Iris 2.3 What's New #3450

trexfeathers · 2019-10-04T11:20:43Z

No description provided.

Merge remote-tracking branch 'upstream/v2.3.x' into v2.3.x

bjlittle · 2019-10-04T12:56:29Z

docs/iris/src/whatsnew/2.3.rst

+What's New in Iris 2.3
+**********************
+
+:Release: 2.3


@trexfeathers Can we explicitly clarify this as 2.3.0

bjlittle · 2019-10-04T13:00:05Z

docs/iris/src/whatsnew/2.3.rst

+  * :class:`~iris.analysis.RMS` (more detail below)
+  * :class:`~iris.analysis.MEAN`
+
+|


@trexfeathers Is this | intentional, if so what does it do?

It adds a blank line, making a clearer distinction between the final showcase and the first bullet point:

@trexfeathers How does it look with a divider instead? i.e., see reStructuredText transitions

@bjlittle I think your idea looks better so I've switched to that

lbdreyer

@trexfeathers Could you also delete the contributions_2.3.0 directory as part of this PR

docs/iris/src/whatsnew/2.3.rst

lbdreyer · 2019-10-04T13:25:19Z

docs/iris/src/whatsnew/2.3.rst

+Bugs Fixed
+==========
+* Cube equality of boolean data is now handled correctly.
+* Iris now supports NetCDF Climate and Forecast (CF) Metadata Conventions 1.7 (see `CF 1.7 Conventions Document <http://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/cf-conventions.html>`_ for more information)


This shouldn't be a bug fix.
I think the original whats new contribution (that I wrote!) was incorrectly labelled as bugfix
Could you remove?

I've moved this to new features

lbdreyer · 2019-10-04T13:30:08Z

docs/iris/src/whatsnew/2.3.rst

+* The name of cubes loaded from abf/abl files has been corrected.
+* Fixed a bug in UM file loading, where any landsea-mask-compressed fields
+  (i.e. with LBPACK=x2x) would cause an error later, when realising the data.
+* :meth:`iris.cube.Cube.coll\apsed` now handles partial collapsing of


Should there be a backslash in coll\apsed?

I will double check all the links next time!

lbdreyer · 2019-10-04T13:57:54Z

docs/iris/src/whatsnew/2.3.rst

+
+
+Iris 2.3.0 Dependency Updates
+===========================


This needs a couple extra =

Thanks, missed that after I added ".0"

lbdreyer · 2019-10-04T13:58:26Z

docs/iris/src/whatsnew/2.3.rst

@@ -0,0 +1,193 @@
+What's New in Iris 2.3.0
+**********************


This underline is too short

Thanks, missed that after I added ".0"

lbdreyer · 2019-10-04T13:58:33Z

docs/iris/src/whatsnew/2.3.rst

+(:doc:`View all changes <index>`.)
+
+Iris 2.3.0 Features
+=================


This underline is too short

Thanks, missed that after I added ".0"

lbdreyer · 2019-10-04T14:05:42Z

docs/iris/src/whatsnew/2.3.rst

+  'bounds' attribute and accompanying 'bnds' boundary variable. See below
+  for an example:
+
+    .. code-block::


This errors when building:
2.3.rst:41: WARNING: Error in "code-block" directive:
And the resulting built page misses the code block completely.

Suggested change

.. code-block::

.. code-block:: none

Interesting that this worked on my local build without "none". Anyway I've made this change and the new formatting still looks good 👍

This may be because I'm using an old version of sphinx. I think more recent versions have a default

It is now allowed to omit the argument in more recent versions of sphinx
sphinx-doc/sphinx#6015
I just need to update my environment!

lbdreyer · 2019-10-04T14:08:34Z

docs/iris/src/whatsnew/2.3.rst

+  When an Iris climatological coordinate is saved in NetCDF, the NetCDF time
+  axis will be given a 'climatology' attribute, and the contents of the


Suggested change

When an Iris climatological coordinate is saved in NetCDF, the NetCDF time

axis will be given a 'climatology' attribute, and the contents of the

coordinate variable will be given a 'climatology' attribute, and the contents of the

From CF conventions:

a climatological time coordinate variable does not have a bounds attribute. Instead, it has a climatology attribute, which names a variable with dimensions (n,2), n being the dimension of the climatological time axis

So its the variable that has a climatology attribute

Thanks, I appreciate the guidance. I've read and re-read that CF section but it's taking me a while to get my head around all the terminology

trexfeathers

Closing this extra review...

lbdreyer · 2019-10-04T14:51:11Z

docs/iris/src/whatsnew/2.3.rst

+.. admonition:: New Chunking Strategy
+
+  Iris now makes better choices of Dask chunk sizes when loading from NetCDF
+  files: If a file variable has specified, small chunks, Iris will now choose


I remember this phrasing tripping me up in the PR it was included.

