BlueBrain / morphoclass

Neuronal morphology preparation and classification using Machine Learning.
https://morphoclass.readthedocs.io
Apache License 2.0
8 stars 4 forks source link

Fix usage of `skip` in MCAR curation `luigi` configuration #72

Closed FrancescoCasalegno closed 2 years ago

FrancescoCasalegno commented 2 years ago

Fixes #71

Description

  1. All stages executed by MCAR curation luigi pipeline are now mentioned in the configuration file mcar-luigi.cfg.
  2. This configuration file specifies the value of the skip parameter for any given stage iff (if and only if) the stage supports it, i.e. iff the stage inherits from SkippableMixin.

    These stages inherit from SkippableMixin, so one can skip:

    • class Align(SkippableMixin(True), ElementValidationTask):
    • class DetectErrors(SkippableMixin(), ElementValidationTask):
    • class EnsureNeuritesOutsideSoma(SkippableMixin(True), ElementValidationTask):
    • class ErrorsReport(SkippableMixin(), SetValidationTask):
    • class ExtractMarkers(SkippableMixin(), ElementValidationTask):
    • class PlotErrors(SkippableMixin(), ElementValidationTask):
    • class PlotMarkers(SkippableMixin(), ElementValidationTask):
    • class PlotMorphologies(SkippableMixin(), ElementValidationTask):
    • class Recenter(SkippableMixin(), ElementValidationTask):
    • class Resample(SkippableMixin(), ElementValidationTask):

These stages don't inherit from SkippableMixin, so one cannot skip:

Note

After this PR the output of the workflow should not change, this PR just cleans up the configurations to make sure that they correspond to what is actually being run.

Checklist