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

.github/workflows/stale.yml

@@ -14,7 +14,7 @@ jobs:
     if: "github.repository == 'SciTools/iris'"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/stale@v6
+      - uses: actions/stale@v7
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
 

.pre-commit-config.yaml

@@ -43,18 +43,17 @@ repos:
         args: [--config=./setup.cfg]
 
 -   repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.11.4
     hooks:
     -   id: isort
         types: [file, python]
         args: [--filter-files]
 
 -   repo: https://github.com/asottile/blacken-docs
-    rev: v1.12.1
+    rev: 1.13.0
     hooks:
     -   id: blacken-docs
         types: [file, rst]
-        additional_dependencies: [black==21.6b0]
 
 -   repo: https://github.com/aio-libs/sort-all
     rev: v1.2.0

benchmarks/benchmarks/experimental/ugrid/__init__.py

@@ -50,7 +50,7 @@ def time_create(self, *params):
 
 class Connectivity(UGridCommon):
     def setup(self, n_faces):
-        self.array = np.zeros([n_faces, 3], dtype=np.int)
+        self.array = np.zeros([n_faces, 3], dtype=int)
         super().setup(n_faces)
 
     def create(self):

docs/Makefile

@@ -20,11 +20,6 @@ html-quick:
         echo "make html-quick in $$i..."; \
         (cd $$i; $(MAKE) $(MFLAGS) $(MYMAKEFLAGS) html-quick); done
 
-spelling:
-	@for i in $(SUBDIRS); do \
-        echo "make spelling in $$i..."; \
-        (cd $$i; $(MAKE) $(MFLAGS) $(MYMAKEFLAGS) spelling); done
-
 all:
 	@for i in $(SUBDIRS); do \
 		echo "make all in $$i..."; \

docs/src/Makefile

@@ -62,11 +62,6 @@ html-quick:
 	@echo
 	@echo "Build finished. The HTML (no gallery or api docs) pages are in $(BUILDDIR)/html"
 
-spelling:
-	$(SPHINXBUILD) -b spelling $(SRCDIR) $(BUILDDIR)
-	@echo
-	@echo "Build finished. The HTML (no gallery) pages are in $(BUILDDIR)/html"
-
 dirhtml:
 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
 	@echo
@@ -156,4 +151,5 @@ doctest:
 	      "results in $(BUILDDIR)/doctest/output.txt."
 
 show:
-	@python -c "import webbrowser; webbrowser.open_new_tab('file://$(shell pwd)/$(BUILDDIR)/html/index.html')"
+	@python -c "import webbrowser; webbrowser.open_new_tab('file://$(shell pwd)/$(BUILDDIR)/html/index.html')"
+

docs/src/_templates/layout.html

@@ -11,7 +11,7 @@
         <div id="slim-red-box-banner">
             You are viewing the <b>latest</b> unreleased documentation
             <b>v{{ version }}</b>. You can switch to a <b>stable</b> version
-            via the flyout menu in the bottom-right of the screen.
+            via the flyout menu in the bottom corner of the screen.
         </div>
         <p></p>
     {%- endif %}

docs/src/conf.py

@@ -158,8 +158,6 @@ def _dotv(version):
     "sphinx_copybutton",
     "sphinx.ext.napoleon",
     "sphinx_panels",
-    # TODO: Spelling extension disabled until the dependencies can be included
-    # "sphinxcontrib.spelling",
     "sphinx_gallery.gen_gallery",
     "matplotlib.sphinxext.mathmpl",
     "matplotlib.sphinxext.plot_directive",
@@ -193,16 +191,6 @@ def _dotv(version):
 napoleon_use_keyword = True
 napoleon_custom_sections = None
 
-# -- spellingextension --------------------------------------------------------
-# See https://sphinxcontrib-spelling.readthedocs.io/en/latest/customize.html
-spelling_lang = "en_GB"
-# The lines in this file must only use line feeds (no carriage returns).
-spelling_word_list_filename = ["spelling_allow.txt"]
-spelling_show_suggestions = False
-spelling_show_whole_line = False
-spelling_ignore_importable_modules = True
-spelling_ignore_python_builtins = True
-
 # -- copybutton extension -----------------------------------------------------
 # See https://sphinx-copybutton.readthedocs.io/en/latest/
 copybutton_prompt_text = r">>> |\.\.\. "
@@ -311,6 +299,9 @@ def _dotv(version):
     ],
     "use_edit_page_button": True,
     "show_toc_level": 1,
+    # Omitted `theme-switcher` below to disable it
+    # Info: https://pydata-sphinx-theme.readthedocs.io/en/stable/user_guide/light-dark.html#configure-default-theme-mode
+    "navbar_end": ["navbar-icon-links"],
 }
 