I think the ordering of the adjectives are wrong. I think it should be:
If a file variable has small, specified chunks, Iris will now choose

lbdreyer · 2019-10-04T14:57:15Z

docs/iris/src/whatsnew/2.3.rst

+  Previously, Iris compared cube data arrays using "abs(a - b) < 1.e-8".
+  We now apply the default operation of :func:`numpy.allclose` instead,
+  which is equivalent to "abs(a - b) < (1.e-8 + 1.e-5 * b)".
+* Added support to render HTML for :class:`iris.cube.CubeList`s in Jupyter Notebooks and JupyterLab.


This may be due to my old version of Sphinx, but it is complaining about this line and in the built copy it doesn't correctly create the link to iris.cube.CubeList

You could also argue that we should use the ~ i.e. :class:~iris.cube.CubeListso that it reads more nicely:
Added support to render HTML for CubeList in Jupyter Notebooks and JupyterLab
where cube list would link off to the ref for CubeList

I caught this one. I'm pretty sure the cause is the "s" immediately following.
I'm sure there is a way to fix this ...

In the 2.2 whatsnew I found :

:class:`iris.coords.AuxCoord`'s can now test as 'equal'

That at least seems to work.

Went for @lbdreyer's idea

lbdreyer · 2019-10-04T14:59:29Z

docs/iris/src/whatsnew/2.3.rst

+  which is equivalent to "abs(a - b) < (1.e-8 + 1.e-5 * b)".
+* Added support to render HTML for :class:`iris.cube.CubeList`s in Jupyter Notebooks and JupyterLab.
+* Loading CellMeasures with non-float values is now supported.
+* New coordinate system: :class:`iris.coord_systems.Geostationary`, based on


This should be in the showcase as Geostationary was introduced in CF1.7

pp-mo

Quite a few points, but all a bit trivial I hope.

pp-mo · 2019-10-04T14:08:06Z

docs/iris/src/whatsnew/2.3.rst

+  * climatological coordinate support
+  * standard name modifier support
+  * name tokens enforcement in cell methods
+  * coordinate var_name, CF_CONVENTIONS_VERSION advanced to 1.7


The "coordinate var_name" and "CF_CONVENTIONS_VERSION advanced to 1.7" are separate points.

What "coordinate var_name" means needs explaining.
I don't get this myself : is it actually part of the previous point ?

This wasn't how I intended, hence it read strangely. Have fixed to what I wanted originally

I have also added links to internal anchors. Unfortunately anchors can't be placed in the middle of a bullet list so the links will only take you to the relevant section. See what you think

pp-mo · 2019-10-04T14:10:21Z

docs/iris/src/whatsnew/2.3.rst

+
+  * climatological coordinate support
+  * standard name modifier support
+  * name tokens enforcement in cell methods


This point either needs more explaining or, if there was some more detail below, we could maybe treat it as a sort of title and turn it into a link?

I don't think we should mention this as it is a bugfix so isn't really suitable in this section

OK it's gone

pp-mo · 2019-10-04T14:21:17Z

docs/iris/src/whatsnew/2.3.rst

+* The :data:`iris.analysis.RMS` aggregator now supports a lazy calculation.
+  However, the "weights" keyword is not currently supported by this, so a
+  *weighted* calculation will still return a realised result, *and* force
+  realisation of the original cube data. **NOTE:** lazy calculation with RMS
+  is currently only supported for un-masked arrays.


The "NOTE" bit just seems to repeat the same information.
Sorry if this was my fault ??

Having read in more detail I see your point, have remoted the NOTE

pp-mo · 2019-10-04T14:21:53Z

docs/iris/src/whatsnew/2.3.rst

+* Cube data equality testing (and hence cube equality) now uses a more relaxed
+  tolerance : This means that some cubes may now test 'equal' that previously
+  did not.
+  Previously, Iris compared cube data arrays using "abs(a - b) < 1.e-8".
+  We now apply the default operation of :func:`numpy.allclose` instead,
+  which is equivalent to "abs(a - b) < (1.e-8 + 1.e-5 * b)".


Can we get those maths expressions to display on one line somehow?
Otherwise it's a bit unreadable.
I know there are special forms for maths -- see the docstring for iris.analysis.calculus.curl,
but that may well be overkill for this, especially if you need to do learning just for this..
Maybe there is a simpler way ?

