nocollier
commented
11 months ago 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 Cell 13 line 1 ----> 1 dsd = cat.to_dataset_dict()
File ~/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 for key, files in ds.items(): 387 if len(files) == 1: --> 388 ds[key] = xr.open_dataset(files[0]) 389 elif len(files) > 1: 390 ds[key] = xr.open_mfdataset(sorted(files))
File ~/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 kwargs.update(backend_kwargs) 552 if engine is None: --> 553 engine = plugins.guess_engine(filename_or_obj) 555 if from_array_kwargs is None: 556 from_array_kwargs = {}
File ~/mambaforge/envs/esgf-cookbook-dev/lib/python3.10/site-packages/xarray/backends/plugins.py:197, in guess_engine(store_spec) 189 else: 190 error_msg = ( 191 "found the following matches with the input file in xarray's IO " 192 f"backends: {compatible_engines}. But their dependencies may not be installed, see:\n" 193 "https://docs.xarray.dev/en/stable/user-guide/io.html \n" 194 "https://docs.xarray.dev/en/stable/getting-started-guide/installing.html" 195 ) --> 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
netcdf4andh5netcdfas a part of environment.yml