DOCS: replace napolean with numpydoc for the API docs.

docs/Makefile

@@ -10,6 +10,11 @@ html:
 		echo "make html in $$i..."; \
 		(cd $$i; $(MAKE) $(MFLAGS) $(MYMAKEFLAGS) html); done
 
+html-nitpicky:
+	@for i in $(SUBDIRS); do \
+		echo "make html-nitpicky in $$i..."; \
+		(cd $$i; $(MAKE) $(MFLAGS) $(MYMAKEFLAGS) html-nitpicky); done
+
 html-noplot:
 	@for i in $(SUBDIRS); do \
 		echo "make html-noplot in $$i..."; \
@@ -48,4 +53,4 @@ show:
 livehtml:
 	@for i in $(SUBDIRS); do \
 		echo "Running show in $$i..."; \
-		(cd $$i; $(MAKE) $(MFLAGS) $(MYMAKEFLAGS) livehtml); done
+		(cd $$i; $(MAKE) $(MFLAGS) $(MYMAKEFLAGS) livehtml); done

docs/src/Makefile

@@ -20,24 +20,30 @@ ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  help         to view this help"
-	@echo "  html         to make standalone HTML files"
-	@echo "  html-noplot  to make standalone HTML files, skip gallery"
-	@echo "  html-noapi   to make standalone HTML files, skip the API"
-	@echo "  html-quick   to make standalone HTML files, skip the gallery and API"
-	@echo "  clean        to remove all built files"
-	@echo "  doctest      to run all doctests embedded in the documentation (if enabled)"
-	@echo "  linkcheck    to check all external links for integrity"
-	@echo "  show         to open the built documentation in the default browser"
-	@echo "  livehtml     to auto build the docs when any file changes are detected."
-	@echo "               You need to install sphinx-autobuild first:"
-	@echo "                   conda install -c conda-forge sphinx-autobuild"
+	@echo "  help          to view this help"
+	@echo "  html          to make standalone HTML files"
+	@echo "  html-noplot   to make standalone HTML files, skip gallery"
+	@echo "  html-nitpicky to make standalone HTML files and  use sphinx nitpicky"	
+	@echo "  html-noapi    to make standalone HTML files, skip the API"
+	@echo "  html-quick    to make standalone HTML files, skip the gallery and API"
+	@echo "  clean         to remove all built files"
+	@echo "  doctest       to run all doctests embedded in the documentation (if enabled)"
+	@echo "  linkcheck     to check all external links for integrity"
+	@echo "  show          to open the built documentation in the default browser"
+	@echo "  livehtml      to auto build the docs when any file changes are detected."
+	@echo "                You need to install sphinx-autobuild first:"
+	@echo "                    conda install -c conda-forge sphinx-autobuild"
 
 html:
 	$(SPHINXBUILD) $(WARNING_TO_ERROR) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html"
 
+html-nitpicky:
+	$(SPHINXBUILD) -n -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML (no api docs) pages are in $(BUILDDIR)/html"
+
 html-noplot:
 	$(SPHINXBUILD) -D plot_gallery=0 -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo

docs/src/conf.py

@@ -144,10 +144,15 @@ def _dotv(version):
 .. |build_date| replace:: ({datetime.datetime.now().strftime('%d %b %Y')})
 """
 
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-suppress_warnings
+# suppress warning "WARNING: cannot cache unpickable configuration value: 'sphinx_gallery_conf'"
+suppress_warnings = ["config.cache"]
+
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named "sphinx.ext.*") or your custom
 # ones.
 extensions = [
+    "numpydoc",
     "sphinx.ext.todo",
     "sphinx.ext.duration",
     "sphinx.ext.coverage",
@@ -158,7 +163,6 @@ def _dotv(version):
     "sphinx.ext.autodoc",
     "sphinx.ext.intersphinx",
     "sphinx_copybutton",
-    "sphinx.ext.napoleon",
     "sphinx_design",
     "sphinx_gallery.gen_gallery",
     "matplotlib.sphinxext.mathmpl",
@@ -171,23 +175,31 @@ def _dotv(version):
     extensions.extend(["sphinxcontrib.apidoc"])
     extensions.extend(["api_rst_formatting"])
 
