Iris ❤ Xarray docs page. (#5025)

trexfeathers · dcherian · web-flow · commit 4a945ec111cf · 2023-01-24T12:07:20.000Z
* Iris Xarray docs page. * Add links. * Xarray page styling. * What's New entry. * Minor docs fixes. * Overall experience section. * Xarray supports other plotting backends through external packages. Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com> * Section on converting between Iris and Xarray. * Clearer language around laziness and multi-processing. * To-do note about dates and fill values. * Move iris_xarray page into a new Community section. * Language fixes from @bjlittle review. Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com>
diff --git a/docs/src/common_links.inc b/docs/src/common_links.inc
@@ -40,6 +40,7 @@
 .. _CF-UGRID: https://ugrid-conventions.github.io/ugrid-conventions/
 .. _issues on GitHub: https://github.com/SciTools/iris/issues?q=is%3Aopen+is%3Aissue+sort%3Areactions-%2B1-desc
 .. _python-stratify: https://github.com/SciTools/python-stratify
+.. _iris-esmf-regrid: https://github.com/SciTools-incubator/iris-esmf-regrid
 
 
 .. comment
diff --git a/docs/src/community/index.rst b/docs/src/community/index.rst
@@ -0,0 +1,48 @@
+.. include:: ../common_links.inc
+
+.. todo:
+    consider scientific-python.org
+    consider scientific-python.org/specs/
+
+Iris in the Community
+=====================
+
+Iris aims to be a valuable member of the open source scientific Python
+community.
+
+We listen out for developments in our dependencies and neighbouring projects,
+and we reach out to them when we can solve problems together; please feel free
+to reach out to us!
+
+We are aware of our place in the user's wider 'toolbox' - offering unique
+functionality and interoperating smoothly with other packages.
+
+We welcome contributions from all; whether that's an opinion, a 1-line
+clarification, or a whole new feature 🙂
+
+Quick Links
+-----------
+
+* `GitHub Discussions`_
+* :ref:`Getting involved<development_where_to_start>`
+* `Twitter <https://twitter.com/scitools_iris>`_
+
+Interoperability
+----------------
+
+There's a big choice of Python tools out there! Each one has strengths and
+weaknesses in different areas, so we don't want to force a single choice for your
+whole workflow - we'd much rather make it easy for you to choose the right tool
+for the moment, switching whenever you need. Below are our ongoing efforts at
+smoother interoperability:
+
+.. not using toctree due to combination of child pages and cross-references.
+
+* The :mod:`iris.pandas` module
+* :doc:`iris_xarray`
+
+.. toctree::
+   :maxdepth: 1
+   :hidden:
+
+   iris_xarray
diff --git a/docs/src/community/iris_xarray.rst b/docs/src/community/iris_xarray.rst
@@ -0,0 +1,154 @@
+.. include:: ../common_links.inc
+
+======================
+Iris ❤️ :term:`Xarray`
+======================
+
+There is a lot of overlap between Iris and :term:`Xarray`, but some important
+differences too. Below is a summary of the most important differences, so that
+you can be prepared, and to help you choose the best package for your use case.
+
+Overall Experience
+------------------
+
+Iris is the more specialised package, focussed on making it as easy
+as possible to work with meteorological and climatological data. Iris
+is built to natively handle many key concepts, such as the CF conventions,
+coordinate systems and bounded coordinates. Iris offers a smaller toolkit of
+operations compared to Xarray, particularly around API for sophisticated
+computation such as array manipulation and multi-processing.
+
+Xarray's more generic data model and community-driven development give it a
+richer range of operations and broader possible uses. Using Xarray
+specifically for meteorology/climatology may require deeper knowledge
+compared to using Iris, and you may prefer to add Xarray plugins
+such as :ref:`cfxarray` to get the best experience. Advanced users can likely
+achieve better performance with Xarray than with Iris.
+
+Conversion
+----------
+There are multiple ways to convert between Iris and Xarray objects.
+
+* Xarray includes the :meth:`~xarray.DataArray.to_iris` and
+  :meth:`~xarray.DataArray.from_iris` methods - detailed in the
+  `Xarray IO notes on Iris`_. Since Iris evolves independently of Xarray, be
+  vigilant for concepts that may be lost during the conversion.
+* Because both packages are closely linked to the :term:`NetCDF Format`, it is
+  feasible to save a NetCDF file using one package then load that file using
+  the other package. This will be lossy in places, as both Iris and Xarray
+  are opinionated on how certain NetCDF concepts relate to their data models.
+* The Iris development team are exploring an improved 'bridge' between the two
+  packages. Follow the conversation on GitHub: `iris#4994`_. This project is
+  expressly intended to be as lossless as possible.
+
+Regridding
+----------
+Iris and Xarray offer a range of regridding methods - both natively and via
+additional packages such as `iris-esmf-regrid`_ and `xESMF`_ - which overlap
+in places
+but tend to cover a different set of use cases (e.g. Iris handles unstructured
+meshes but offers access to fewer ESMF methods). The behaviour of these
+regridders also differs slightly (even between different regridders attached to
