Xarray support

[elbeejay]

Updated (9/28/2020)

This PR makes CubeVariable an xarray-accessor rather than a subclass of numpy.ndarray. So changes are all over the place, but are relatively minor and largely preserve the prior API.

The changes

1. In io.py instead of reading the NetCDF4 as a dictionary, we load it as an xarray.DataSet. This retains the benefits of the original scheme ("lazy" loading without reading the file into memory). In this way we can keep the .read() function to give the user the option of fully reading the dataset into memory whenever they wish (presumably prior to running a serious computation). What is a bit clumsy right now is the definition of the "coords" which are the dimensions of the data arrays. This might be better addressed in pyDeltaRCM (related to Add ability to save sediment discharge pyDeltaRCM#99) as there we could just create a better netCDF file to read (and for other datasets encourage people to preprocess or prep their datasets per the expected standard).

2. Turns out NetCDF4 and HDF5 are very similar (see this and this). The built-in xarray loading supports most NetCDF4 and HDF5 files so now we use that and have therefore added support for HDF5 files. A small HDF5 example file has been added to allow us to unit test this functionality (as well as generalize DeltaMetrics by incorporating example Landsat data).

3. The developers of xarray have been pretty consistent (back from when it was xray even), that they do not support or encourage subclassing (their issues 728, 3959, and 3980 to name a few). Instead they suggest using an "accessor" to extend the functionality of xarray objects. So now CubeVariable is an accessor to xarray allowing us to add custom functions to CubeVariable, but retain an xarray object as CubeVariable.data.

4. Rudimentary 3D plotting support added for show_cube() via PyVista. Returns an error if pyvista is not installed.

Conclusions

This passes the unit tests as well as the documentation tests which suggests that this change does not break everything. But I do suspect that some of the stratigraphy functions are a bit less stable than they were before due to changes in the way some of the dimensions (think self.x or self._y etc) are handled. Started tracking things down, but realized that we might want to convert components of plan.py and section.py to be xarray accessors too (such as SectionVariable). So stopped messing with things and have settled for the PR as it is now. Implementing this might just be an incremental step towards true xarray compatibility, details regarding coordinates and dimensions are incomplete as mentioned above.

[codecov-commenter]

Codecov Report

Merging #23 into develop will increase coverage by 1.21%.
The diff coverage is 94.36%.

@@             Coverage Diff             @@
##           develop      #23      +/-   ##
===========================================
+ Coverage    87.25%   88.46%   +1.21%     
===========================================
  Files           10        7       -3     
  Lines         1106     1118      +12     
===========================================
+ Hits           965      989      +24     
+ Misses         141      129      -12     

Impacted Files	Coverage Δ
deltametrics/utils.py	54.16% <ø> (+12.50%)	⬆️
deltametrics/io.py	86.58% <87.87%> (+3.97%)	⬆️
deltametrics/plot.py	84.90% <100.00%> (ø)
deltametrics/section.py	96.96% <100.00%> (ø)
deltametrics/strat.py	87.83% <100.00%> (+1.04%)	⬆️
deltametrics/sample_data/__init__.py
deltametrics/_version.py

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[amoodie]

Hi @elbeejay. This was a huge effort and you have pushed the project way forward with it, thank you.

My only major suggestion is adding a __getitem__ to the CubeVariable that points to the xarray data. This allows the API for accessing data to stay the same, and would remove a lot of the needed .data calls (for example in the mask codes).

[codecov-io]

Codecov Report

Merging #23 into develop will increase coverage by 0.98%.
The diff coverage is 93.10%.

@@             Coverage Diff             @@
##           develop      #23      +/-   ##
===========================================
+ Coverage    88.56%   89.55%   +0.98%     
===========================================
  Files           11        8       -3     
  Lines         1251     1254       +3     
===========================================
+ Hits          1108     1123      +15     
+ Misses         143      131      -12     

Impacted Files	Coverage Δ
deltametrics/utils.py	68.57% <ø> (+8.57%)	⬆️
deltametrics/io.py	86.58% <87.87%> (+3.97%)	⬆️
deltametrics/plot.py	84.90% <100.00%> (ø)
deltametrics/section.py	96.96% <100.00%> (ø)
deltametrics/strat.py	87.22% <100.00%> (+0.44%)	⬆️
deltametrics/_version.py
deltametrics/sample_data/__init__.py

---

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[elbeejay]

I think between your commits @amoodie and some of the smaller commits I made today we've made this into a better PR. In the future I'm sure there are many more xarray related methods/PRs that'll come up, but I think this is enough to get us started on the path of "easy" dimensioning for our plots/computations...

[amoodie]

Cool, thanks for cleaning up. I agree, there will be more to do, but this is a huge first step. Thanks!