__DimensionalMetadata.py

@@ -28,10 +28,7 @@
 
 class Test___init____abstractmethod(tests.IrisTest):
     def test(self):
-        emsg = (
-            "Can't instantiate abstract class _DimensionalMetadata with "
-            "abstract methods __init__"
-        )
+        emsg = "Can't instantiate abstract class _DimensionalMetadata"
         with self.assertRaisesRegex(TypeError, emsg):
             _ = _DimensionalMetadata(0)
 

lib/iris/tests/unit/experimental/ugrid/load/test_load_mesh.py

@@ -24,7 +24,8 @@ def test_calls_load_meshes(self):
         args = [("file_1", "file_2"), "my_var_name"]
         with PARSE_UGRID_ON_LOAD.context():
             _ = load_mesh(args)
-        self.assertTrue(self.load_meshes_mock.called_with(args))
+        assert self.load_meshes_mock.call_count == 1
+        assert self.load_meshes_mock.call_args == ((args, None),)
 
     def test_returns_mesh(self):
         with PARSE_UGRID_ON_LOAD.context():

noxfile.py

@@ -15,7 +15,7 @@
 nox.options.reuse_existing_virtualenvs = True
 
 #: Python versions we can run sessions under
-_PY_VERSIONS_ALL = ["3.9", "3.10", "3.11"]
+_PY_VERSIONS_ALL = ["3.10", "3.11", "3.12"]
 _PY_VERSION_LATEST = _PY_VERSIONS_ALL[-1]
 
 #: One specific python version for docs builds

pyproject.toml

@@ -22,9 +22,9 @@ classifiers = [
     "Operating System :: Unix",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: Implementation :: CPython",
     "Topic :: Scientific/Engineering",
     "Topic :: Scientific/Engineering :: Atmospheric Science",
@@ -50,7 +50,7 @@ keywords = [
 ]
 license = {text = "BSD-3-Clause"}
 name = "scitools-iris"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 
 [project.urls]
 Code = "https://github.com/SciTools/iris"
@@ -73,7 +73,6 @@ src = [
     "lib",
     "docs/src",
 ]
-target-version = "py39"
 
 [tool.ruff.format]
 preview = false

requirements/iris.yml

@@ -1 +1 @@
-py311.yml
+py312.yml

requirements/locks/py310-linux-64.lock

@@ -23,7 +23,7 @@ https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.11-hd590300_1.conda
 https://conda.anaconda.org/conda-forge/linux-64/aom-3.8.2-h59595ed_0.conda#625e1fed28a5139aed71b3a76117ef84
 https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.1-h166bdaf_1.tar.bz2#d9c69a24ad678ffce24c6543a0176b00
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
-https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.0-hd590300_0.conda#a6d86d33ddb84cde21de214cce563823
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
 https://conda.anaconda.org/conda-forge/linux-64/dav1d-1.2.1-hd590300_0.conda#418c6ca5929a611cbd69204907a83995
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@@ -155,7 +155,7 @@ https://conda.anaconda.org/conda-forge/noarch/cloudpickle-3.0.0-pyhd8ed1ab_0.con
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-https://conda.anaconda.org/conda-forge/linux-64/cython-3.0.9-py310hc6cd4ac_0.conda#987a8359726157c7a7cdd198f882f82d
+https://conda.anaconda.org/conda-forge/linux-64/cython-3.0.10-py310hc6cd4ac_0.conda#bd1d71ee240be36f1d85c86177d6964f
 https://conda.anaconda.org/conda-forge/linux-64/dbus-1.13.6-h5008d03_3.tar.bz2#ecfff944ba3960ecb334b9a2663d708d
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@@ -192,7 +192,7 @@ https://conda.anaconda.org/conda-forge/noarch/packaging-24.0-pyhd8ed1ab_0.conda#
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-https://conda.anaconda.org/conda-forge/noarch/pycparser-2.21-pyhd8ed1ab_0.tar.bz2#076becd9e05608f8dc72757d5f3a91ff
+https://conda.anaconda.org/conda-forge/noarch/pycparser-2.22-pyhd8ed1ab_0.conda#844d9eb3b43095b031874477f7d70088
 https://conda.anaconda.org/conda-forge/noarch/pygments-2.17.2-pyhd8ed1ab_0.conda#140a7f159396547e9799aa98f9f0742e
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 https://conda.anaconda.org/conda-forge/noarch/pyshp-2.3.1-pyhd8ed1ab_0.tar.bz2#92a889dc236a5197612bc85bee6d7174
@@ -290,7 +290,7 @@ https://conda.anaconda.org/conda-forge/linux-64/aiohttp-3.9.3-py310h2372a71_1.co
 https://conda.anaconda.org/conda-forge/linux-64/cftime-1.6.3-py310h1f7b6fc_0.conda#31beda75384647959d5792a1a7dc571a
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 https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.2.0-py310hd41b1e2_0.conda#85d2aaa7af046528d339da1e813c3a9f
-https://conda.anaconda.org/conda-forge/noarch/dask-core-2024.3.1-pyhd8ed1ab_0.conda#52dd56ce3afa6a52c2f3d3116875ff32
+https://conda.anaconda.org/conda-forge/noarch/dask-core-2024.4.0-pyhd8ed1ab_0.conda#291ae1e1179a934cfb7dfbbb802206d6
 https://conda.anaconda.org/conda-forge/linux-64/gst-plugins-base-1.22.9-h8e1006c_0.conda#614b81f8ed66c56b640faee7076ad14a
 https://conda.anaconda.org/conda-forge/noarch/identify-2.5.35-pyhd8ed1ab_0.conda#9472bfd206a2b7bb8143835e37667054
 https://conda.anaconda.org/conda-forge/linux-64/libass-0.17.1-h8fe9dca_1.conda#c306fd9cc90c0585171167d09135a827
@@ -305,7 +305,7 @@ https://conda.anaconda.org/conda-forge/linux-64/scipy-1.12.0-py310hb13e2d6_2.con
 https://conda.anaconda.org/conda-forge/linux-64/shapely-2.0.3-py310hc3e127f_0.conda#fbc825d13cbcb2d5d3fbba22c83fd203
 https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-apidoc-0.3.0-py_1.tar.bz2#855b087883443abb10f5faf6eef40860
 https://conda.anaconda.org/conda-forge/linux-64/cf-units-3.2.0-py310h1f7b6fc_4.conda#0ca55ca20891d393846695354b32ebc5
-https://conda.anaconda.org/conda-forge/noarch/distributed-2024.3.1-pyhd8ed1ab_0.conda#b0ad5ef44595ef37c3008fc04ecd2abf
+https://conda.anaconda.org/conda-forge/noarch/distributed-2024.4.0-pyhd8ed1ab_0.conda#5085b4511ddca32d600783bed80a420f
 https://conda.anaconda.org/conda-forge/linux-64/esmf-8.6.0-nompi_h7b237b1_0.conda#a5f1925a75d9fcf0bffd07a194f83895
 https://conda.anaconda.org/conda-forge/linux-64/ffmpeg-6.1.1-gpl_h38e077a_106.conda#23fe0f8b47e7b5527bcc1dfb6087dba6
 https://conda.anaconda.org/conda-forge/linux-64/gtk2-2.24.33-h280cfa0_4.conda#410f86e58e880dcc7b0e910a8e89c05c

