search

NCAR / pynio

PyNIO is a multi-format data I/O package with a NetCDF-style interface
http://www.pyngl.ucar.edu/Nio.shtml
Apache License 2.0
112 stars 37 forks source link

Errors opening GRIB file with xarray, engine="pynio" (using python 3 pynio developer branch) #14

Open lukelbd opened 6 years ago

lukelbd commented 6 years ago

Hi folks,

Thanks for updating pynio for python3 (#10). I created a virtual environment for the developer branch (as advised) with conda create -n pynio -c ncar -c conda-forge pynio=dev python=3, activated it with . activate pynio, and installed xarray to the virtual environment with conda install xarray. Unfortunately when trying to open an ERA-Interim GRIB file I get a ModuleNotFound error (the module Nio can't be found); included is the full traceback.

In [1]: import xarray as xr

In [2]: f = xr.open_dataset('ei.moda.an.sfc.regn128sc.2012120100.grb', engine='pynio')
---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-2-9da81691cb02> in <module>()
----> 1 f = xr.open_dataset('ei.moda.an.sfc.regn128sc.2012120100.grb', engine='pynio')

/home/user/anaconda3/lib/python3.6/site-packages/xarray/backends/api.py in open_dataset(filename_or_obj, group, decode_cf, mask_and_scale, decode_times, autoclose, concat_characters, decode_coords, engine, chunks, lock, cache, drop_variables)
    291         elif engine == 'pynio':
    292             store = backends.NioDataStore(filename_or_obj,
--> 293                                           autoclose=autoclose)
    294         else:
    295             raise ValueError('unrecognized engine for open_dataset: %r'

/home/user/anaconda3/lib/python3.6/site-packages/xarray/backends/pynio_.py in __init__(self, filename, mode, autoclose)
     40     """
     41     def __init__(self, filename, mode='r', autoclose=False):
---> 42         import Nio
     43         opener = functools.partial(Nio.open_file, filename, mode=mode)
     44         self.ds = opener()

ModuleNotFoundError: No module named 'Nio'

Also, for what it's worth, I also tried installing pynio without creating a virtual environment into my existing anaconda environment; in this case, I get an entirely different error having to do with a missing object file from the library "libkea":

In [1]: import xarray as xr
In [2]: f = xr.open_dataset('ei.moda.an.sfc.regn128sc.2012120100.grb', engine='pynio')
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-4-9da81691cb02> in <module>()
----> 1 f = xr.open_dataset('ei.moda.an.sfc.regn128sc.2012120100.grb', engine='pynio')

/home/user/anaconda3/lib/python3.6/site-packages/xarray/backends/api.py in open_dataset(filename_or_obj, group, decode_cf, mask_and_scale, decode_times, autoclose, concat_characters, decode_coords, engine, chunks, lock, cache, drop_variables)
    291         elif engine == 'pynio':
    292             store = backends.NioDataStore(filename_or_obj,
--> 293                                           autoclose=autoclose)
    294         else:
    295             raise ValueError('unrecognized engine for open_dataset: %r'

/home/user/anaconda3/lib/python3.6/site-packages/xarray/backends/pynio_.py in __init__(self, filename, mode, autoclose)
     40     """
     41     def __init__(self, filename, mode='r', autoclose=False):
---> 42         import Nio
     43         opener = functools.partial(Nio.open_file, filename, mode=mode)
     44         self.ds = opener()

/home/user/anaconda3/lib/python3.6/site-packages/PyNIO/Nio.py in <module>()
     81 '''
     82 from __future__ import print_function
---> 83 from _nio import *
     84 
     85 #

ImportError: libkea.so.1.4: cannot open shared object file: No such file or directory

Any idea what these issues could be?

cbarrick commented 6 years ago

IIRC, you also have to build xarray from their master branch. When I did it about a month ago, I just took the conda-forge feedstocks for both pynio and xarray, changed the URLs to the proper branches, built them with conda-build, and installed them with conda install --use-local xarray pynio.

It's been working for me, so I hope the official release comes soon.

chiaral commented 5 years ago

In case people are still getting this error. This issue was helpful to me.

