ValueError: unrecognized engine zarr must be one of: ['netcdf4', 'scipy', 'store']

[iuryt]

Hi,

I am trying to load MUR data from AWS on Google Colab just as Chelle did for her Pangeo tutorial.
https://github.com/pangeo-gallery/osm2020tutorial/blob/master/AWS-notebooks/aws_mur_sst_tutorial_long.ipynb

What happened:

---------------------------------------------------------------------------

ValueError                                Traceback (most recent call last)

<ipython-input-15-363886c4b27b> in <module>()
      1 import xarray as xr
      2 
----> 3 ds = xr.open_zarr('https://mur-sst.s3.us-west-2.amazonaws.com/zarr-v1',consolidated=True)

2 frames

/usr/local/lib/python3.7/dist-packages/xarray/backends/plugins.py in get_backend(engine)
    133         if engine not in engines:
    134             raise ValueError(
--> 135                 f"unrecognized engine {engine} must be one of: {list(engines)}"
    136             )
    137         backend = engines[engine]

ValueError: unrecognized engine zarr must be one of: ['netcdf4', 'scipy', 'store']

What you expected to happen:

Load Zarr data from S3.

Minimal Complete Verifiable Example:

import xarray as xr
ds = xr.open_zarr('https://mur-sst.s3.us-west-2.amazonaws.com/zarr-v1',consolidated=True)

Anything else we need to know?:

I am using Google Colab.

Environment:

Output of xr.show_versions()

INSTALLED VERSIONS

commit: None
python: 3.7.10 (default, May 3 2021, 02:48:31)
[GCC 7.5.0]
python-bits: 64
OS: Linux
OS-release: 5.4.109+
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.12.0
libnetcdf: 4.7.4

xarray: 0.18.2
pandas: 1.1.5
numpy: 1.19.5
scipy: 1.4.1
netCDF4: 1.5.6
pydap: None
h5netcdf: None
h5py: 3.1.0
Nio: None
zarr: 2.8.3
cftime: 1.5.0
nc_time_axis: None
PseudoNetCDF: None
rasterio: None
cfgrib: None
iris: None
bottleneck: 1.3.2
dask: 2.12.0
distributed: 1.25.3
matplotlib: 3.2.2
cartopy: None
seaborn: 0.11.1
numbagg: None
pint: None
setuptools: 56.1.0
pip: 19.3.1
conda: None
pytest: 3.6.4
IPython: 5.5.0
sphinx: 1.8.5

[keewis]

I got the same error without zarr installed, but this does work for me after installing zarr so I'm inclined to believe there's something wrong with your environment. How did you set it up?

[iuryt]

As I am using Google Colab I simply installed zarr and xarray using pip (as they suggest) and tried to run the command.

!pip install zarr xarray

Maybe this is something with the way Colab setup things, but it would be nice to have a way to make it work. I am planning to use it in a course and Colab helps to save time on the installing process.

[keewis]

I had to install a few other packages, but it did work for me. Here's what I did:

mamba env create -n test python=3.7; conda activate test  # to get a fresh environment with py37
python -m pip install ipython
ipython

In [1]: !pip install zarr xarray fsspec aiohttp requests
In [2]: import xarray as xr
   ...: ds = xr.open_zarr('https://mur-sst.s3.us-west-2.amazonaws.com/zarr-v1',consolidated=True)

I don't know anything about Google Colab, though, so there might be something specific you have to do.

output of xr.show_versions()

INSTALLED VERSIONS
------------------
commit: None
python: 3.7.10 | packaged by conda-forge | (default, Feb 19 2021, 16:07:37) 
[GCC 9.3.0]
python-bits: 64
OS: Linux
OS-release: 4.19.0-16-amd64
machine: x86_64
processor: 
byteorder: little
libhdf5: None
libnetcdf: None

xarray: 0.18.2
pandas: 1.2.4
numpy: 1.20.3
scipy: None
netCDF4: None
pydap: None
h5netcdf: None
h5py: None
Nio: None
zarr: 2.8.3
cftime: None
nc_time_axis: None
PseudoNetCDF: None
rasterio: None
cfgrib: None
iris: None
bottleneck: None
dask: None
distributed: None
matplotlib: None
cartopy: None
seaborn: None
numbagg: None
pint: None
setuptools: 49.6.0.post20210108
pip: 21.1.2
conda: None
pytest: None
IPython: 7.23.1
sphinx: None

[keewis]

actually, did you try !pip install xarray[complete]?

[iuryt]

actually, did you try !pip install xarray[complete]?

That worked! Thanks!

[ryanjdillon]

zarr and other formats can be installed with only xarray[io] if you don't need all the other bits.

http://xarray.pydata.org/en/stable/getting-started-guide/installing.html#instructions