Test input data processing identifies issues

[ALGW71]

Upon running pytest test_input_data_processing.py I get the following message:

nanobind: leaked 4 instances!
 - leaked instance 0x7fc4f13ba7c8 of type "gemmi.MmcifOutputGroups"
 - leaked instance 0x7fc4f13ba788 of type "gemmi.MmcifOutputGroups"
 - leaked instance 0x7fc4f13ba7a8 of type "gemmi.MmcifOutputGroups"
 - leaked instance 0x7fc4f1c39908 of type "gemmi.PdbWriteOptions"
nanobind: leaked 8 types!
 - leaked type "gemmi.PdbWriteOptions"
 - leaked type "gemmi.FastaSeq"
 - leaked type "CoorFormat"
 - leaked type "gemmi.Chain"
 - leaked type "gemmi.MmcifOutputGroups"
 - leaked type "gemmi.iterator"
 - leaked type "gemmi.iterator"
 - leaked type "gemmi.Structure"
nanobind: leaked 226 functions!
 - leaked function ""
 - leaked function "setup_cell_images"
 - leaked function "__iter__"
 - leaked function ""
 - leaked function ""
 - leaked function ""
 - leaked function ""
 - leaked function ""
 - leaked function "add_model"
 - leaked function ""
 - leaked function ""
 - ... skipped remainder
nanobind: this is likely caused by a reference counting issue in the binding code.

[ALGW71]

This will likely change as part of our solutions to #83

[ALGW71]

Does not occur in python 3.9