Migration to v2 version

• Neuron object now extends morphio.Morphology.

• Soma is not considered as a section anymore. Soma is skipped when iterating over neuron’s sections. It means that section indexing offset needs to be adjusted by -(number of soma sections) which is usually -1.

• drop benchmarks

• drop neurom.check.structural_checks as MorphIO does not allow to load invalid morphologies, and it does not give access to raw data.

• drop Tree class. Use Section instead as it includes its functionality but if you need Tree separately then copy-paste Tree code from v1 version to your project.

• Section and Neurite class can’t be copied anymore because their underlying MorphIO objects can’t be copied (pickled). Only copying of Neuron is preserved.

• drop FstNeuron. It functionality is included in Neuron class. Use Neuron instead of FstNeuron.

• Validation of morphologies changed.

  The following is not an invalid morphology anymore: - 2 point soma - non-sequential ids