POD5 has encountered an error: ''return_dtype' of function python_udf must be set

[etwatson]

Issue Description

I am trying to subset my pod5 files as described on the nanopore website for duplex calling. .

When I enter pod5 subset -r pod5_skip/ --summary summary.tsv --columns channel --output /scratch/raw/run_06_09_25_split_by_channel I get the error:

POD5 has encountered an error: ''return_dtype' of function python_udf must be set

A later expression might fail because the output type is not known. Set return_dtype=pl.self_dtype() if the type is unchanged, or set the proper output data type.

Resolved plan until failure:

        ---> FAILED HERE RESOLVING 'sink' <---
SELECT [col("__dest_fname").unique()]
   WITH_COLUMNS:
   ["/scratch/raw/run_06_09_25_split_by_channel".str.concat_horizontal([col("__dest_fname")]).strict_cast(Categorical(Categories { name: "", namespace: "", physical: U32 }, CategoricalMapping { max_categories: 4294967295, upper_bound: 1 })).alias("__dest_fname")]
     WITH_COLUMNS:
     ["channel-".str.concat_horizontal([col("channel"), ".pod5"]).strict_cast(Categorical(Categories { name: "", namespace: "", physical: U32 }, CategoricalMapping { max_categories: 4294967295, upper_bound: 1 })).alias("__dest_fname"), col("read_id").alias("__read_id")]
      DF ["read_id", "channel"]; PROJECT */2 COLUMNS'

For detailed information set POD5_DEBUG=1'

Logs

Setting POD5_DEBUG=1 does not change the error reporting behavior.

Specifications

• Pod5 Version: 0.3.28
• Python Version: 3.12.9
• Platform: Ubuntu 22.04 LTS

[HalfPhoton]

Hi @etwatson, a recent breaking change in Polars has changed the requirements of a function that we are using.

An update to POD5 will be released to fix this. In the meantime you can install the last working version of polars with:

pip install --force-reinstall polars==1.31

Kind regards
Rich