-# -- Napoleon extension -------------------------------------------------------
-# See https://sphinxcontrib-napoleon.readthedocs.io/en/latest/sphinxcontrib.napoleon.html
-napoleon_google_docstring = True
-napoleon_numpy_docstring = True
-napoleon_include_init_with_doc = False
-napoleon_include_private_with_doc = False
-napoleon_include_special_with_doc = True  # includes dunders in api doc
-napoleon_use_admonition_for_examples = False
-napoleon_use_admonition_for_notes = False
-napoleon_use_admonition_for_references = False
-napoleon_use_ivar = False
-napoleon_use_param = True
-napoleon_use_rtype = True
-napoleon_use_keyword = True
-napoleon_custom_sections = None
-
-# -- copybutton extension -----------------------------------------------------
+# -- numpydoc options --------------------------------------------------------
+# See https://numpydoc.readthedocs.io/en/latest/index.html
+numpydoc_attributes_as_param_list = True  # GV is True
+numpydoc_class_members_toctree = True  # GB is False
+numpydoc_show_class_members = False  # GV is False
+numpydoc_use_plots = True  # GV is True
+# note, the dict index is case sensitive
+numpydoc_xref_aliases = {
+    "ArrayLike": "numpy.typing.ArrayLike",
+    "Cube": "iris.cube.Cube",
+}
+numpydoc_xref_ignore = {"optional", "default", "of"}
+numpydoc_xref_param_type = True
+
+# -- nitpicky ----------------------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-nitpicky
+#
+# Use "make html-nitpicky" to enable.
+nitpick_ignore_regex = [
+    (r"py:class", r"iris.tests.*"),  # iris.tests not included in the API docs
+    (r"py:meth", r"iris.tests.*"),  # iris.tests not included in the API docs
+    (r"py:.*", r"iris.tests.*"),  # iris.tests not included in the API docs
+]
+
+# -- copybutton extension ----------------------------------------------------
 # See https://sphinx-copybutton.readthedocs.io/en/latest/
 copybutton_prompt_text = r">>> |\.\.\. "
 copybutton_prompt_is_regexp = True
@@ -246,16 +258,17 @@ def _dotv(version):
 # See https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html
 intersphinx_mapping = {
     "cartopy": ("https://scitools.org.uk/cartopy/docs/latest/", None),
+    "cf-units": ("https://cf-units.readthedocs.io/en/stable/", None),
     "dask": ("https://docs.dask.org/en/stable/", None),
+    "geovista": ("https://geovista.readthedocs.io/en/latest/", None),
     "iris-esmf-regrid": ("https://iris-esmf-regrid.readthedocs.io/en/stable/", None),
     "matplotlib": ("https://matplotlib.org/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
-    "python": ("https://docs.python.org/3/", None),
-    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
     "pandas": ("https://pandas.pydata.org/docs/", None),
-    "dask": ("https://docs.dask.org/en/stable/", None),
-    "geovista": ("https://geovista.readthedocs.io/en/latest/", None),
+    "python": ("https://docs.python.org/3/", None),
     "pyvista": ("https://docs.pyvista.org/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+    "xarray": ("https://docs.xarray.dev/en/stable/", None),
 }
 
 # The name of the Pygments (syntax highlighting) style to use.

docs/src/whatsnew/latest.rst

@@ -91,7 +91,12 @@ This document explains the changes made to Iris for this release
 📚 Documentation
 ================
 
-#. `@hsteptoe`_ added more detailed examples to :class:`~iris.cube.Cube` functions :func:`~iris.cube.Cube.slices` and :func:`~iris.cube.Cube.slices_over`. (:pull:`5735`)
+#. `@hsteptoe`_ added more detailed examples to :class:`~iris.cube.Cube` functions
+   :func:`~iris.cube.Cube.slices` and :func:`~iris.cube.Cube.slices_over`.
+   (:pull:`5735`)
+#. `@tkknight`_ introduced ``make html-nitpicky`` target to check all the references
+   in the Iris documentation, including the API documentation.  This is not the
+   default.  (:pull:`5910`)
 
 
 💼 Internal

lib/iris/analysis/__init__.py

@@ -2138,7 +2138,7 @@ def interp_order(length):
 
 Parameters
 ----------
-ddof : int, optioonal
+ddof : int, optional
     Delta degrees of freedom. The divisor used in calculations is N - ddof,
     where N represents the number of elements. Defaults to 1.
 

lib/iris/analysis/maths.py

@@ -733,11 +733,11 @@ def apply_ufunc(ufunc, cube, other=None, new_unit=None, new_name=None, in_place=
 
         cube = apply_ufunc(numpy.sin, cube, in_place=True)
 
-    .. note::
-
-        This function maintains laziness when called; it does not realise data. This is dependent on `ufunc` argument
-        being a numpy operation that is compatible with lazy operation.
-        See more at :doc:`/userguide/real_and_lazy_data`.
+    Notes
+    -----
+    This function maintains laziness when called; it does not realise data.
+    This is dependent on `ufunc` argument being a numpy operation that is compatible
+    with lazy operation.  See more at :doc:`/userguide/real_and_lazy_data`.
 
