Migrate configuration files to YAML

[dzhoshkun]

This is a sub-task of #166

For a roadmap, see the following comment: https://github.com/NifTK/NiftyNet/issues/166#issuecomment-407015033

Basically:

• [x] deprecate the current INI parser
• [ ] implement a new parser along the lines of:
  • [ ] loading, and
  • [ ] parsing functionalities.

[dzhoshkun]

• [x] modify the CI script to read (only?) YAML files

[dzhoshkun]

Deprecation warnings are ignored by default, hence no user output in the above build. Apparently this decision has been (and continues to be) strongly debated.

[dzhoshkun]

• [x] use UserWarning instead?

[dzhoshkun]

• [ ] compare new YAML files on this branch to INI files on dev branch before merging! (by reverting 9666eb9)

[dzhoshkun]

• [x] remove INI files?

[dzhoshkun]

• [ ] default CI sections do not load any configuration files, should test these changes using the slow tests etc.

[dzhoshkun]

• [x] the last commit fails because there are hard-coded filenames featuring the .ini extension. Those should be replaced, possibly using a global file extension constant

[dzhoshkun]

• [ ] references to / examples of INI files in documentation should be revised as well

[dzhoshkun]

• [ ] depends on https://github.com/NifTK/NiftyNetModelZoo/issues/2

[dzhoshkun]

• [x] set the environment variable niftynet_model_zoo to point the dowload utility to the https://github.com/NifTK/NiftyNetModelZoo/issues/2 branch for YAML files

[dzhoshkun]

• [ ] revert above commit before merging

[dzhoshkun]

• [ ] possibly implement a new class with same interface as ConfigParser but which can also parse YAML files, that way all the current parameter validation can be kept intact => #203
  • [ ] ConfigParser is used in many places, so make sure the new impersonator ConfigParser does not break existing configuration parsing (possibly put INI files back and run CI)

[dzhoshkun]

• [ ] add a test checking equivalence of INI and (mirrored-from-INI) YAML files

[dzhoshkun]

• [ ] use assertEqual instead of assertTrue ?

[dzhoshkun]

• [ ] make sure tests make sense

[dzhoshkun]

• [ ] overridden methods with default parameter values cause problems (see above commit, and also fix a369e3e if applicable)

[dzhoshkun]

• [ ] ConfigParser.items returns a list of tuples, not a dict