add support for writing parquet files#642
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haimasree merged 6 commits intokipoi:masterfrom Feb 10, 2022
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haimasree
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Feb 10, 2022
| chunk_size = 10000 | ||
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| # optional import of pyarrow | ||
| import pyarrow as pa |
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So CI is telling me that pyarrow is not installed. I dont see it in any dev-requirements-py*. yml either. Perhaps try adding pyarrow in kipoi setup.py?
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The exact error is ModuleNotFoundError: No module named 'pyarrow'
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Thanks! Yes, I have to add it as an optional dependency 👍
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I will merge this and remove the coverall for now. I will check tomorrow why the REPO token is not working anymore. |
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This PR adds support for writing parquet files.
In particular, it adds two additional parquet writer implementations:
ParquetFileBatchWriter: Writes to a single parquet file and depends on PyArrow.ParquetDirBatchWriter: Writes a directory of parquet files usingpandas.to_parquet(). Supports both PyArrow and fastparquet. This implementation is predestined for multi-processing / asynchronous writing since no file-locking is necessary for it. Nevertheless, I'm not sure yet how Kipoi would take advantage of that.My very long-term goal is that we directly provide schemas as Arrow schemas to be able to pass them around cross-language without any kind of conversion/serialization:
https://arrow.apache.org/docs/python/api/datatypes.html
This PR is the first step in that direction.
Future work: