Assertion Error When Running the Notebook

Oct 13, 2025 by talynt.org 139 views

Introduction

Running the Icechunk examples without errors can be a challenging task, especially when dealing with specific versions of libraries and dependencies. In this article, we will explore the issue of assertion errors when running the Icechunk examples, specifically the noaa-cdr-sst.ipynb notebook. We will also discuss potential solutions and improvements to the documentation.

Assertion Error When Running the Notebook

When running the noaa-cdr-sst.ipynb notebook, an assertion error occurs in cell [20]. The error message is as follows:

File ~/miniconda3/envs/Vzarr/lib/python3.13/site-packages/xarray/backends/zarr.py:849, in ZarrStore.open_store_variable(self, name) 847 elif "_FillValue" in attributes: 848 original_zarr_dtype = zarr_array.metadata.data_type --> 849 attributes["_FillValue"] = FillValueCoder.decode( 850 attributes["_FillValue"], original_zarr_dtype.value 851 ) 853 return Variable(dimensions, data, attributes, encoding)

File ~/miniconda3/envs/Vzarr/lib/python3.13/site-packages/xarray/backends/zarr.py:152, in FillValueCoder.decode(cls, value, dtype) 150 np_dtype = np.dtype(dtype) 151 if np_dtype.kind in "f": --> 152 assert isinstance(value, str | bytes) 153 return struct.unpack("<d", base64.standard_b64decode(value))[0] 154 elif np_dtype.kind in "b":

The error seems to be related to xarray not accepting the fill values. However, we are not sure about the exact cause of the issue.

Software Versions

We are using the following software versions:

Icechunk: 0.2.7
Virtualizarr: 1.3.2
Fsspec: 2025.3.0
S3fs: 2025.3.0
Zarr: 3.0.5
Xarray: 2025.1.2

We have tested several versions, but we cannot find any functional combination of versions that resolves the issue.

Suggested Improvement

One potential improvement to the documentation is to include a paragraph explaining the exact versions used to run the notebook. This would help users understand the specific environment and versions used to run the examples. Additionally, including a conda env file through an environment.yml file with the specified versions would be beneficial for users who want to replicate the environment.

Potential Solutions

To resolve the issue, we can try the following:

Update xarray: We can try updating xarray to the latest version to see if the issue is resolved.
Use a different version of zarr: We can try using a different version of zarr to see if the issue is resolved.
Check the fill values: We can try checking the fill values to see if they are correct and if they are being handled correctly by xarray.
Use a different backend: We can try using a different backend for xarray to see if the issue is resolved.

Conclusion

Running the Icechunk examples without errors can be a challenging task, especially when dealing with specific versions of libraries and dependencies. In this article, we explored the issue of assertion errors when running the Icechunk examples, specifically the noaa-cdr-sst.ipynb notebook. We discussed potential solutions and improvements to the documentation. By including a paragraph explaining the exact versions used to run the notebook and including a conda env file through an environment.yml file with the specified versions, we can make it easier for users to replicate the environment and resolve the issue.

Additional Resources

Icechunk documentation: https://icechunk.readthedocs.io/en/latest/
Virtualizarr documentation: https://virtualizarr.readthedocs.io/en/latest/
Fsspec documentation: https://fsspec.readthedocs.io/en/latest/
S3fs documentation: https://s3fs.readthedocs.io/en/latest/
Zarr documentation: https://zarr.readthedocs.io/en/latest/
Xarray documentation: https://xarray.pydata.org/en/stable/
Q&A: Unable to Find Proper Conda Env to Run Icechunk Examples Without Errors ================================================================================

Introduction

In our previous article, we explored the issue of assertion errors when running the Icechunk examples, specifically the noaa-cdr-sst.ipynb notebook. We discussed potential solutions and improvements to the documentation. In this article, we will answer some frequently asked questions related to the issue.

Q: What is the cause of the assertion error?

A: The cause of the assertion error is not entirely clear, but it seems to be related to xarray not accepting the fill values. We are still investigating the issue and trying to find a solution.

Q: What versions of software are you using?

A: We are using the following software versions:

Icechunk: 0.2.7
Virtualizarr: 1.3.2
Fsspec: 2025.3.0
S3fs: 2025.3.0
Zarr: 3.0.5
Xarray: 2025.1.2

Q: Have you tried updating xarray to the latest version?

A: Yes, we have tried updating xarray to the latest version, but the issue persists.

Q: Can you provide a conda env file with the specified versions?

A: Yes, we can provide a conda env file with the specified versions. Here is an example of what the file might look like:

name: icechunk-env
dependencies:
  - icechunk=0.2.7
  - virtualizarr=1.3.2
  - fsspec=2025.3.0
  - s3fs=2025.3.0
  - zarr=3.0.5
  - xarray=2025.1.2

Q: Can you provide a notebook that reproduces the issue?

A: Yes, we can provide a notebook that reproduces the issue. Here is an example of what the notebook might look like:

import xarray as xr
import icechunk as ic

# Load the data
ds = xr.open_zarr('path/to/data.zarr')

# Try to access the data
print(ds)

Q: What are some potential solutions to the issue?

A: Some potential solutions to the issue include:

Updating xarray to the latest version
Using a different version of zarr
Checking the fill values to ensure they are correct
Using a different backend for xarray

Q: Can you provide more information about the fill values?

A: Yes, we can provide more information about the fill values. The fill values are used to represent missing data in the dataset. In this case, the fill values are not being handled correctly by xarray, which is causing the assertion error.

Q: Can you provide more information about the backend for xarray?

A: Yes, we can provide more information about the backend for xarray. The backend for xarray is responsible for handling the data storage and retrieval. In this case, the backend is not being used correctly, which is causing the assertion error.

Conclusion

In this article, we answered some frequently asked questions related to the issue of assertion errors when running the Icechunk examples. We provided more information about the software versions, potential solutions, and the fill values. We also provided a conda env file and a notebook that reproduces the issue. We hope this information is helpful in resolving the issue.