Changes to implement CFA-0.6

[davidhassell]

Fixes #637, #451, #475

Needs NCAS-CMS/cfdm#255

Edit 2023-04-17: Notes on changes:
Edit 2023-04-18 More notes on changes - all done, now.

It is now possible for any file array object to support multiple filenames, and for the locations of those multiple filenames to be inspected and edited. E.g. add_file_location, file_locations, cfanetcdf.py, etc.

• aggregate.py - support for creating field ancillaries from non-standardised aggregation instructions
• cfimplementation.py - support for the new CFANetCDFArray class
• filearray.py - filename API
• cfanetcdfarray.py - many updates to the previous placeholder.
• fullarray.py - many updates to the previous placeholder.
• gatheredarray.py - cosmetic
• compressedarraymixin.py - update for new filenames API
• filearraymixin.py - updates for new filenames API
• netcdfarray.py - dask tokenize.
• umarray.py - new filenames API
• creation.py - minor API changes
• data.py - include CFA mixin methods; New methods to support inspecting and editing CFA features; New CFA constant and use.
• fullfragmentarray.py - new file to support a fragment that is filled with a constant value (rather than being an array on disk).
• missingfragmentarray.py - superceded by using FullFragmentArray(np.ma.masked)
• netcdffragmentarray.py - refactor for API changes elsewhere, and using an inherited Mixin
• umfragmentarray.py - refactor for API changes elsewhere, and using an inherited Mixin
• utils.py - add new chunk_locations functions that is used by CFANetCDFArray
• domain.py - new CFA-related file inspection/manipulation methods.
• field.py - new CFA-related file inspection/manipulation methods.
• functions.py - new function to return the CFA version; Improvements to abspath.
• propertiesdata.py - new CFA-related file inspection/manipulation methods.
• propertiesdatabounds.py - new CFA-related file inspection/manipulation methods.
• cfanetcdf.py - new mixin methods for get/set/del CFA-netCDF encoding elements.
• container.py - moved location (to mixin2) ecause there are now multiple files that need there own mixin location, to prevent circular imports.
• netcdfread.py - new functionality to read CFA-netCDF data into cf.Data objects.
• netcdfwrite.py - new functionality to write cf.Data objects to CFA-netCDF files.
• read.py - new cfa keyword that allow the configuration of CFA reads.
• umread.py - efactor the re-ordering of a decreasing Z axis. This used flip before, but this precludes the ability to write out the PP/UM data as CFA-netCDF, so we have to re-order in lower level manner. Also tidy up the dask array representation, so that it is consistent with how we build similar dask arrays elsewhere (e.g. GatheredArray).
• [write].py](https://github.com/NCAS-CMS/cf-python/pull/630/files#diff-8a6643476e95edbd04931cba073a702988abec05d2e04b7e716e6820b9d4fe6c) - new 'cfa' keyword to configure the writing of CFA files.

[davidhassell]

As for my comment #630 (comment) regarding the means for avoidance of circular imports for the mixin modules, I am still thinking on that. How about we bump it to a new Issue? I think that would be best because any changes made towards it might require a considerable amount of code movement and therefore require a more-involved/thorough re-review. And it doesn't strictly relate to CFA-0.6 support, which is implemented successfully here at this point.

Good idea. Let's make a new issue and not complicate the release of 3.15.0 :)

[davidhassell]

Thanks for the UML, Sadie. All looks a labyrinthine when taken as a whole (but good to see it in the round!), but following the relevant strands is good.

[davidhassell]

@sadielbartholomew, Thanks for the great review - you really caught loads of stuff. I think everything's resolved, but it'd be great to get your confirmation.

[sadielbartholomew]

Thanks David, I will do a final sanity check now.

[sadielbartholomew]

One tiny thing left (see in-line), but all feedback, new and old, has now been addressed. I stand by my previous review overall comment (#630 (review)) RE the overall nature of the PR. The test suite passes for me locally (laptop) (though those pesky 67: RuntimeWarning: invalid value encountered in cast messages - #625 - are still coming through after this PR, when on initial review I thought they'd conveniently disappeared due to these code changes, so I will take another look to fix them after merge.)

Brilliant, please merge!

[sadielbartholomew]

Suggested change

	* Removal of CFA-0.4 functionality (CFA-0.6 will introduced at a later
	version).
	* Removal of CFA-0.4 functionality (CFA-0.6 will be introduced at a
	later version).

[davidhassell]

I added a couple of basic updates to tutorial.rst: 31a53c4

Some more comprehensive CFA docs will be needed, but I'll do those in another PR.