I was getting the same error. I had a stable but out of date environment:

# packages in environment at /home/clepore/.conda/envs/general_python2_7:
#
affine                    2.1.0                      py_1    conda-forge
asciitree                 0.3.3                    py27_1    conda-forge
asn1crypto                0.22.0                   py27_0    conda-forge
attrs                     17.3.0                     py_0    conda-forge
backports                 1.0                      py27_1    conda-forge
backports.functools_lru_cache 1.4                      py27_1    conda-forge
backports.lzma            0.0.11                   py27_0    conda-forge
backports.shutil_get_terminal_size 1.0.0                      py_3    conda-forge
backports_abc             0.5                      py27_0    conda-forge
basemap                   1.1.0                    py27_3    conda-forge
beautifulsoup4            4.6.0                     <pip>
beautifulsoup4            4.6.0                    py27_0    conda-forge
blas                      1.0                         mkl  
bleach                    2.0.0                    py27_0    conda-forge
blosc                     1.12.0                        1    conda-forge
bokeh                     0.12.10                  py27_0    conda-forge
boost                     1.65.1                   py27_0    conda-forge
boost-cpp                 1.65.1                        1    conda-forge
boto3                     1.4.7                    py27_0    conda-forge
botocore                  1.5.92                   py27_0    conda-forge
bottleneck                1.2.1                    py27_1    conda-forge
bzip2                     1.0.6                         1    conda-forge
ca-certificates           2017.7.27.1                   0    conda-forge
cairo                     1.14.6                        5    conda-forge
cartopy                   0.16.0                   py27_0    conda-forge
certifi                   2017.7.27.1              py27_0    conda-forge
cffi                      1.10.0                   py27_0    conda-forge
chardet                   3.0.4                    py27_0    conda-forge
click                     6.7                      py27_0    conda-forge
click-plugins             1.0.3                    py27_0    conda-forge
cligj                     0.4.0                    py27_0    conda-forge
cloudpickle               0.4.0                    py27_0    conda-forge
colorcet                  1.0.0                      py_0    conda-forge
configparser              3.5.0                    py27_0    conda-forge
coverage                  4.4.2                     <pip>
coveralls                 1.2.0                     <pip>
cryptography              2.0.3                    py27_0    conda-forge
curl                      7.55.1                        0    conda-forge
cycler                    0.10.0                   py27_0    conda-forge
cyordereddict             1.0.0                    py27_1    conda-forge
cython                    0.27.3                   py27_0    conda-forge
cytoolz                   0.8.2                    py27_0    conda-forge
dask                      0.15.4                     py_0    conda-forge
dask-core                 0.15.4                     py_0    conda-forge
dask-glm                  0.1.1.dev1+g64e01eb           <pip>
dask-searchcv             0.1.0                      py_0    conda-forge
datashader                0.6.2                      py_0    conda-forge
datashape                 0.5.4                    py27_0    conda-forge
dbus                      1.10.22                       0    conda-forge
decorator                 4.1.2                    py27_0    conda-forge
distributed               1.19.3                   py27_0    conda-forge
docopt                    0.6.2                     <pip>
docutils                  0.14                     py27_0    conda-forge
ecmwf_grib                1.23.1                        1    conda-forge
entrypoints               0.2.3                    py27_1    conda-forge
enum34                    1.1.6                    py27_1    conda-forge
expat                     2.1.0                         3    conda-forge
fasteners                 0.14.1                   py27_2    conda-forge
fastparquet               0.1.3                    py27_0    conda-forge
fontconfig                2.12.1                        5    conda-forge
freetype                  2.7                           2    conda-forge
freexl                    1.0.2                         2    conda-forge
funcsigs                  1.0.2                      py_2    conda-forge
functools32               3.2.3.2                  py27_1    conda-forge
futures                   3.0.5                    py27_0    conda-forge
g2clib                    1.6.0                         4    conda-forge
