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Missed dependencies error for netcdf4
and h5netcdf
#7
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I saw this on a few participants, thanks for the report. I think we just
need to manually include netcdf4 in the Python installs.
…On Mon, Dec 11, 2023 at 8:51 PM Jiwoo Lee ***@***.***> wrote:
I have created my conda env using the enviroment.yml following the
instructions in the README.md
<https://github.com/esgf2-us/esgf-cookbook/blob/main/README.md>, and ran
below code which I am getting following error that complains it cannot find
netcdf4, h5netcdf.
I resolved it by manually installing those two libraries. I think a
possible solution could be adding netcdf4 and h5netcdf as a part of
environment.yml
<https://github.com/esgf2-us/esgf-cookbook/blob/main/environment.yml#L17>
cat = ESGFCatalog(esgf1_indices="esgf-node.llnl.gov")
cat.search(
experiment_id="historical",
source_id="CanESM5",
frequency="mon",
variable_id=["gpp", "tas", "pr"],
variant_label="r1i1p1f1", # addition from the last search
)
dsd = cat.to_dataset_dict()
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
[/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/intro-search_AGU_tutorial.ipynb](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/intro-search_AGU_tutorial.ipynb) Cell 13 line 1
----> [1](vscode-notebook-cell:/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/intro-search_AGU_tutorial.ipynb#X15sZmlsZQ%3D%3D?line=0) dsd = cat.to_dataset_dict()
File [~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/intake_esgf/catalog.py:388](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/intake_esgf/catalog.py:388), in ESGFCatalog.to_dataset_dict(self, minimal_keys, ignore_facets, separator, num_threads, quiet, add_measures, operators)
[386](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/intake_esgf/catalog.py:386) for key, files in ds.items():
[387](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/intake_esgf/catalog.py:387) if len(files) == 1:
--> [388](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/intake_esgf/catalog.py:388) ds[key] = xr.open_dataset(files[0])
[389](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/intake_esgf/catalog.py:389) elif len(files) > 1:
[390](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/intake_esgf/catalog.py:390) ds[key] = xr.open_mfdataset(sorted(files))
File [~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/xarray/backends/api.py:553](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/xarray/backends/api.py:553), in open_dataset(filename_or_obj, engine, chunks, cache, decode_cf, mask_and_scale, decode_times, decode_timedelta, use_cftime, concat_characters, decode_coords, drop_variables, inline_array, chunked_array_type, from_array_kwargs, backend_kwargs, **kwargs)
[550](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/xarray/backends/api.py:550) kwargs.update(backend_kwargs)
[552](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/xarray/backends/api.py:552) if engine is None:
--> [553](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/xarray/backends/api.py:553) engine = plugins.guess_engine(filename_or_obj)
[555](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/xarray/backends/api.py:555) if from_array_kwargs is None:
[556](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/xarray/backends/api.py:556) from_array_kwargs = {}
File [~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/xarray/backends/plugins.py:197](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/xarray/backends/plugins.py:197), in guess_engine(store_spec)
[189](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/xarray/backends/plugins.py:189) else:
[190](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/xarray/backends/plugins.py:190) error_msg = (
[191](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/xarray/backends/plugins.py:191) "found the following matches with the input file in xarray's IO "
[192](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/xarray/backends/plugins.py:192) f"backends: {compatible_engines}. But their dependencies may not be installed, see:\n"
[193](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/xarray/backends/plugins.py:193) "https://docs.xarray.dev/en/stable/user-guide/io.html \n"
[194](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/xarray/backends/plugins.py:194) "https://docs.xarray.dev/en/stable/getting-started-guide/installing.html"
[195](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/xarray/backends/plugins.py:195) )
--> [197](https://file+.vscode-resource.vscode-cdn.net/Users/lee1043/Documents/Research/git/esgf-cookbook/notebooks/~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/xarray/backends/plugins.py:197) raise ValueError(error_msg)
ValueError: found the following matches with the input file in xarray's IO backends: ['netcdf4', 'h5netcdf']. But their dependencies may not be installed, see:https://docs.xarray.dev/en/stable/user-guide/io.html https://docs.xarray.dev/en/stable/getting-started-guide/installing.html
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I have created my conda env using the enviroment.yml following the instructions in the README.md, and ran below code which I am getting following error that complains it cannot find
netcdf4
,h5netcdf
.I resolved it by manually installing those two libraries. I think a possible solution could be adding
netcdf4
andh5netcdf
as a part of environment.ymlThe text was updated successfully, but these errors were encountered: