Refactor mtrain_api to remove dependencies on visual_behavior_analysis and mtrain repos

[nicain]

The code should instead go to allensdk. Requires moving:

• [x] ExtendedTrialSchema from VBA to allensdk (Done in #612 https://github.com/AllenInstitute/AllenSDK/blob/44b66b59685416d2301cb637ccc532a89404310c/allensdk/brain_observatory/behavior/mtrain.py#L134)
• [ ] Implement get_extended_trials (drop-in replacement for create_extended_dataframe) for:
  • [x] Image behavior sessions
  • [ ] Gratings behavior sessions (CC @nickponvert)
• [ ] Remove visual_behavior references from mtrain_lims:
  • [ ]

    from visual_behavior.translator.core import create_extended_dataframe
    # from allensdk.brain_observatory.behavior.trails_processing import create_extended_trials
    from visual_behavior.schemas.extended_trials import ExtendedTrialSchema
    # from allensdk.brain_observatory.behavior.mtrain import ExtendedTrialSchema 
    # from visual_behavior.translator import foraging2

  • [ ] redeploy mtrain_lims environment to production (http://bamboo.corp.alleninstitute.org/deploy/config/configureDeploymentProject.action?id=164855829&environmentId=164986911)
• [x] remove mtrain dependencies from mtrain_api
  • [x] move "criteria.py" module and all dependencies (session_metrics) from mtrain to mtrain_api (or allensdk)
  • [x] visual_behavior.change_detection.trials.masks can be moved whole-sale
  • [x] visual_behavior.utilities.get_response_rates functionality is already in allensdk (roughly allensdk.brain_observatory.behavior.dprime)
  • [ ] visual_behavior.utilities.flatten_list can be moved whole-sale
  • [x] visual_behavior.metrics.d_prime is already in allensdk (allensdk.brain_observatory.behavior.dprime). Also the VBA implementation has a bug
  • [x] assign_trial_description is easy enough, but it has a kinda tricky sub-dependency: trial_translator. However, allensdk.brain_observatory.behavior.trials_processing.categorize_one_trial might be an equivalent function.
  • [x] Unfoobar Mouse class; currently implemented twice in mtrain and mtrain_api. Should keep the mtrain_api implmenetation. Create criteria.py submodule in allensdk.brain_observatory.behavior with atomic functions whose names correspond to the advancement criteria in mtrain_regimens.regimens.yml. import these functions (that really implemetn the guts of the state machine transition) in the mouse.py class in mtrain_api; same-named methods on that class then wrap the behavior.
  • [x] Consider refactoring interface.py/Interface class to be simply a library/module, that can be handed to the mouse object.
  • [x] Update Makefile and Dockerfile in mtrain_api to no longer reference (i.e. pull and use as a dependency to build the image) mtrain

[nicain]

Work in progress to build out associated issues. @kschelonka an I will pick this up tomorrow to fully scope.