+the same package) so the appropriate package to use depends highly on the
+particulars of the use case.
+
+Plotting
+--------
+Xarray and Iris have a large overlap of functionality when creating
+:term:`Matplotlib` plots and both support the plotting of multidimensional
+coordinates. This means the experience is largely similar using either package.
+
+Xarray supports further plotting backends through external packages (e.g. Bokeh through `hvPlot`_)
+and, if a user is already familiar with `pandas`_, the interface should be
+familiar. It also supports some different plot types to Iris, and therefore can
+be used for a wider variety of plots. It also has benefits regarding "out of
+the box", quick customisations to plots. However, if further customisation is
+required, knowledge of matplotlib is still required.
+
+In both cases, :term:`Cartopy` is/can be used. Iris does more work
+automatically for the user here, creating Cartopy
+:class:`~cartopy.mpl.geoaxes.GeoAxes` for latitude and longitude coordinates,
+whereas the user has to do this manually in Xarray.
+
+Statistics
+----------
+Both libraries are quite comparable with generally similar capabilities,
+performance and laziness. Iris offers more specificity in some cases, such as
+some more specific unique functions and masked tolerance in most statistics.
+Xarray seems more approachable however, with some less unique but more
+convenient solutions (these tend to be wrappers to :term:`Dask` functions).
+
+Laziness and Multi-Processing with :term:`Dask`
+-----------------------------------------------
+Iris and Xarray both support lazy data and out-of-core processing through
+utilisation of Dask.
+
+While both Iris and Xarray expose :term:`NumPy` conveniences at the API level
+(e.g. the `ndim()` method), only Xarray exposes Dask conveniences. For example
+:attr:`xarray.DataArray.chunks`, which gives the user direct control
+over the underlying Dask array chunks. The Iris API instead takes control of
+such concepts and user control is only possible by manipulating the underlying
+Dask array directly (accessed via :meth:`iris.cube.Cube.core_data`).
+
+:class:`xarray.DataArray`\ s comply with `NEP-18`_, allowing NumPy arrays to be
+based on them, and they also include the necessary extra members for Dask
+arrays to be based on them too. Neither of these is currently possible with
+Iris :class:`~iris.cube.Cube`\ s, although an ambition for the future.
+
+NetCDF File Control
+-------------------
+(More info: :term:`NetCDF Format`)
+
+Unlike Iris, Xarray generally provides full control of major file structures,
+i.e. dimensions + variables, including their order in the file.  It mostly
+respects these in a file input, and can reproduce them on output.
+However, attribute handling is not so complete: like Iris, it interprets and
+modifies some recognised aspects, and can add some extra attributes not in the
+input.
+
+.. todo:
+    More detail on dates and fill values (@pp-mo suggestion).
+
+Handling of dates and fill values have some special problems here.
+
+Ultimately, nearly everything wanted in a particular desired result file can
+be achieved in Xarray, via provided override mechanisms (`loading keywords`_
+and the '`encoding`_' dictionaries).
+
+Missing Data
+------------
+Xarray uses :data:`numpy.nan` to represent missing values and this will support
+many simple use cases assuming the data are floats. Iris enables more
+sophisticated missing data handling by representing missing values as masks
+(:class:`numpy.ma.MaskedArray` for real data and :class:`dask.array.Array`
+for lazy data) which allows data to be any data type and to include either/both
+a mask and :data:`~numpy.nan`\ s.
+
+.. _cfxarray:
+
+`cf-xarray`_
+-------------
+Iris has a data model entirely based on :term:`CF Conventions`. Xarray has a
+data model based on :term:`NetCDF Format` with cf-xarray acting as translation
+into CF. Xarray/cf-xarray methods can be
+called and data accessed with CF like arguments (e.g. axis, standard name) and
+there are some CF specific utilities (similar
+to Iris utilities). Iris tends to cover more of and be stricter about CF.
+
+
+.. seealso::
+
+    * `Xarray IO notes on Iris`_
+    * `Xarray notes on other NetCDF libraries`_
+
+.. _Xarray IO notes on Iris: https://docs.xarray.dev/en/stable/user-guide/io.html#iris
+.. _Xarray notes on other NetCDF libraries: https://docs.xarray.dev/en/stable/getting-started-guide/faq.html#what-other-netcdf-related-python-libraries-should-i-know-about
+.. _loading keywords: https://docs.xarray.dev/en/stable/generated/xarray.open_dataset.html#xarray.open_dataset
+.. _encoding: https://docs.xarray.dev/en/stable/user-guide/io.html#writing-encoded-data
+.. _xESMF: https://github.com/pangeo-data/xESMF/
+.. _seaborn: https://seaborn.pydata.org/
+.. _hvPlot: https://hvplot.holoviz.org/
+.. _pandas: https://pandas.pydata.org/
+.. _NEP-18: https://numpy.org/neps/nep-0018-array-function-protocol.html
+.. _cf-xarray: https://github.com/xarray-contrib/cf-xarray
+.. _iris#4994: https://github.com/SciTools/iris/issues/4994
diff --git a/docs/src/conf.py b/docs/src/conf.py
@@ -223,6 +223,7 @@ def _dotv(version):
     "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),
 }
 
