Decode times adds micro-second noise to standard calendar

[mankoff]

Code Sample, a copy-pastable example if possible

I have a simplified NetCDF file with the following header:

netcdf foo {
dimensions:
	time = UNLIMITED ; // (366 currently)
	x = 2 ;
	y = 2 ;
variables:
	float time(time) ;
		time:standard_name = "time" ;
		time:long_name = "time" ;
		time:units = "DAYS since 2000-01-01 00:00:00" ;
		time:calendar = "standard" ;
		time:axis = "T" ;
...
}

I would expect xarray to be able to decode these times. It does, but appears to do so incorrectly and without reporting any issues. Note the fractional time added to each date.

In [4]: xr.open_dataset('foo.nc').time
Out[4]:
<xarray.DataArray 'time' (time: 366)>
array(['2000-01-01T00:00:00.000000000', '2000-01-02T00:00:00.003211264',
       '2000-01-03T00:00:00.006422528', ..., '2000-12-29T00:00:01.962606592',
       '2000-12-30T00:00:01.672216576', '2000-12-31T00:00:01.381826560'], dtype='datetime64[ns]')
Coordinates:
  * time     (time) datetime64[ns] 2000-01-01 2000-01-02T00:00:00.003211264 ...
Attributes:
    standard_name:  time
    long_name:      time
    axis:           T

Problem description

Days since a valid date on a standard calendar should not add microseconds.

I know that xarray has time issues, for example #118 #521 numpy:#6207 #531 #789 and #848. But all of those appear to address non-standard times. This bug (if it is a bug) seems to occur with a very simple and straight forward calendar, and is silent, so it took me 2 days to figure out what was going on.

Output of xr.show_versions()

In [5]: xr.show_versions()

INSTALLED VERSIONS

commit: None
python: 3.5.4.final.0
python-bits: 64
OS: Darwin
OS-release: 16.7.0
machine: x86_64
processor: i386
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: en_US.UTF-8

xarray: 0.10.0
pandas: 0.22.0
numpy: 1.12.1
scipy: 0.19.1
netCDF4: 1.3.1
h5netcdf: None
Nio: None
bottleneck: 1.2.1
cyordereddict: 1.0.0
dask: 0.16.0
matplotlib: 2.1.1
cartopy: 0.15.1
seaborn: 0.8.1
setuptools: 38.4.0
pip: 9.0.1
conda: None
pytest: None
IPython: 6.2.1
sphinx: None

[shoyer]

Can you share a file that reproduces the issue?

[mankoff]

foo.nc.zip

[shoyer]

I just tested this out, and it appears that the issue is fixed on master -- see #1859.

[jhamman]

@mankoff - can you try with xarray v0.10.1 (released today)?

[mankoff]

Appears fixed. Thank you!