 rev_parse = run(["git", "rev-parse", "--short", "HEAD"], capture_output=True)
@@ -322,6 +313,9 @@ def _dotv(version):
     "github_user": "scitools",
     "github_version": "main",
     "doc_path": "docs/src",
+    # default theme.  Also disabled the button in the html_theme_options.
+    # Info: https://pydata-sphinx-theme.readthedocs.io/en/stable/user_guide/light-dark.html#configure-default-theme-mode
+    "default_mode": "light",
     # custom
     "on_rtd": on_rtd,
     "rtd_version": rtd_version,
@@ -365,8 +359,6 @@ def _dotv(version):
     "http://www.esrl.noaa.gov/psd/data/gridded/conventions/cdc_netcdf_standard.shtml",
     "http://www.nationalarchives.gov.uk/doc/open-government-licence",
     "https://www.metoffice.gov.uk/",
-    # TODO: try removing this again in future - was raising an SSLError.
-    "http://www.ecmwf.int/",
 ]
 
 # list of sources to exclude from the build.

docs/src/developers_guide/contributing_documentation_full.rst

@@ -113,18 +113,6 @@ adding it to the ``linkcheck_ignore`` array that is defined in the
 If this fails check the output for the text **broken** and then correct
 or ignore the url.
 
-.. comment
-    Finally, the spelling in the documentation can be checked automatically via the
-    command::
-
-        make spelling
-
-    The spelling check may pull up many technical abbreviations and acronyms.  This
-    can be managed by using an **allow** list in the form of a file.  This file,
-    or list of files is set in the `conf.py`_ using the string list
-    ``spelling_word_list_filename``.
-
-
 .. note:: In addition to the automated `Iris GitHub Actions`_ build of all the
           documentation build options above, the
           https://readthedocs.org/ service is also used.  The configuration

docs/src/developers_guide/release.rst

@@ -277,6 +277,11 @@ Post Release Steps
 #. On main, make a new ``latest.rst`` from ``latest.rst.template`` and update
    the include statement and the toctree in ``index.rst`` to point at the new
    ``latest.rst``.
+#. Consider updating ``docs/src/userguide/citation.rst`` on ``main`` to include 
+   the version number, date and `Zenodo DOI <https://doi.org/10.5281/zenodo.595182>`_ 
+   of the new release. Ideally this would be updated before the release, but 
+   the DOI for the new version is only available once the release has been 
+   created in GitHub.
 
 
 .. _SciTools/iris: https://github.com/SciTools/iris

docs/src/further_topics/metadata.rst

@@ -389,10 +389,10 @@ instances. Normally, this would cause issues. For example,
 
 .. doctest:: richer-metadata
 
-    >>> simply = {"one": np.int(1), "two": np.array([1.0, 2.0])}
+    >>> simply = {"one": np.int32(1), "two": np.array([1.0, 2.0])}
     >>> simply
     {'one': 1, 'two': array([1., 2.])}
-    >>> fruity = {"one": np.int(1), "two": np.array([1.0, 2.0])}
+    >>> fruity = {"one": np.int32(1), "two": np.array([1.0, 2.0])}
     >>> fruity
     {'one': 1, 'two': array([1., 2.])}
     >>> simply == fruity
@@ -419,7 +419,7 @@ However, metadata class equality is rich enough to handle this eventuality,
 
     >>> metadata1
     CubeMetadata(standard_name='air_temperature', long_name=None, var_name='air_temperature', units=Unit('K'), attributes={'one': 1, 'two': array([1., 2.])}, cell_methods=(CellMethod(method='mean', coord_names=('time',), intervals=('6 hour',), comments=()),))
-    >>> metadata2 = cube.metadata._replace(attributes={"one": np.int(1), "two": np.array([1000.0, 2000.0])})
+    >>> metadata2 = cube.metadata._replace(attributes={"one": np.int32(1), "two": np.array([1000.0, 2000.0])})
     >>> metadata2
     CubeMetadata(standard_name='air_temperature', long_name=None, var_name='air_temperature', units=Unit('K'), attributes={'one': 1, 'two': array([1000., 2000.])}, cell_methods=(CellMethod(method='mean', coord_names=('time',), intervals=('6 hour',), comments=()),))
     >>> metadata1 == metadata2

docs/src/installing.rst

@@ -14,7 +14,7 @@ Subsystem for Linux).  This is a great option to get started with Iris
 for users and developers.  Be aware that we do not currently test against
 any WSL_ distributions.
 
-.. _WSL: https://docs.microsoft.com/en-us/windows/wsl/install-win10
+.. _WSL: https://learn.microsoft.com/en-us/windows/wsl/install
 
 .. note:: Iris is currently supported and tested against |python_support|
           running on Linux.  We do not currently actively test on other