Have reformatted

pp-mo · 2019-10-04T14:22:54Z

docs/iris/src/whatsnew/2.3.rst

+* The Proj4 pin has been moved from version 5 to version 6 pending `fixes to
+  some cartopy tests <https://github
+  .com/SciTools/cartopy/pull/1289#pullrequestreview-272774087>`_.
+* Iris now requires Dask > 1.2 to allow for improved coordinate equality


"> 1.2" should be ">= 1.2"

pp-mo · 2019-10-04T14:43:59Z

docs/iris/src/whatsnew/2.3.rst

+
+Documentation Changes
+=====================
+* Added a gallery example showing how to concatenate NEMO ocean model data.


Could we make "a gallery example" into a link ?

pp-mo · 2019-10-04T14:53:13Z

docs/iris/src/whatsnew/2.3.rst

+=====================
+* Added a gallery example showing how to concatenate NEMO ocean model data.
+* Added an example in the
+  `Loading Iris Cubes: Constraining on Time <https://scitools.org.uk/iris/docs/latest/userguide/loading_iris_cubes.html#constraining-on-time>`_


Because this is written as an external link, it doesn't go to the page in this same docs build, so it doesn't show the changes it ought to !
This was my fault 😱
After some experiment, I think this should instead be ... "Loading Iris Cubes: Constraining on Time <../userguide/loading_iris_cubes.html#constraining-on-time>_"

The initial '..' is probably not the best way, but I'm not quite sure how it goes otherwise. That did at least work for me.

pp-mo · 2019-10-04T14:55:38Z

docs/iris/src/whatsnew/2.3.rst

+  Userguide section, demonstrating how to load data within a specified date
+  range.
+* Added notes to the :func:`iris.load` documentation, and the userguide
+  `Loading Iris Cubes <https://scitools.org.uk/iris/docs/latest/userguide/loading_iris_cubes.html>`_


As above, links to the "wrong docs", i.e. the Scitools release docs.
I think this one should be "Loading Iris Cubes <../userguide/loading_iris_cubes.html>_.

pp-mo · 2019-10-04T15:01:11Z

docs/iris/src/whatsnew/2.3.rst

+  We now apply the default operation of :func:`numpy.allclose` instead,
+  which is equivalent to "abs(a - b) < (1.e-8 + 1.e-5 * b)".
+* Added support to render HTML for :class:`iris.cube.CubeList`s in Jupyter Notebooks and JupyterLab.
+* Loading CellMeasures with non-float values is now supported.


I think this should be "integer values". It won't cope with strings !

pp-mo · 2019-10-04T15:02:45Z

docs/iris/src/whatsnew/2.3.rst

+  which is equivalent to "abs(a - b) < (1.e-8 + 1.e-5 * b)".
+* Added support to render HTML for :class:`iris.cube.CubeList`s in Jupyter Notebooks and JupyterLab.
+* Loading CellMeasures with non-float values is now supported.
+* New coordinate system: :class:`iris.coord_systems.Geostationary`, based on


Do we also load+save these in netcdf ? If so, should say so (like the one below).

lbdreyer · 2019-10-04T15:13:46Z

docs/iris/src/whatsnew/2.3.rst

+* Cubes are now rendered more robustly by Jupyter.
+  :meth:`~iris.cube.Cube._repr_html_` no longer crashes for a cube with
+  attributes containing ``\n``.
+* Variables which reference themselves in ``cell_measures`` can now be read.


This is a bit unclear.
I would specify that the you are talking about netCDF here.
And possibly explicitly say the cell_measures attribute.
Something like:

Suggested change

* Variables which reference themselves in ``cell_measures`` can now be read.

* NetCDF Variables which reference themselves in their ``cell_measures`` attribute can now be read.

docs/iris/src/whatsnew/2.3.rst

lbdreyer · 2019-10-04T16:55:27Z

Brilliant! 🎉 🎉 This all looks good! Thanks for all your hard work on this @trexfeathers !

And as @trexfeathers mentioned offline, the amount of content in this what's new is proof of just how much we have accomplished these past few weeks!

