Mergeback of FEATURE_chunk_control branch (#5588)

* Merge chunk control code into latest iris (#5565)

* Dask chunking control for netcdf loading.

* renamed loader

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* fix indentation error, perhaps also docstring error

* fixed result error in loader, and set tests to treat as big files

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* trial and error, solve non iterable tuple 1.0

* trial and error, solve non iterable tuple 2.0 (used if var is none: instead of if var: )

* commented out docstring

* fixed mock 'no name' failure

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* fixed precommit issues

* corrected docstrings as per review comments

* Removed unnecessary line

Co-authored-by: Martin Yeo <40734014+trexfeathers@users.noreply.github.com>

---------

Co-authored-by: Patrick Peglar <patrick.peglar@metoffice.gov.uk>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Martin Yeo <40734014+trexfeathers@users.noreply.github.com>

* Chunk control modes (#5575)

* added modes

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* added as_dask mode

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* cleaned up enum and as_dask, as per review comments

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* corrected  to  in final place

* unindented lazy_param assignment one indent

---------

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* Corrected required type of dimension_chunksizes. (#5581)

* Chunk Control Tests (#5583)

* converted tests to pytest, added neg_one, and incomplete from_file and as_dask tests

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* trial and error with mocks and patches, may or may not work

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* converted Mock to patch in as_dask test

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* added tests and fixed review comments

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* Chunk control minor fixes (#5593)

* Disallow chunks=None in optimum_chunksize.

* Clearer docstrings.

* Corrected docstring.

* Chunk Control documentation (#5597)

* init PR, skeleton TP

* whoops, missed the TP.

* fixed doctests in rst file

* correct triple chevron to elipses

* updated set doctest to better show functionality

* removed in-progress doctest code

* Review comments, part 1

* Review comments, part 2

* changed numpy docs dict

* wait, this way is better

* fixed linkcheck failures (maybe)

* fixed :meth:

* fixed a couple doc bits

* hopefully fixed doctests

* newest review comments

* fixed rendering, and wording in docstring

* fixed docstring numpyness

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* written whatsnew entry

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docs/src/techpapers/index.rst

@@ -11,3 +11,4 @@ Extra information on specific technical issues.
 
