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openvax / pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Apache License 2.0
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Downloading breaks due to reliance on deprecated numpy feature #276

Closed vluzko closed 1 year ago

vluzko commented 1 year ago

pyensembl relies on the numpy.typeDict value, which has been removed since 2021: https://github.com/numpy/numpy/pull/17586

Specifically downloading data with pyensembl uses datacache, which uses numpy.typeDict in database_types

Error generated by pyensembl install --release 108 --species human.

iskandr commented 1 year ago

Hey Vincent,

Thanks for letting me know. I just put up datacache 1.2.0 which doesn't use typeDict anymore, hopefully this fixes the problem.

--Alex

On Mon, Dec 19, 2022 at 10:18 PM Vincent Luczkow @.***> wrote:

pyensembl relies on the numpy.typeDict value, which has been removed since 2021: numpy/numpy#17586 https://github.com/numpy/numpy/pull/17586

Specifically downloading data with pyensembl uses datacache https://github.com/openvax/datacache, which uses numpy.typeDict in database_types https://github.com/openvax/datacache/blob/master/datacache/database_types.py

Error generated by pyensembl install --release 108 --species human.

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