gcsfs                     0.0.3                    py27_0    conda-forge
gdal                      2.2.3                    py27_0    conda-forge
geos                      3.6.2                         1    conda-forge
geotiff                   1.4.2                         0    conda-forge
geoviews                  1.4.2                    py27_0    ioam
gettext                   0.19.7                        1    conda-forge
giflib                    5.1.4                         0    conda-forge
glib                      2.51.4                        0    conda-forge
gmp                       6.1.2                         0    conda-forge
graphite2                 1.3.9                         0    conda-forge
graphviz                  0.8.1                     <pip>
gsl                       2.4                  h1bed415_3  
gst-plugins-base          1.8.0                         0    conda-forge
gstreamer                 1.8.0                         2    conda-forge
h5netcdf                  0.5.0                      py_0    conda-forge
h5py                      2.7.1                    py27_2    conda-forge
harfbuzz                  1.4.3                         0    conda-forge
hdf4                      4.2.13                        0    conda-forge
hdf5                      1.10.1                        1    conda-forge
hdfeos2                   2.19.1                        8    conda-forge
heapdict                  1.0.0                    py27_0    conda-forge
holoviews                 1.9.1                    py27_0    conda-forge
html5lib                  0.999999999              py27_0    conda-forge
httplib2                  0.10.3                   py27_0    conda-forge
icu                       58.1                          1    conda-forge
idna                      2.6                      py27_1    conda-forge
imageio                   2.2.0                    py27_0    conda-forge
ipaddress                 1.0.18                   py27_0    conda-forge
ipykernel                 4.6.1                    py27_0    conda-forge
ipython                   5.5.0                    py27_0    conda-forge
ipython_genutils          0.2.0                    py27_0    conda-forge
ipywidgets                7.0.3                    py27_1    conda-forge
jasper                    1.900.1                       4    conda-forge
jinja2                    2.9.6                    py27_0    conda-forge
jmespath                  0.9.3                    py27_0    conda-forge
jpeg                      9b                            2    conda-forge
json-c                    0.12.1                        0    conda-forge
jsonschema                2.6.0                    py27_0    conda-forge
jupyter                   1.0.0                    py27_0    conda-forge
jupyter_client            5.1.0                    py27_0    conda-forge
jupyter_console           5.2.0                    py27_0    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
jupyter_dashboards        0.7.0                    py27_0    conda-forge
jupyterlab                0.29.1                   py27_0    conda-forge
jupyterlab_launcher       0.5.5                    py27_0    conda-forge
kealib                    1.4.7                         4    conda-forge
keras                     2.0.6                    py27_0    conda-forge
krb5                      1.14.2                        0    conda-forge
lancet                    0.9.0                    py27_0    conda-forge
libdap4                   3.18.3                        2    conda-forge
libffi                    3.2.1                         3    conda-forge
libgcc                    7.2.0                h69d50b8_2  
libgcc-ng                 7.2.0                h7cc24e2_2  
libgdal                   2.2.3                         1    conda-forge
libgfortran               3.0.0                         1  
libgfortran-ng            7.2.0                hdf63c60_3  
libgpuarray               0.7.4                         0    conda-forge
libiconv                  1.14                          4    conda-forge
libkml                    1.3.0                         4    conda-forge
libnetcdf                 4.4.1.1                      10    conda-forge
libopenblas               0.2.20               h9ac9557_4  
libpng                    1.6.28                        2    conda-forge
libpq                     9.6.3                         0    conda-forge
libsodium                 1.0.10                        0    conda-forge
libspatialite             4.3.0a                       17    conda-forge
libssh2                   1.8.0                         2    conda-forge
libstdcxx-ng              7.2.0                h7a57d05_2  
libtiff                   4.0.7                         1    conda-forge
