They are apparently declared as "output" not "python" because they are not working.
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
Cell In[8], line 34
31 consumer = oms.PlainMSDataWritingConsumer(outputfile)
32 consumer = FilteringConsumer(consumer, filter_string)
---> 34 oms.MzMLFile().transform(inputfile,consumer)
File pyopenms/_pyopenms_7.pyx:10193, in pyopenms._pyopenms_7.MzMLFile.transform()
File pyopenms/_pyopenms_7.pyx:10279, in pyopenms._pyopenms_7.MzMLFile._transform_1()
RuntimeError: - due to that error of type FileNotFound in: /__w/OpenMS/OpenMS/OpenMS/src/openms/source/FORMAT/XMLFile.cpp@107-void OpenMS::Internal::XMLFile::parse_(const OpenMS::String&, OpenMS::Internal::XMLHandler*)
I didn't check but it might be the change from output to python block. Maybe the code is not executable or a file missing. I think a quick fix for your PR would be to change it back to output.
They are apparently declared as "output" not "python" because they are not working.
I didn't check but it might be the change from output to python block. Maybe the code is not executable or a file missing. I think a quick fix for your PR would be to change it back to output.
Originally posted by @timosachsenberg in https://github.com/OpenMS/pyopenms-docs/pull/396#issuecomment-1552067570