pyopenms how to deal with uint64 ?

[timosachsenberg]

in 20 21 file_description.size = feature_map.size() ---> 22 file_description.unique_id = feature_map.getUniqueId() 23 print(file_description.unique_id) 24 file_descriptions[i] = file_description pyopenms\pyopenms_1.pyx in pyopenms.pyopenms_1.ColumnHeader.unique_id.__set__() OverflowError: Python int too large to convert to C unsigned long

[timosachsenberg]

On windows

[jpfeuffer]

I would say don't use unsigned long since it is platform dependent. Just use our UInt64 typedef.

[timosachsenberg]

Ok thanks. Will check where this type comes from and how to change it

[timosachsenberg]

ok what about size? this is wrong? https://github.com/OpenMS/OpenMS/blob/develop/src/pyOpenMS/pxds/UniqueIdInterface.pxd#L13

[hroest]

See

https://github.com/OpenMS/OpenMS/blob/5c51ad02b833986049f250c1cb46fe02b77b79cc/src/pyOpenMS/pxds/Types.pxd#L25

so Size should be size_t - so that makes me wonder if the Windows version is 32 bit? Otherwise, if its compiled for 64 bit then I would assume that size_t is 64 bit?

[timosachsenberg]

on the left side of the assignment we have a UInt64 https://github.com/OpenMS/OpenMS/blob/develop/src/pyOpenMS/pxds/ConsensusMap.pxd#L28 on the right side a Size type

[jpfeuffer]

I meant more this: https://github.com/OpenMS/OpenMS/blob/5c51ad02b833986049f250c1cb46fe02b77b79cc/src/pyOpenMS/pxds/ConsensusMap.pxd#L35

[timosachsenberg]

aah... k will change

[jpfeuffer]

let's hope autowrap knows about typedefs and does not complain about maps with wrapped key+value

[timosachsenberg]

according to uwe that is a wrapper around Map https://github.com/OpenMS/OpenMS/blob/5c51ad02b833986049f250c1cb46fe02b77b79cc/src/pyOpenMS/addons/ConsensusMap.pyx#L23 but we use std::map can't we then not get rid of https://github.com/OpenMS/OpenMS/blob/5c51ad02b833986049f250c1cb46fe02b77b79cc/src/pyOpenMS/addons/ConsensusMap.pyx#L7-L25

[jpfeuffer]

Unless autowrap+msvc complained just about the potential type incompatibility, I would keep the extension and change the types there as well But you could try.

[timosachsenberg]

let's see if this works https://github.com/OpenMS/OpenMS/pull/5634

[jpfeuffer]

Did you test it on windows? Because our night lies still fail because of numpy

[jpfeuffer]

@timosachsenberg didn't you recently fix GitHub actions? Also pyopenms?

[hroest]

@timosachsenberg is there a way you can test this, eg with large integers in Python?

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