     """
     if not isinstance(ufunc, np.ufunc):

lib/iris/cube.py

@@ -1220,8 +1220,8 @@ def __init__(
         aux_coords_and_dims : optional
             A list of coordinates with dimension mappings,
             e.g ``[(lat_coord, 0), (lon_coord, (0, 1))]``.
-            See also :meth:`Cube.add_dim_coord()<iris.cube.Cube.add_dim_coord>`
-            and :meth:`Cube.add_aux_coord()<iris.cube.Cube.add_aux_coord>`.
+            See also :meth:`iris.cube.Cube.add_dim_coord`
+            and :meth:`iris.cube.Cube.add_aux_coord`.
         aux_factories : optional
             A list of auxiliary coordinate factories. See
             :mod:`iris.aux_factory`.

lib/iris/util.py

@@ -1789,7 +1789,7 @@ def find_discontiguities(cube, rel_tol=1e-5, abs_tol=1e-8):
 
     Parameters
     ----------
-    cube : `iris.cube.Cube`
+    cube : Cube
         The cube to be checked for discontinuities in its 'x' and 'y'
         coordinates. These coordinates must be 2D.
     rel_tol : float, default=1e-5
@@ -2131,7 +2131,7 @@ def mask_cube_from_shapefile(cube, shape, minimum_weight=0.0, in_place=False):
 
     Parameters
     ----------
-    cube : :class:`~iris.cube.Cube` object
+    cube : Cube object
         The `Cube` object to masked. Must be singular, rather than a `CubeList`.
     shape : Shapely.Geometry object
         A single `shape` of the area to remain unmasked on the `cube`.
@@ -2146,12 +2146,12 @@ def mask_cube_from_shapefile(cube, shape, minimum_weight=0.0, in_place=False):
 
     Returns
     -------
-    iris.Cube
+    Cube
         A masked version of the input cube, if in_place is False.
 
     See Also
     --------
-    :func:`~iris.util.mask_cube`
+    iris.util.mask_cube
         Mask any cells in the cube’s data array.
 
     Notes

requirements/locks/py310-linux-64.lock

@@ -80,7 +80,6 @@ https://conda.anaconda.org/conda-forge/linux-64/libaec-1.1.3-h59595ed_0.conda#5e
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-https://conda.anaconda.org/conda-forge/linux-64/libcap-2.69-h0f662aa_0.conda#25cb5999faa414e5ccb2c1388f62d3d5
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@@ -116,6 +115,7 @@ https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d05
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 https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb
+https://conda.anaconda.org/conda-forge/linux-64/gettext-0.22.5-h59595ed_2.conda#219ba82e95d7614cf7140d2a4afc0926
 https://conda.anaconda.org/conda-forge/linux-64/gl2ps-1.4.2-h0708190_0.tar.bz2#438718bf8921ac70956d919d0e2cc487
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@@ -149,7 +149,6 @@ https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz
 https://conda.anaconda.org/conda-forge/noarch/colorcet-3.1.0-pyhd8ed1ab_0.conda#4d155b600b63bc6ba89d91fab74238f8
 https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_0.conda#5cd86562580f274031ede6aa6aa24441
 https://conda.anaconda.org/conda-forge/linux-64/cython-3.0.10-py310hc6cd4ac_0.conda#bd1d71ee240be36f1d85c86177d6964f
-https://conda.anaconda.org/conda-forge/linux-64/dbus-1.13.6-h5008d03_3.tar.bz2#ecfff944ba3960ecb334b9a2663d708d
 https://conda.anaconda.org/conda-forge/noarch/distlib-0.3.8-pyhd8ed1ab_0.conda#db16c66b759a64dc5183d69cc3745a52
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 https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.2.0-pyhd8ed1ab_2.conda#8d652ea2ee8eaee02ed8dc820bc794aa
@@ -341,3 +340,4 @@ https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-htmlhelp-2.0.5-pyhd8
 https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-qthelp-1.0.7-pyhd8ed1ab_0.conda#26acae54b06f178681bfb551760f5dd1
 https://conda.anaconda.org/conda-forge/noarch/sphinx-7.3.7-pyhd8ed1ab_0.conda#7b1465205e28d75d2c0e1a868ee00a67
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+