libxcb                    1.12                          1    conda-forge
libxml2                   2.9.5                         1    conda-forge
libxslt                   1.1.29                        5    conda-forge
llvmlite                  0.20.0                   py27_0  
locket                    0.2.0                    py27_1    conda-forge
lxml                      4.1.1                    py27_0    conda-forge
lz4                       0.10.1                   py27_0  
mako                      1.0.7                    py27_0    conda-forge
markupsafe                1.0                      py27_0    conda-forge
matplotlib                2.1.0                    py27_1    conda-forge
metpy                     0.6.1                    py27_0    conda-forge
mistune                   0.8                      py27_0    conda-forge
monotonic                 1.5                        py_0    conda-forge
mpi4py                    3.0.0                    py27_0    conda-forge
mpich                     3.2                           5    conda-forge
msgpack-python            0.4.8                    py27_0    conda-forge
multipledispatch          0.4.9                    py27_0    conda-forge
nbconvert                 5.3.1                      py_1    conda-forge
nbformat                  4.4.0                    py27_0    conda-forge
ncurses                   5.9                          10    conda-forge
netcdf4                   1.3.1                    py27_1    conda-forge
networkx                  1.11                     py27_0    conda-forge
nodejs                    6.11.0                        0    conda-forge
nomkl                     1.0                           0  
notebook                  5.2.1                    py27_2    conda-forge
numba                     0.35.0             np113py27_10  
numcodecs                 0.5.5                    py27_0    conda-forge
numpy                     1.13.3          py27_nomklh2b20989_4  [nomkl]
oauth2client              4.1.2                    py27_0    conda-forge
olefile                   0.44                     py27_0    conda-forge
openblas                  0.2.19                        2    conda-forge
openjpeg                  2.3.0                         1    conda-forge
openssl                   1.0.2l                        0    conda-forge
owslib                    0.15.0                     py_0    conda-forge
pandas                    0.21.0                   py27_0    conda-forge
pandoc                    2.0.0.1                       1    conda-forge
pandocfilters             1.4.1                    py27_0    conda-forge
pango                     1.40.4                        0    conda-forge
param                     1.5.1                    py27_0    conda-forge
partd                     0.3.8                    py27_0    conda-forge
pathlib2                  2.3.0                    py27_0    conda-forge
patsy                     0.4.1                    py27_0    conda-forge
pcre                      8.39                          0    conda-forge
pexpect                   4.2.1                    py27_0    conda-forge
pickleshare               0.7.4                    py27_0    conda-forge
pillow                    4.3.0                    py27_1    conda-forge
pint                      0.8.1                    py27_0    conda-forge
pip                       9.0.1                    py27_0    conda-forge
pixman                    0.34.0                        0    conda-forge
poppler                   0.61.1                        2    conda-forge
poppler-data              0.4.8                         0    conda-forge
proj4                     4.9.3                         5    conda-forge
prompt_toolkit            1.0.15                   py27_0    conda-forge
protobuf                  3.5.0                    py27_0    conda-forge
psutil                    5.4.0                    py27_0    conda-forge
ptyprocess                0.5.2                    py27_0    conda-forge
py                        1.4.34                   py27_0    conda-forge
pyasn1                    0.3.7                      py_0    conda-forge
pyasn1-modules            0.1.5                      py_0    conda-forge
pycparser                 2.18                     py27_0    conda-forge
Pydap                     3.2.2                     <pip>
pyepsg                    0.3.2                    py27_0    conda-forge
pygments                  2.2.0                    py27_0    conda-forge
pygpu                     0.7.4                    py27_0    conda-forge
pygrib                    2.0.2                    py27_1    conda-forge
pynio                     1.5.0                    py27_1    conda-forge
pyopenssl                 17.2.0                   py27_0    conda-forge
pyparsing                 2.2.0                    py27_0    conda-forge