    um_files_loading.rst
    missing_data_handling.rst
+   netcdf_io.rst

docs/src/techpapers/netcdf_io.rst

@@ -0,0 +1,140 @@
+.. testsetup:: chunk_control
+
+    import iris
+    from iris.fileformats.netcdf.loader import CHUNK_CONTROL
+
+    from pathlib import Path
+    import dask
+    import shutil
+    import tempfile
+
+    tmp_dir = Path(tempfile.mkdtemp())
+    tmp_filepath = tmp_dir / "tmp.nc"
+
+    cube = iris.load(iris.sample_data_path("E1_north_america.nc"))[0]
+    iris.save(cube, tmp_filepath, chunksizes=(120, 37, 49))
+    old_dask = dask.config.get("array.chunk-size")
+    dask.config.set({'array.chunk-size': '500KiB'})
+
+
+.. testcleanup:: chunk_control
+
+    dask.config.set({'array.chunk-size': old_dask})
+    shutil.rmtree(tmp_dir)
+
+.. _netcdf_io:
+
+=============================
+NetCDF I/O Handling in Iris
+=============================
+
+This document provides a basic account of how Iris loads and saves NetCDF files.
+
+.. admonition:: Under Construction
+
+    This document is still a work in progress, so might include blank or unfinished sections,
+    watch this space!
+
+
+Chunk Control
+--------------
+
+Default Chunking
+^^^^^^^^^^^^^^^^
+
+Chunks are, by default, optimised by Iris on load. This will automatically
+decide the best chunksize for your data without any user input. This is
+calculated based on a number of factors, including:
+
+- File Variable Chunking
+- Full Variable Shape
+- Dask Default Chunksize
+- Dimension Order: Earlier (outer) dimensions will be prioritised to be split over later (inner) dimensions.
+
+.. doctest:: chunk_control
+
+    >>> cube = iris.load_cube(tmp_filepath)
+    >>>
+    >>> print(cube.shape)
+    (240, 37, 49)
+    >>> print(cube.core_data().chunksize)
+    (60, 37, 49)
+
+For more user control, functionality was updated in :pull:`5588`, with the
+creation of the :data:`iris.fileformats.netcdf.loader.CHUNK_CONTROL` class.
+
+Custom Chunking: Set
+^^^^^^^^^^^^^^^^^^^^
+
+There are three context manangers within :data:`~iris.fileformats.netcdf.loader.CHUNK_CONTROL`. The most basic is
+:meth:`~iris.fileformats.netcdf.loader.ChunkControl.set`. This allows you to specify the chunksize for each dimension,
+and to specify a ``var_name`` specifically to change.
+
+Using ``-1`` in place of a chunksize will ensure the chunksize stays the same
+as the shape, i.e. no optimisation occurs on that dimension.
+
+.. doctest:: chunk_control
+
+    >>> with CHUNK_CONTROL.set("air_temperature", time=180, latitude=-1, longitude=25):
+    ...     cube = iris.load_cube(tmp_filepath)
+    >>>
+    >>> print(cube.core_data().chunksize)
+    (180, 37, 25)
+
+Note that ``var_name`` is optional, and that you don't need to specify every dimension. If you
+specify only one dimension, the rest will be optimised using Iris' default behaviour.
+
+.. doctest:: chunk_control
+
+    >>> with CHUNK_CONTROL.set(longitude=25):
+    ...     cube = iris.load_cube(tmp_filepath)
+    >>>
+    >>> print(cube.core_data().chunksize)
+    (120, 37, 25)
+
+Custom Chunking: From File
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The second context manager is :meth:`~iris.fileformats.netcdf.loader.ChunkControl.from_file`.
+This takes chunksizes as defined in the NetCDF file. Any dimensions without specified chunks
+will default to Iris optimisation.
+
+.. doctest:: chunk_control
+
+    >>> with CHUNK_CONTROL.from_file():
+    ...     cube = iris.load_cube(tmp_filepath)
+    >>>
+    >>> print(cube.core_data().chunksize)
+    (120, 37, 49)
+
+Custom Chunking: As Dask
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+The final context manager, :meth:`~iris.fileformats.netcdf.loader.ChunkControl.as_dask`, bypasses
+Iris' optimisation all together, and will take its chunksizes from Dask's behaviour.
+
+.. doctest:: chunk_control
+
+    >>> with CHUNK_CONTROL.as_dask():
+    ...    cube = iris.load_cube(tmp_filepath)
+    >>>
+    >>> print(cube.core_data().chunksize)
+    (70, 37, 49)
+
+
+Split Attributes
+-----------------
+
+TBC
+
+
+Deferred Saving
+----------------
+
+TBC
+
+
+Guess Axis
+-----------
+
+TBC

docs/src/whatsnew/latest.rst

@@ -59,6 +59,10 @@ This document explains the changes made to Iris for this release
    intervention preventing :func:`~iris.util.guess_coord_axis` from acting on a
    coordinate. (:pull:`5551`)
 
+#. `@pp-mo`_, `@trexfeathers`_ and `@ESadek-MO`_ added more control over
+   NetCDF chunking with the use of the :data:`iris.fileformats.netcdf.loader.CHUNK_CONTROL`
+   context manager. (:pull:`5588`)
+
 
 🐛 Bugs Fixed
 =============
@@ -118,6 +122,10 @@ This document explains the changes made to Iris for this release
 #. `@ESadek-MO`_ added a phrasebook for synonymous terms used in similar
    packages. (:pull:`5564`)
 
+#. `@ESadek-MO`_ and `@trexfeathers`_ created a technical paper for NetCDF
+   saving and loading, :ref:`netcdf_io` with a section on chunking, and placeholders
+   for further topics. (:pull:`5588`)
+
 
 💼 Internal
 ===========