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OpenMS / pyopenms-docs

pyOpenMS readthedocs documentation, additional utilities, addons, scripts, and examples.
https://pyopenms.readthedocs.io
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Deisotoping fails #197

Closed poshul closed 3 years ago

poshul commented 3 years ago

The deisotoping tutorial fails with the error: TypeError: __static_Deisotoper_deisotopeAndSingleCharge() takes exactly 10 positional arguments (14 given)

jpfeuffer commented 3 years ago

I think then you have an older version. It runs fine in the tests.

jpfeuffer commented 3 years ago

This is really strange. I encounter it, too, in binder. But the version says: 2.7.0-pre-nightly-2021-10-21

And this is exactly the version that is also installed in the github actions: Successfully installed numpy-1.21.3 pyopenms-nightly-2.7.0.dev20211021

jpfeuffer commented 3 years ago

Ah @timosachsenberg broke the function yesterday by overwriting it. Probably if you do changes in deisotoping and it is tested, it will fail in the PR, too. @timosachsenberg I think autowrap does not do overloading of "wrap-attach"ed methods. See the last function. https://github.com/OpenMS/OpenMS/blame/develop/src/pyOpenMS/pxds/Deisotoper.pxd

timosachsenberg commented 3 years ago

snap hmm yet another strange behavior of autowrap :)

timosachsenberg commented 3 years ago

so what should we do about it. Ithink it was broken before that is why I added the 10 argument version. A fix would be to add all 14 parameters.

jpfeuffer commented 3 years ago

I added all 14 already when I fixed all notebooks.

jpfeuffer commented 3 years ago

You can also wrap it with another name as mentioned.

timosachsenberg commented 3 years ago

ok I undid the change to the pxd. having another version with wrap-as .... not sure if needed. so that should do it right?

jpfeuffer commented 3 years ago

Yes removal should work as well.