pyproj                    1.9.5.1                  py27_0    conda-forge
pyqt                      5.6.0                    py27_4    conda-forge
pyshp                     1.2.12                     py_0    conda-forge
pysocks                   1.6.7                    py27_0    conda-forge
pytest                    3.2.3                    py27_0    conda-forge
pytest-cov                2.5.1                     <pip>
python                    2.7.14                        1    conda-forge
python-blosc              1.4.4                    py27_0    conda-forge
python-dateutil           2.6.1                    py27_0    conda-forge
pytz                      2017.3                     py_2    conda-forge
pywavelets                0.5.2                    py27_1    conda-forge
pyyaml                    3.12                     py27_1    conda-forge
pyzmq                     16.0.2                   py27_2    conda-forge
qt                        5.6.2                         6    conda-forge
qtconsole                 4.3.1                    py27_0    conda-forge
r-base                    3.4.1                         1    conda-forge
rasterio                  0.36.0           py27h453aca2_1  
readline                  6.2                           0    conda-forge
requests                  2.18.4                   py27_1    conda-forge
rpy2                      2.8.5              py27r3.4.1_0    conda-forge
rsa                       3.4.2                    py27_0    conda-forge
s3fs                      0.1.2                    py27_0    conda-forge
s3transfer                0.1.11                   py27_0    conda-forge
scandir                   1.6                      py27_0    conda-forge
scikit-image              0.13.0                   py27_3    conda-forge
scikit-learn              0.19.1          py27_nomklh6479e79_0  [nomkl]
scipy                     1.1.0           py27_nomklh9d22d0a_0  [nomkl]
seaborn                   0.8.1                    py27_0    conda-forge
setuptools                36.6.0                   py27_1    conda-forge
shapely                   1.6.2                    py27_1    conda-forge
simplegeneric             0.8.1                    py27_0    conda-forge
singledispatch            3.4.0.3                  py27_0    conda-forge
sip                       4.18                     py27_1    conda-forge
siphon                    0.6.1                    py27_0    conda-forge
six                       1.11.0                   py27_1    conda-forge
snappy                    1.1.7                         1    conda-forge
snuggs                    1.4.1                    py27_0    conda-forge
sortedcontainers          1.5.7                    py27_0    conda-forge
sqlite                    3.13.0                        1    conda-forge
ssl_match_hostname        3.5.0.1                  py27_1    conda-forge
statsmodels               0.8.0                    py27_0    conda-forge
subprocess32              3.2.7                    py27_0    conda-forge
tblib                     1.3.2                    py27_0    conda-forge
terminado                 0.6                      py27_0    conda-forge
testpath                  0.3.1                    py27_0    conda-forge
theano                    0.9.0                    py27_1    conda-forge
thrift                    0.10.0                   py27_0    conda-forge
tk                        8.5.19                        2    conda-forge
toolz                     0.8.2                      py_2    conda-forge
tornado                   4.5.2                    py27_0    conda-forge
traitlets                 4.3.2                    py27_0    conda-forge
urllib3                   1.22                     py27_0    conda-forge
util-linux                2.21                          0  
wcwidth                   0.1.7                    py27_0    conda-forge
webencodings              0.5                      py27_0    conda-forge
WebOb                     1.7.3                     <pip>
wheel                     0.30.0                     py_1    conda-forge
widgetsnbextension        3.0.6                    py27_0    conda-forge
xarray                    0.10.2                   py27_0  
xerces-c                  3.2.0                         0    conda-forge
xorg-libxau               1.0.8                         3    conda-forge
xorg-libxdmcp             1.1.2                         3    conda-forge
xz                        5.2.3                         0    conda-forge
yaml                      0.1.6                         0    conda-forge
zarr                      2.2.0                      py_1    conda-forge
zeromq                    4.2.1                         1    conda-forge
zict                      0.1.3                      py_0    conda-forge
zlib                      1.2.11                        0    conda-forge

