pod5 breaks with new numpy 2.0.0 about pod5-file-format HOT 7 CLOSED

Hi @Psy-Fer,

0.3.11 is now out, and is compatible with numpy 2.0 - please let us know if you have any issues.

Thanks,

• George

from pod5-file-format.

Hi James,

We will take a look at this!

Thanks,

• George

from pod5-file-format.

Hi @tamalarafat ,

It looks like you may be running bash commands inside a python file - the line you have:

>  pod5 convert to_fast5 *.pod5 --output pod5_to_fast5/

Is a bash command, i believe.

We have an internal pod5 build which is numpy 2.0 compatible, due out shortly.

Thanks,

• George

from pod5-file-format.

Okay i tried it out and it all works!

We also released new pyslow5 wheels with a new version which also fixed all of our problems.

So all sorted. Thanks George.

James

from pod5-file-format.

I solved the issue by downgrading numpy from version 2.0 to 1.26.4.

Although the error "ImportError: numpy.core.multiarray failed to import" was resolved, I am now encountering a new error while trying to convert my ".pod5" files to ".fast5" files.

The error I am getting now is:
"
cmd: pod5 convert to_fast5 *.pod5 --output pod5_to_fast5/

error: File "", line 1
pod5 convert to_fast5 *.pod5 --output pod5_to_fast5/
^^^^^^^
SyntaxError: invalid syntax
"

Any idea?

from pod5-file-format.

Great to hear 😁

from pod5-file-format.

Thanks, George!

from pod5-file-format.