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DOCS: replace napolean with numpydoc for the API docs. #5910

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7 changes: 6 additions & 1 deletion docs/Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -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 $$i..."; \
Expand Down Expand Up @@ -48,4 +53,4 @@ show:
livehtml:
@for i in $(SUBDIRS); do \
echo "Running show in $$i..."; \
(cd $$i; $(MAKE) $(MFLAGS) $(MYMAKEFLAGS) livehtml); done
(cd $$i; $(MAKE) $(MFLAGS) $(MYMAKEFLAGS) livehtml); done
30 changes: 18 additions & 12 deletions docs/src/Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
57 changes: 35 additions & 22 deletions docs/src/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -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",
Expand All @@ -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
Expand Down Expand Up @@ -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.
Expand Down
7 changes: 6 additions & 1 deletion docs/src/whatsnew/latest.rst
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion lib/iris/analysis/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -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.

Expand Down
10 changes: 5 additions & 5 deletions lib/iris/analysis/maths.py
Original file line number Diff line number Diff line change
Expand Up @@ -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):
Expand Down
4 changes: 2 additions & 2 deletions lib/iris/cube.py
Original file line number Diff line number Diff line change
Expand Up @@ -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`.
Expand Down
8 changes: 4 additions & 4 deletions lib/iris/util.py
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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`.
Expand All @@ -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
Expand Down
4 changes: 2 additions & 2 deletions requirements/locks/py310-linux-64.lock
Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,6 @@ https://conda.anaconda.org/conda-forge/linux-64/libaec-1.1.3-h59595ed_0.conda#5e
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Expand Down Expand Up @@ -116,6 +115,7 @@ https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d05
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Expand Down Expand Up @@ -149,7 +149,6 @@ https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz
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Expand Down Expand Up @@ -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
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4 changes: 2 additions & 2 deletions requirements/locks/py311-linux-64.lock
Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,6 @@ https://conda.anaconda.org/conda-forge/linux-64/libaec-1.1.3-h59595ed_0.conda#5e
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Expand Down Expand Up @@ -116,6 +115,7 @@ https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d05
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Expand Down Expand Up @@ -149,7 +149,6 @@ https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz
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Expand Down Expand Up @@ -339,3 +338,4 @@ https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-htmlhelp-2.0.5-pyhd8
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4 changes: 2 additions & 2 deletions requirements/locks/py312-linux-64.lock
Original file line number Diff line number Diff line change
Expand Up @@ -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/libgettextpo-devel-0.22.5-h59595ed_2.conda#b63d9b6da3653179a278077f0de20014
Expand Down Expand Up @@ -116,6 +115,7 @@ https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d05
https://conda.anaconda.org/conda-forge/linux-64/blosc-1.21.5-hc2324a3_1.conda#11d76bee958b1989bd1ac6ee7372ea6d
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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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

1 change: 1 addition & 0 deletions requirements/py310.yml
Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,7 @@ dependencies:
- requests

# Documentation dependencies.
- numpydoc
- sphinx
- sphinxcontrib-apidoc
- sphinx-copybutton
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