requirements/locks/py311-linux-64.lock

@@ -80,7 +80,6 @@ https://conda.anaconda.org/conda-forge/linux-64/libaec-1.1.3-h59595ed_0.conda#5e
 https://conda.anaconda.org/conda-forge/linux-64/libasprintf-0.22.5-h661eb56_2.conda#dd197c968bf9760bba0031888d431ede
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 https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.1.0-hd590300_1.conda#5fc11c6020d421960607d821310fcd4d
-https://conda.anaconda.org/conda-forge/linux-64/libcap-2.69-h0f662aa_0.conda#25cb5999faa414e5ccb2c1388f62d3d5
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@@ -116,6 +115,7 @@ https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d05
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 https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb
+https://conda.anaconda.org/conda-forge/linux-64/gettext-0.22.5-h59595ed_2.conda#219ba82e95d7614cf7140d2a4afc0926
 https://conda.anaconda.org/conda-forge/linux-64/gl2ps-1.4.2-h0708190_0.tar.bz2#438718bf8921ac70956d919d0e2cc487
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@@ -149,7 +149,6 @@ https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz
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-https://conda.anaconda.org/conda-forge/linux-64/dbus-1.13.6-h5008d03_3.tar.bz2#ecfff944ba3960ecb334b9a2663d708d
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@@ -339,3 +338,4 @@ https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-htmlhelp-2.0.5-pyhd8
 https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-qthelp-1.0.7-pyhd8ed1ab_0.conda#26acae54b06f178681bfb551760f5dd1
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+

requirements/locks/py312-linux-64.lock

@@ -80,7 +80,6 @@ https://conda.anaconda.org/conda-forge/linux-64/libaec-1.1.3-h59595ed_0.conda#5e
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 https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.1.0-hd590300_1.conda#39f910d205726805a958da408ca194ba
 https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb
+https://conda.anaconda.org/conda-forge/linux-64/gettext-0.22.5-h59595ed_2.conda#219ba82e95d7614cf7140d2a4afc0926
 https://conda.anaconda.org/conda-forge/linux-64/gl2ps-1.4.2-h0708190_0.tar.bz2#438718bf8921ac70956d919d0e2cc487
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
 https://conda.anaconda.org/conda-forge/linux-64/libasprintf-devel-0.22.5-h661eb56_2.conda#02e41ab5834dcdcc8590cf29d9526f50
@@ -149,7 +149,6 @@ https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz
 https://conda.anaconda.org/conda-forge/noarch/colorcet-3.1.0-pyhd8ed1ab_0.conda#4d155b600b63bc6ba89d91fab74238f8
 https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_0.conda#5cd86562580f274031ede6aa6aa24441
 https://conda.anaconda.org/conda-forge/linux-64/cython-3.0.10-py312h30efb56_0.conda#b119273bff37284cbcb9281c1e85e67d
-https://conda.anaconda.org/conda-forge/linux-64/dbus-1.13.6-h5008d03_3.tar.bz2#ecfff944ba3960ecb334b9a2663d708d
 https://conda.anaconda.org/conda-forge/noarch/distlib-0.3.8-pyhd8ed1ab_0.conda#db16c66b759a64dc5183d69cc3745a52
 https://conda.anaconda.org/conda-forge/noarch/docutils-0.21.2-pyhd8ed1ab_0.conda#e8cd5d629f65bdf0f3bb312cde14659e
 https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.2.0-pyhd8ed1ab_2.conda#8d652ea2ee8eaee02ed8dc820bc794aa
@@ -339,3 +338,4 @@ https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-htmlhelp-2.0.5-pyhd8
 https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-qthelp-1.0.7-pyhd8ed1ab_0.conda#26acae54b06f178681bfb551760f5dd1
 https://conda.anaconda.org/conda-forge/noarch/sphinx-7.3.7-pyhd8ed1ab_0.conda#7b1465205e28d75d2c0e1a868ee00a67
 https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.10-pyhd8ed1ab_0.conda#e507335cb4ca9cff4c3d0fa9cdab255e
+

requirements/py310.yml

@@ -48,6 +48,7 @@ dependencies:
   - requests
 
 # Documentation dependencies.
+  - numpydoc
   - sphinx
   - sphinxcontrib-apidoc
   - sphinx-copybutton