Well done team! 💯

* Manual elements of What's New * renamed manual 2.3 What's New entries * Created 2.3 What's New document. * Referencing 2.3 What's New in index.html * Explicit reference to 2.3.0 * Added separator underneath showcases * Deleted contributions folder. * Referenced CF conventions for NetCDF format example * Moved CF 1.7 support from bugfix to new feature. * Typo in Cube.collapsed. * Underlines, code-block language and CF terminology fixes. * Correction to climatological docstring and What's New. * Correction to climatological docstring and What's New. * Added Geostationary projection to CF 1.7 showcase. * Chunking strategy phrasing. * CubeList link for render HTML point. * Removed reference to latest.rst from What's New index. * CF 1.7 section links. * Removed duplicate note about realisation with iris.analysis.RMS * Improved formatting for cube equality point. * Fixed Dask dependency to by >=1.2. * Proj4 dependency phrasing. * with masked arrays -> with arrays with missing points. * var_name name token phrasing. * Removed reference to private method Cube._html_repr_. * abf/abl cube pluralisation. * Link for NEMO example. * Corrected internal documentation links. * Corrected *integer* value support. * Geostationary includes load and save support. * Clarified self-referencing NetCDF variables. * Reworded CF 1.7 showcase. * Internal address fixes. * Removed name tokens from the CF 1.7 showcase.

trexfeathers added 5 commits October 3, 2019 17:32

Manual elements of What's New

f708cd0

renamed manual 2.3 What's New entries

8f18124

Bringing in new What's New additions

2abecce

Merge remote-tracking branch 'upstream/v2.3.x' into v2.3.x

Created 2.3 What's New document.

42ce665

Referencing 2.3 What's New in index.html

8d344a6

trexfeathers requested a review from pp-mo October 4, 2019 11:30

bjlittle added Release: Minor Type: Documentation labels Oct 4, 2019

bjlittle added this to the v2.3.0 milestone Oct 4, 2019

bjlittle reviewed Oct 4, 2019

View reviewed changes

Explicit reference to 2.3.0

c48c0ef

lbdreyer requested changes Oct 4, 2019

View reviewed changes

trexfeathers added 6 commits October 4, 2019 15:15

Added separator underneath showcases

df6e4c8

Deleted contributions folder.

4c26070

Referenced CF conventions for NetCDF format example

a5ddbf8

Moved CF 1.7 support from bugfix to new feature.

e870a91

Typo in Cube.collapsed.

1437aea

Underlines, code-block language and CF terminology fixes.

a4dbfbe

trexfeathers commented Oct 4, 2019

View reviewed changes

lbdreyer reviewed Oct 4, 2019

View reviewed changes

trexfeathers added 4 commits October 4, 2019 16:00

Correction to climatological docstring and What's New.

46c2800

Correction to climatological docstring and What's New.

ac6e8bb

Added Geostationary projection to CF 1.7 showcase.

36e0254

Chunking strategy phrasing.

33c5291

pp-mo reviewed Oct 4, 2019

View reviewed changes

CubeList link for render HTML point.

66e78a3

lbdreyer reviewed Oct 4, 2019

View reviewed changes

Removed reference to latest.rst from What's New index.

4d68bc1

lbdreyer reviewed Oct 4, 2019

View reviewed changes

docs/iris/src/whatsnew/2.3.rst Show resolved Hide resolved

trexfeathers added 17 commits October 4, 2019 16:35

CF 1.7 section links.

814e0cd

Removed duplicate note about realisation with iris.analysis.RMS

9f9260e

Improved formatting for cube equality point.

7075750

Fixed Dask dependency to by >=1.2.

9aef9f3

Proj4 dependency phrasing.

d242248

with masked arrays -> with arrays with missing points.

ae4b4c0

var_name name token phrasing.

b82215b

Removed reference to private method Cube._html_repr_.

28b509a

abf/abl cube pluralisation.

f51562d

Link for NEMO example.

48abcaf

Corrected internal documentation links.

2cd1abb

Corrected *integer* value support.

c868fa6

Geostationary includes load and save support.

aff6bc3

Clarified self-referencing NetCDF variables.

5cc4fdf

Reworded CF 1.7 showcase.

a93d688

Internal address fixes.

6688f35

Removed name tokens from the CF 1.7 showcase.

72a5c1f

lbdreyer merged commit dee6e32 into SciTools:v2.3.x Oct 4, 2019

trexfeathers deleted the v2.3.x branch July 31, 2020 11:27

		@@ -0,0 +1,193 @@
		What's New in Iris 2.3.0
		**********************

		When an Iris climatological coordinate is saved in NetCDF, the NetCDF time
		axis will be given a 'climatology' attribute, and the contents of the

	When an Iris climatological coordinate is saved in NetCDF, the NetCDF time
	axis will be given a 'climatology' attribute, and the contents of the
	coordinate variable will be given a 'climatology' attribute, and the contents of the

	* Variables which reference themselves in ``cell_measures`` can now be read.
	* NetCDF Variables which reference themselves in their ``cell_measures`` attribute can now be read.

Uh oh!

Iris 2.3 What's New #3450

Iris 2.3 What's New #3450

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