 # The name of the Pygments (syntax highlighting) style to use.
diff --git a/docs/src/further_topics/ugrid/partner_packages.rst b/docs/src/further_topics/ugrid/partner_packages.rst
@@ -1,3 +1,5 @@
+.. include:: ../../common_links.inc
+
 .. _ugrid partners:
 
 Iris' Mesh Partner Packages
@@ -97,4 +99,3 @@ Applications
 
 .. _GeoVista: https://github.com/bjlittle/geovista
 .. _PyVista: https://docs.pyvista.org/index.html
-.. _iris-esmf-regrid: https://github.com/SciTools-incubator/iris-esmf-regrid
diff --git a/docs/src/index.rst b/docs/src/index.rst
@@ -136,6 +136,15 @@ The legacy support resources:
    developers_guide/contributing_getting_involved
 
 
+.. toctree::
+   :caption: Community
+   :maxdepth: 1
+   :name: community_index
+   :hidden:
+
+   Community <community/index>
+
+
 .. toctree::
    :caption: Iris API
    :maxdepth: 1
diff --git a/docs/src/whatsnew/latest.rst b/docs/src/whatsnew/latest.rst
@@ -82,6 +82,14 @@ This document explains the changes made to Iris for this release
    and removed an ECMWF link in the ``v1.0`` What's New that was failing the
    linkcheck CI. (:pull:`5109`)
 
+#. `@trexfeathers`_ added a new top-level :doc:`/community/index` section,
+   as a one-stop place to find out about getting involved, and how we relate
+   to other projects. (:pull:`5025`)
+
+#. The **Iris community**, with help from the **Xarray community**, produced
+   the :doc:`/community/iris_xarray` page, highlighting the similarities and
+   differences between the two packages. (:pull:`5025`)
+
 💼 Internal
 ===========
 
diff --git a/lib/iris/_lazy_data.py b/lib/iris/_lazy_data.py
@@ -39,7 +39,7 @@ def is_lazy_data(data):
     """
     Return whether the argument is an Iris 'lazy' data array.
 
-    At present, this means simply a Dask array.
+    At present, this means simply a :class:`dask.array.Array`.
     We determine this by checking for a "compute" property.
 
     """
@@ -67,7 +67,8 @@ def _optimum_chunksize_internals(
     * shape (tuple of int):
         The full array shape of the target data.
     * limit (int):
-        The 'ideal' target chunk size, in bytes.  Default from dask.config.
+        The 'ideal' target chunk size, in bytes.  Default from
+        :mod:`dask.config`.
     * dtype (np.dtype):
         Numpy dtype of target data.
 
@@ -77,7 +78,7 @@ def _optimum_chunksize_internals(
 
     .. note::
         The purpose of this is very similar to
-        `dask.array.core.normalize_chunks`, when called as
+        :func:`dask.array.core.normalize_chunks`, when called as
         `(chunks='auto', shape, dtype=dtype, previous_chunks=chunks, ...)`.
         Except, the operation here is optimised specifically for a 'c-like'
         dimension order, i.e. outer dimensions first, as for netcdf variables.
@@ -174,13 +175,13 @@ def _optimum_chunksize(
 
 def as_lazy_data(data, chunks=None, asarray=False):
     """
-    Convert the input array `data` to a dask array.
+    Convert the input array `data` to a :class:`dask.array.Array`.
 