requirements/locks/py311-linux-64.lock

@@ -23,7 +23,7 @@ https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.11-hd590300_1.conda
 https://conda.anaconda.org/conda-forge/linux-64/aom-3.8.2-h59595ed_0.conda#625e1fed28a5139aed71b3a76117ef84
 https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.1-h166bdaf_1.tar.bz2#d9c69a24ad678ffce24c6543a0176b00
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
-https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.0-hd590300_0.conda#a6d86d33ddb84cde21de214cce563823
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
 https://conda.anaconda.org/conda-forge/linux-64/dav1d-1.2.1-hd590300_0.conda#418c6ca5929a611cbd69204907a83995
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@@ -155,7 +155,7 @@ https://conda.anaconda.org/conda-forge/noarch/cloudpickle-3.0.0-pyhd8ed1ab_0.con
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 https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_0.conda#5cd86562580f274031ede6aa6aa24441
-https://conda.anaconda.org/conda-forge/linux-64/cython-3.0.9-py311hb755f60_0.conda#c49924051b8336f6031eb3d019619cba
+https://conda.anaconda.org/conda-forge/linux-64/cython-3.0.10-py311hb755f60_0.conda#f3a8a500a2e743ff92f418f0eaf9bf71
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@@ -192,7 +192,7 @@ https://conda.anaconda.org/conda-forge/noarch/packaging-24.0-pyhd8ed1ab_0.conda#
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-https://conda.anaconda.org/conda-forge/noarch/pycparser-2.21-pyhd8ed1ab_0.tar.bz2#076becd9e05608f8dc72757d5f3a91ff
+https://conda.anaconda.org/conda-forge/noarch/pycparser-2.22-pyhd8ed1ab_0.conda#844d9eb3b43095b031874477f7d70088
 https://conda.anaconda.org/conda-forge/noarch/pygments-2.17.2-pyhd8ed1ab_0.conda#140a7f159396547e9799aa98f9f0742e
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@@ -288,7 +288,7 @@ https://conda.anaconda.org/conda-forge/linux-64/ukkonen-1.0.1-py311h9547e67_4.co
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 https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.2.0-py311h9547e67_0.conda#40828c5b36ef52433e21f89943e09f33
-https://conda.anaconda.org/conda-forge/noarch/dask-core-2024.3.1-pyhd8ed1ab_0.conda#52dd56ce3afa6a52c2f3d3116875ff32
+https://conda.anaconda.org/conda-forge/noarch/dask-core-2024.4.0-pyhd8ed1ab_0.conda#291ae1e1179a934cfb7dfbbb802206d6
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 https://conda.anaconda.org/conda-forge/linux-64/libass-0.17.1-h8fe9dca_1.conda#c306fd9cc90c0585171167d09135a827
@@ -304,7 +304,7 @@ https://conda.anaconda.org/conda-forge/linux-64/shapely-2.0.3-py311h2032efe_0.co
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-https://conda.anaconda.org/conda-forge/noarch/distributed-2024.3.1-pyhd8ed1ab_0.conda#b0ad5ef44595ef37c3008fc04ecd2abf
+https://conda.anaconda.org/conda-forge/noarch/distributed-2024.4.0-pyhd8ed1ab_0.conda#5085b4511ddca32d600783bed80a420f
 https://conda.anaconda.org/conda-forge/linux-64/esmf-8.6.0-nompi_h7b237b1_0.conda#a5f1925a75d9fcf0bffd07a194f83895
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