Allensdk

Added
- Improved Neuropixels data download performance by enabling asynchronous transfers. Data downloads will now raise timeout errors when data cannot be retrieved in a reasonable timeframe.

Changed
- Updated AllenSDK readme and contributing documentation

Bug Fixes
- https://github.com/AllenInstitute/AllenSDK/issues/1214 Fix hanging downloads for Neuropixels NWB files

Added
- Support for Brain Observatory - Visual Coding Neuropixels data.
- https://github.com/AllenInstitute/AllenSDK/issues/447 Implemented improved eye tracking module based on DeepLabCut

Changed
- Python 2.x is no longer supported.
- statsmodels is now pinned at 0.9.0

Bug Fixes
- https://github.com/AllenInstitute/AllenSDK/commit/f76678 Fix integer division bug in receptive field analysis

Bug Fixes
- https://github.com/AllenInstitute/AllenSDK/issues/660 Use pillow/Image.resize instead of scipy.misc.imresize
- https://github.com/AllenInstitute/AllenSDK/issues/659 Same
- https://github.com/AllenInstitute/AllenSDK/issues/661 Update example notebooks

Added
- https://github.com/AllenInstitute/AllenSDK/issues/549 Transforms for tissuecyte registration accessible from allensdk
- https://github.com/AllenInstitute/AllenSDK/pull/568 Release instructions for future maintainers.

Changed
- https://github.com/AllenInstitute/AllenSDK/issues/582 Documentation builds from a yml config in python 3.7

Bug Fixes
- https://github.com/AllenInstitute/AllenSDK/issues/523 pip no longer fails on new conda environment because of tables

Added
- Added tools for working with itksnap label descriptions (https://github.com/AllenInstitute/AllenSDK/issues/312)

Changed
- Update pytest version number (now requires pytest>=4.1.1)
- Update numpy version number (now requires numpy>=1.15.1)
- Removed deprecated functions from BrainObservatoryNwbDataSet
- Updated documentation

Bug Fixes
- https://github.com/AllenInstitute/AllenSDK/issues/256 Examples python3 compatible
- https://github.com/AllenInstitute/AllenSDK/issues/267 Fix get_cell_specimens filter argument
- https://github.com/AllenInstitute/AllenSDK/pull/226 Fix pandas sorting behavior warning
- https://github.com/AllenInstitute/AllenSDK/issues/207 Fix "two celltypes features"
- https://github.com/AllenInstitute/AllenSDK/issues/273 Fix "make notebook"
- https://github.com/AllenInstitute/AllenSDK/issues/275 Fix inconsistent numpy requirement
- https://github.com/AllenInstitute/AllenSDK/issues/295 Fix BiophysicalApi.get_neuronal_models
- https://github.com/AllenInstitute/AllenSDK/issues/309 Fix tests to use updated pytest
- https://github.com/AllenInstitute/AllenSDK/issues/307 Fix openjpeg dependency in python3 in the CI build
- https://github.com/AllenInstitute/AllenSDK/issues/311 Fix locally sparse noise test
- https://github.com/AllenInstitute/AllenSDK/issues/330 Fix numpy warning message
- https://github.com/AllenInstitute/AllenSDK/issues/330 Fix Pillow dependency install
- https://github.com/AllenInstitute/AllenSDK/issues/405 Fix session analysis regression test (passing CI in python2 and python3)
- https://github.com/AllenInstitute/AllenSDK/issues/420 Fix installation bug resulting from pytables 3.5
- https://github.com/AllenInstitute/AllenSDK/commit/1ef88046a58a36d870d3f1048a778806d1db2954 Fix scikit-image dependency install

Added
- BrainObservatoryCache.get_ophys_experiment_events
- BrainObservatoryCache.get_ophys_experiments and get_experiment_containers accept reporter_lines argument
- BrainObservatoryCache.ge_ophys_experiment_analysis
- Cache subclasses can have their manifest locations set via environment variable