add porting-notes to the documentation

[khoffschlag]

Notes on porting from the old PUMI version to the new one: I will use the terms „NP“ for „new PUMI“ and „OP“ for „old PUMI“.

• Use NP NestedNodes and NestedWorkflow instead of nipype nodes and workflows
  • You only have to change the nipype-node-import to from PUMI.engine import NestedNode as Node and the nipype-workflow-import to from PUMI.engine import NestedWorkflow as Workflow
• Every workflow of NP must use a (suitable) decorator.
  • Anatomical related workflows use „AnatPipeline“, functional ones „FuncPipelines“ and QC-Workflows use „QcPipeline“
  • You have to specify the inputspec_fields and the outputspec_fields when using the decorator
  • It‘s possible to specify your own DataSinker regex-substitutions with regexp_sub=[]
  • You can deactivate the default regex substitutions with default_regexp_sub=False (not advised if you don‘t really know what you do)
  • Example usage with comments can seen here in https://github.com/pni-lab/PUMI/blob/main/PUMI/pipelines/anat/segmentation.py at the qc_bet definition
• Don‘t create workflow objects in your NP workflow methods. The decorator will create a workflow object and you can access it simply via using „wf“.
  • Example: wf.connect('inputspec', 'in_file', plot, 'registered_brain')
• Don‘t create inputspec, outputspec, and SinkDir objects in NP. The decorator will handle this.
  • You can utilize these in connect-statements by using the strings „inputspec“, „outputspec“ and „sinker“.
  • Example 1: wf.connect(bet, 'out_file', 'outputspec', 'out_file')
  • Example 2: wf.connect(bet, 'out_file', 'sinker', 'out_file')
  • The inputspec_fields that you specify in the decorator are the IdentityInterface fields of the inputspec object in OP
  • The outputspec_fields that you specify in the decorator are the IdentityInterface fields of the outputspec object in OP
• The first parameter of you workflow has to be „wf“ and the last one „**kwargs“. You do not need to pass wf yourself, the decorator will handle this
• Currently you have to pass "qc_dir=wf.qc_dir" when creating a qc object. We will fix this in the future. This can be seen in https://github.com/pni-lab/PUMI/blob/main/PUMI/pipelines/anat/segmentation.py in the bet_fsl workflow
• Don‘t use MapNodes. Most times it‘s enough to change MapNode to Node and delete the iterfields but verify that this makes sense when doing it!
• You may stumble across such connection statements in OP (note the „outputspec.[...]“ and „inputspec.[...]“): wf_mc.connect(mytmpfilt, 'outputspec.func_tmplfilt', fmri_qc_mc_dspk_nuis_bpf, 'inputspec.func').Don‘t explicitly mention inputspec/outputspec in NP when connecting nested workflows. The NP equivalent would be: wf_mc.connect(mytmpfilt, 'func_tmplfilt', fmri_qc_mc_dspk_nuis_bpf, 'func').

Also note the coding conventions mentioned in NP README (https://github.com/pni-lab/PUMI)