Allensdk

Changed
- bumped lower limit of pandas to 0.17, removed upper limit
- changed CellTypesCache cell data structure to be less nested, more flat. Requires update to manifest and re-download of cells.json.
- simplified MouseConnectivityCache data structure. Requires update to manifest and re-download of experiments.json.
- stopped using deprecated function in SimpleTree

Added
- regression tests for Brain Observatory analysis

Changed

- Numerous Python 2/3 compatibility fixes
- Improved spike filtering in ephys.ephys_features

Added

- CellTypesCache.get_cells has a new `species` argument.

Changed

- MouseConnectivityCache downloads structure masks instead of computing them.

Added

- ABS-64; Jupyterhub Dockerfiles
- PR 13; Manifest error check

Changed

ABS-132; changed to Allen Institute Software License
ABS-129; StructureTree converts color hex triplet to 8-bit color triplet
ABS-125; update expected data for unmocked tests
PBS-358; update extract_trace module to deal with motion border case
ABS-85; allow variable long square start time in ephys feature extractor

Added

- BrainObservatoryNwbDataSet.get_demixed_traces
- BrainObservatoryNwbDataSet.get_pupil_location
- BrainObservatoryNwbDataSet.get_pupil_size
- BrainObservatoryApi.get_cell_specimen_id_mapping
- allensdk.brain_observatory.receptive_field_analysis
- allensdk.brain_observatory.demixer

Changed

- BrainObservatoryCache.get_ophys_experiments returns "acquisition_age_days" instead of "age_days". The new field describes the age of the animal on the day of experiment acquisition.
- BrainObservatoryCache.get_experiment_containers no longer returns "age_days".
- BrainObservatoryCache.get_ophys_experiments accepts a list of cell_specimen_ids for additional filtering
- json_utilities uses simplejson for better NaN handling

Fixed

- issue 42: Caching behavior in MouseConnectivityCache for CCF volumes fixed
- GLIF examples, documentation fixed