     Args:
 
     * data (array-like):
         An indexable object with 'shape', 'dtype' and 'ndim' properties.
-        This will be converted to a dask array.
+        This will be converted to a :class:`dask.array.Array`.
 
     Kwargs:
 
@@ -192,7 +193,7 @@ def as_lazy_data(data, chunks=None, asarray=False):
         Set to False (default) to pass passed chunks through unchanged.
 
     Returns:
-        The input array converted to a dask array.
+        The input array converted to a :class:`dask.array.Array`.
 
     .. note::
         The result chunk size is a multiple of 'chunks', if given, up to the
@@ -284,15 +285,16 @@ def multidim_lazy_stack(stack):
     """
     Recursively build a multidimensional stacked dask array.
 
-    This is needed because dask.array.stack only accepts a 1-dimensional list.
+    This is needed because :meth:`dask.array.Array.stack` only accepts a
+    1-dimensional list.
 
     Args:
 
     * stack:
-        An ndarray of dask arrays.
+        An ndarray of :class:`dask.array.Array`.
 
     Returns:
-        The input array converted to a lazy dask array.
+        The input array converted to a lazy :class:`dask.array.Array`.
 
     """
     if stack.ndim == 0:
diff --git a/lib/iris/cube.py b/lib/iris/cube.py
@@ -884,7 +884,8 @@ def __init__(
             This object defines the shape of the cube and the phenomenon
             value in each cell.
 
-            ``data`` can be a dask array, a NumPy array, a NumPy array
+            ``data`` can be a :class:`dask.array.Array`, a
+            :class:`numpy.ndarray`, a NumPy array
             subclass (such as :class:`numpy.ma.MaskedArray`), or
             array_like (as described in :func:`numpy.asarray`).
 
diff --git a/lib/iris/experimental/ugrid/mesh.py b/lib/iris/experimental/ugrid/mesh.py
@@ -131,7 +131,7 @@ def __init__(
 
         Args:
 
-        * indices (numpy.ndarray or numpy.ma.core.MaskedArray or dask.array.Array):
+        * indices (:class:`numpy.ndarray` or :class:`numpy.ma.core.MaskedArray` or :class:`dask.array.Array`):
             2D array giving the topological connection relationship between
             :attr:`location` elements and :attr:`connected` elements.
             The :attr:`location_axis` dimension indexes over the
@@ -501,7 +501,7 @@ def core_indices(self):
         NumPy array or a Dask array.
 
         Returns:
-            numpy.ndarray or numpy.ma.core.MaskedArray or dask.array.Array
+            :class:`numpy.ndarray` or :class:`numpy.ma.core.MaskedArray` or :class:`dask.array.Array`
 
         """
         return super()._core_values()
diff --git a/lib/iris/pandas.py b/lib/iris/pandas.py
@@ -238,7 +238,7 @@ def as_cubes(
     A :class:`~pandas.DataFrame` using columns as a second data dimension will
     need to be 'melted' before conversion. See the Examples for how.
 
-    Dask ``DataFrame``\\s are not supported.
+    :class:`dask.dataframe.DataFrame`\\ s are not supported.
 
     Examples
     --------
@@ -686,7 +686,7 @@ def as_data_frame(
 
     Notes
     -----
-    Dask ``DataFrame``\\s are not supported.
+    :class:`dask.dataframe.DataFrame`\\ s are not supported.
 
     A :class:`~pandas.MultiIndex` :class:`~pandas.DataFrame` is returned by default.
     Use the :meth:`~pandas.DataFrame.reset_index` to return a
diff --git a/lib/iris/util.py b/lib/iris/util.py

Original file line number	Diff line number	Diff line change
`@@ -223,6 +223,7 @@ def _dotv(version):`
`223`	`223`	`"python": ("https://docs.python.org/3/", None),`
`224`	`224`	`"scipy": ("https://docs.scipy.org/doc/scipy/", None),`
`225`	`225`	`"pandas": ("https://pandas.pydata.org/docs/", None),`
	`226`	`+ "dask": ("https://docs.dask.org/en/stable/", None),`
`226`	`227`	`}`
`227`	`228`
`228`	`229`	`# The name of the Pygments (syntax highlighting) style to use.`