Fix issues in from_array

[adehecq]

Despite our best efforts, PR #265 seems to have introduced bugs that are not caught by current tests.
The backbone is in from_array and some checks seem to have been lost in the PR after this line, e.g.:

• the dimension of data is not forced to be 3D (as in rasterio)
• the mask is likely not always preserved

[rhugonnet]

Also potentially after this line of _update, that doesn't exist anymore.

[adehecq]

Actually, the issue does not seem to be in from_array, or at least I was not able to find one. But an issue occurs with reproject for rasters with masked values, e.g.:

import geoutils as gu
# Take any raster with gaps
r = gu.Raster('/Users/adehecq/work/RAGMAC/ragmac_xdem/data/raw/experiment_2/PK_Baltoro/DEM_2002.75631975.tif')
r2 = r.reproject(dst_res=20)
print(r2.data)
print(r.data)

-> r2.data and r.data have different fill_value. This might cause issues later.

[rhugonnet]

Maybe the added lines in reproject here?
More tomorrow...