xenium PyArrow OSError: Unexpected end of stream

[ArneDefauw]

When reading xenium data, pyarrow==22.0.0 throws E OSError: Unexpected end of stream, see scverse/spatialdata-io#334

Stay at pyarrow 21.0.0 until apache/arrow@main...pitrou:arrow:gh47981-pq-impala-file gets released

[hiraksarkar]

Naive question, I am new to this, can you please tell me how can I install spatialdata-io while piining pyarrow to 21.0.0?

[ArneDefauw]

You can do
pip install pyarrow==21.0.0`

in your active environment on the command line.

Please let me know if this would not work!

[hiraksarkar]

Thanks for replying.

I tried this and unfortunately it broke the scipy and linked cpp libraries -- and I got this next time I tried importing spatialdata-io.

ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.15' not found
(required by .../scipy/optimize/_highspy/_core.cpython-313-...so)

[hiraksarkar]

I think this new error is not related to spatialdata-io. I pinned 'scipy < 2.13' and created a clean environment it works. Full set of commands

mamba create -n xenium_clean -c conda-forge --strict-channel-priority \
    python=3.12 \
    pyarrow=21 \
    scipy=1.12

mamba activate xenium_clean
mamba install -c conda-forge \
    scanpy \
    leidenalg \
    igraph \
    matplotlib \
    seaborn \
    jupyterlab

pip install spatialdata-io

[ArneDefauw]

FYI, for xenium there is a tutorial available here https://harpy.readthedocs.io/en/latest/tutorials/advanced/Harpy_transcriptomics_xenium.html

you can install harpy from the main branch in your conda environment with:

pip install "git+https://github.com/saeyslab/harpy.git#egg=harpy-analysis[extra]"

[hiraksarkar]

Thanks, this is really cool.