and loading a grib file works.

Python 2.7.14 | packaged by conda-forge | (default, Nov  4 2017, 10:15:28) 
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import xarray as xr
>>> temp = xr.open_dataset('/Data2/SubX/EMC/GEFS/pr_sfc/1999/01/pr_sfc_GEFS_06jan1999_00z_d01_d35_m00.grb2', engine='pynio')
>>> temp
<xarray.Dataset>
Dimensions:          (forecast_time0: 35, lat_0: 181, lon_0: 360)
Coordinates:
  * forecast_time0   (forecast_time0) timedelta64[ns] 01:00:00 02:00:00 ...
  * lon_0            (lon_0) float32 0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 ...
  * lat_0            (lat_0) float32 90.0 89.0 88.0 87.0 86.0 85.0 84.0 83.0 ...
Data variables:
    APCP_P1_L1_GLL0  (forecast_time0, lat_0, lon_0) float32 ...

I was trying to create a new python 3 environment, but when I try to use xarray and pynio, I got the same error.

One of the main difference was that I was mixing channels: 

# Name                    Version                   Build  Channel
blas                      1.1                    openblas    conda-forge
bokeh                     0.13.0                   py36_0  
boost-cpp                 1.67.0               h14c3975_4  
bottleneck                1.2.1            py36h035aef0_1  
bzip2                     1.0.6                h14c3975_5  
ca-certificates           2018.03.07                    0  
cairo                     1.14.12              he6fea26_5    conda-forge
certifi                   2018.10.15               py36_0  
cftime                    1.0.0b1          py36h035aef0_0  
click                     7.0                      py36_0  
cloudpickle               0.6.1                    py36_0  
curl                      7.61.1               hbc83047_0  
cycler                    0.10.0                   py36_0  
cytoolz                   0.9.0.1          py36h14c3975_1  
dask                      0.19.4                   py36_0  
dask-core                 0.19.4                   py36_0  
dbus                      1.13.0               h3a4f0e9_0    conda-forge
distributed               1.23.3                   py36_0  
esmf                      7.1.0r               ha678704_2    conda-forge
expat                     2.2.6                he6710b0_0  
fontconfig                2.13.0               h9420a91_0  
freetype                  2.9.1                h8a8886c_1  
freexl                    1.0.5                h14c3975_0  
g2clib                    1.6.0                h838ce51_4  
geos                      3.6.2                heeff764_2  
geotiff                   1.4.2                h8e81d37_0  
gettext                   0.19.8.1             hd7bead4_3  
giflib                    5.1.4                h14c3975_1  
glib                      2.55.0               h464dc38_2    conda-forge
gsl                       2.2.1                h0c605f7_3  
gst-plugins-base          1.12.5               hde13a9d_0    conda-forge
gstreamer                 1.12.5               h61a6719_0    conda-forge
h5netcdf                  0.6.2                      py_0    conda-forge
h5py                      2.8.0            py36h989c5e5_3  
hdf4                      4.2.13               h3ca952b_2  
hdf5                      1.10.2               hba1933b_1  
hdfeos2                   2.20                 h64bfcee_0  
hdfeos5                   5.1.16               h647bee3_2    conda-forge
heapdict                  1.0.0                    py36_2  
icu                       58.2                 h9c2bf20_1  
intel-openmp              2019.0                      118  
jasper                    1.900.1              hd497a04_4  
jinja2                    2.10                     py36_0  
jpeg                      9c                   h470a237_1    conda-forge
json-c                    0.12.1               ha6a3662_2  
kealib                    1.4.9                h0bee7d0_2    conda-forge
kiwisolver                1.0.1            py36hf484d3e_0  
krb5                      1.16.1               hc83ff2d_6  
libboost                  1.67.0               h46d08c1_4  
libcurl                   7.61.1               heec0ca6_0  
libdap4                   3.19.1               h6ec2957_0  
libedit                   3.1.20170329         h6b74fdf_2  
libffi                    3.2.1                hd88cf55_4  
libgcc-ng                 8.2.0                hdf63c60_1  
libgdal                   2.2.4                he036fc0_8    conda-forge
libgfortran               3.0.0                         1  
libgfortran-ng            7.3.0                hdf63c60_0  
libiconv                  1.15                 h63c8f33_5  
libkml                    1.3.0                h590aaf7_4  
libnetcdf                 4.6.1                h10edf3e_1  
libopenblas               0.2.20               h9ac9557_7  
libpng                    1.6.35               hbc83047_0  
libpq                     10.5                 h1ad7b7a_0  
libspatialite             4.3.0a              h72746d6_18  
libssh2                   1.8.0                h9cfc8f7_4  
libstdcxx-ng              8.2.0                hdf63c60_1  
libtiff                   4.0.9                he85c1e1_2  
libuuid                   1.0.3                h1bed415_2  
libxcb                    1.13                 h1bed415_1  
libxml2                   2.9.8                h26e45fe_1  
locket                    0.2.0                    py36_1  
markupsafe                1.0              py36h14c3975_1  
matplotlib                2.2.2            py36hb69df0a_2  
mkl                       2019.0                      118  
mkl_fft                   1.0.1            py36h3010b51_0  
mkl_random                1.0.1            py36h629b387_0  
mpi                       1.0                       mpich    conda-forge
mpich                     3.2.1                h26a2512_4    conda-forge
msgpack-python            0.5.6            py36h6bb024c_1  
ncl                       6.5.0           blas_openblashd40de8d_1  [blas_openblas]  conda-forge
ncurses                   6.1                  hf484d3e_0  
netcdf-fortran            4.4.4                h4363f12_9    conda-forge
netcdf4                   1.4.1            py36h4b4f87f_0  
numpy                     1.14.3           py36h28100ab_1  
numpy-base                1.14.3           py36h0ea5e3f_1  
openblas                  0.2.20                        4  
openblas-devel            0.2.20                        7  
openjpeg                  2.3.0                h05c96fa_1  
openssl                   1.0.2p               h14c3975_0  
packaging                 18.0                     py36_0  
pandas                    0.23.4           py36h04863e7_0  
partd                     0.3.9                    py36_0  
pcre                      8.42                 h439df22_0  
pip                       10.0.1                   py36_0  
pixman                    0.34.0               hceecf20_3  
poppler                   0.67.0               h4d7e492_3    conda-forge
poppler-data              0.4.9                         0  
proj4                     4.9.3                hc8507d1_7  
psutil                    5.4.7            py36h14c3975_0  
pyngl                     1.6.0            py36h4217dbb_0    conda-forge
pynio                     1.5.2            py36h36f4ed2_0    conda-forge
pyparsing                 2.2.2                    py36_0  
pyqt                      5.6.0            py36h22d08a2_6  
python                    3.6.6                h6e4f718_2  
python-dateutil           2.7.3                    py36_0  
pytz                      2018.5                   py36_0  
pyyaml                    3.13             py36h14c3975_0  
qt                        5.6.2                hf70d934_9    conda-forge
readline                  7.0                  h7b6447c_5  
scipy                     1.1.0           py36_nomklh9d22d0a_0  [nomkl]
setuptools                40.4.3                   py36_0  
sip                       4.18.1           py36hf484d3e_2  
six                       1.11.0                   py36_1  
sortedcontainers          2.0.5                    py36_0  
sqlite                    3.25.2               h7b6447c_0  
tblib                     1.3.2                    py36_0  
tk                        8.6.8                hbc83047_0  
toolz                     0.9.0                    py36_0  
tornado                   5.1.1            py36h7b6447c_0  
udunits2                  2.2.25               hd30922c_1  
util-linux                2.21                          0  
wheel                     0.32.1                   py36_0  
xarray                    0.10.9                   py36_0  
xerces-c                  3.2.0                h524ea4d_2  
xorg-imake                1.0.7                         0    conda-forge
xorg-kbproto              1.0.7                h470a237_2    conda-forge
xorg-libice               1.0.9                h470a237_4    conda-forge
xorg-libsm                1.2.2                h470a237_5    conda-forge
xorg-libx11               1.6.6                h470a237_0    conda-forge
xorg-libxaw               1.0.13               h470a237_2    conda-forge
xorg-libxext              1.3.3                h470a237_4    conda-forge
xorg-libxmu               1.1.2                h470a237_2    conda-forge
xorg-libxpm               3.5.12               h470a237_2    conda-forge
xorg-libxrender           0.9.10               h470a237_2    conda-forge
xorg-libxt                1.1.5                h470a237_2    conda-forge
xorg-makedepend           1.0.5                         0    conda-forge
xorg-renderproto          0.11.1               h470a237_2    conda-forge
xorg-xextproto            7.3.0                h470a237_2    conda-forge
xorg-xproto               7.0.31               h470a237_7    conda-forge
xz                        5.2.4                h14c3975_4  
yaml                      0.1.7                had09818_2  
zict                      0.1.3                    py36_0  
zlib                      1.2.11               ha838bed_2

based on this issue I updated all the packages from the channel conda-forge

conda update --all -c conda-forge

and now it works.

Keep in mind that my environment was brand new so I didn't have any reason to use other channels, but some specific packages in your environment might need a specific channel which is not conda-forge.