read_ncdf refactor and improvements

[dblodgett-usgs]

This PR includes a significant chunk of work from @mdsumner that I've picked up and tried to make some progress on.

1. A number of the commits are related to a file ncdf_tidync.R that has been temporarily moved into inst/nc I'm planning on using that for future work on ncdf.R and thought it would be worth preserving.

2. There's work here to fix TRMM netCDF file is fliped / rotated  #199 and Handle non-canonical NetCDF axis order #89 non-canonical axis order. I'm not 100% happy with how that's all handled, but this is a good start and reasonably well tested for both 1d and 2d coordinate variables.

3. This has not been tested with the latest RNetCDF so does not address read_ncdf regression? #183. I plan on doing that testing in the future as v2 RNetCDF gets closer to CRAN.

4. This work is largely a refactor in preparation for work on Support for reading station data timeseries (NetCDF example) #30 and NetCDF Geometry and Subsetting Functionality #86 -- A timeseries.nc file from rasterwise reads with no errors but is not where it should be at all.

5. There is work included here to handle bounds as requested in coordinates with bounds not correctly read for ncdf #175. Additional work is needed before we can consider that fixed.

Before I go any further I felt it was important to get this work at least reviewed if not merged. All tests pass and all rasterwise sample data read with no error -- although copious warnings!!

[edzer]

Great work! Right now, units are ignored, and this causes a few errors; also, I see while checking

  1. Failure: curvilinear (@test_ncdf.R#79) 
  2. Failure: curvilinear broked (@test_ncdf.R#97) 

and a lot of not so helpful warnings of the kind of

< time    1   1     NA    NA     NA    NA   1460    
< Warning messages:
< 1: Unknown or uninitialised column: 'name'. 
< 2: Unknown or uninitialised column: 'name'. 
< 3: Unknown or uninitialised column: 'name'. 
< 4: In .get_nc_time(dimensions, make_time, coord_var, var[1], meta) :
<   ignoring units of time dimension, not able to interpret

so not ready to be merged IMO. Do you want me to help out here, or to review the PR as a whole?

[dblodgett-usgs]

Happy to fix things up unless you want to take time to help out!

How are you creating the curvilinear failures? Tests all pass for me (running tests in Rstudio) but I have to admit I'm unfamiliar with the testing style you are using with .Rout.save files. Are those issues showing up during R CMD CHECK?

[dblodgett-usgs]

OK -- I see the issues in the travis tests. Turns out I'm using RNetCDF 2.0 -- and I can't get 1.9 installed anymore. Will work on that install a little more and try and deal with these issues.

[edzer]

Things check clean locally now, with RNetCDF 1.9-1, but both travis & appveyor give the same error - any ideas where that could come from?

[dblodgett-usgs]

The errors seem to be related to a warning (not) coming from try_as_units.

Locally, with the units 0.6-3 linked to udunits 2.2.26

as_units("kg m^-2")
Error: ‘`kg` `m`^-2’ is not a unit recognized by udunits or a user-defined unit
In addition: Warning message:
Could not parse expression: ‘`kg` `m`^-2’. Returning as a single symbolic unit() 

Apparently not in CI which is on udunits 2.2.0-1?

[dblodgett-usgs]

Derp... hadn't pulled down the most recent upstream main changes. The warning is suppressed now.

[edzer]

Does this mean that parameter curvilinear is being overwritten, and hence ignored as input?

[dblodgett-usgs]

It does! Will fix.

[dblodgett-usgs]

Tracked this down and fixed for now. Lon and Lat order matter or we need to make this a named vector using "X" and "Y" to denote canonical axes. I'm asssuming Lon/Lat order for now.

[edzer]

Ready to merge?

[dblodgett-usgs]

I think so. I'm starting to work on a couple other additions but those deserve a separate PR.

[edzer]

Great -- thanks so much!!