Allensdk

Added
- CCF locations for ecephys neuropixels electrodes have been added to their respective nwb electrodes tables
- Examples for accessing eye tracking ellipse fit and screen gaze location data have been added to ecephys example notebooks

Changed
- pynwb and hdmf version pinning has been relaxed
- The organization of data for ecephys neuropixels Neurodata Without Borders (NWB) files has been significantly changed to conform with NWB specifications and best practices

**Important Note**:
Due to newer versions of pynwb/hdmf having issues reading previously released Visual Coding Neuropixels NWB files and due to the significant reorganization of their NWB file contents, this release contains breaking changes that necessitate a major version revision. NWB files released prior to 6/11/2020 are not guaranteed to work with the 2.0.0 version of AllenSDK. If you cannot or choose not to re-download the updated NWB files, you can continue using a prior version of AllenSDK (< 2.0.0) to access them. However, no further features or bugfixes for AllenSDK (< 2.0.0) are planned. Data released for other projects (Cell Types, Mouse Connectivity, etc.) are *NOT* affected and will *NOT* need to be re-downloaded

Added
- The biophysical module can now run both current and legacy all-active models.
- Internal users can now access `date_of_acquisition` for behavior-only Session data.
- A pull request template was added to the repository.

Changed
- The CSV log was removed from `BehaviorProjectCache` (internal users).
- Duplicated demixer module was deprecated, and test coverage was added.
- Docker image for AllenSDK was updated.

Bug Fixes
- Internal LIMS data served to `BehaviorDataSession` class now all use the same timestamp source

Bug Fixes
- Time sync tests were failing because of removed content. Tests were running only on nightly.
- Notebook tests failing on nightly because of down server, switched tests to production server.

Added
- Internal users can now access `eye_tracking` ellipse fit data from behavior + ophys Session objects
- A new mixin for managing processing parameters for Session objects
- Added support for additional sync file line labels

Changed
- Monitor delay calculation is updated to properly handle photodiode streams that end
on a rising edge. We are no longer providing a default delay value in case of error.

Bug Fixes
- experiment\_table from behavior project cache has NaNs in the 'imaging\_depth' column for MultiScope experiments due to incorrect join in behavior\_project\_lims\_api.py and 4 other places where ophys\_sessions was incorrectly queried for imaging\_depth\_id
- get_keys method for sync datasets was returning the wrong line labels and creating incorrect key, value pairs for
data loading from sync files

Added
- tutorial for optotagging for ecephys notebook
- get\_receptive\_field() method in ecephys receptive field mapping

Changed
- remove redundant sham\_change column in behavior sessions.trials table
- versions for NWB output for ecephys and ophys behavior.
- monitor delay is now calculated for BehaviorOphysLimsApi rather than defaulting to 0.0351

Bug Fixes
- Fixed a bug where auto-rewarded trials were not properly attributed in the rewards property of a visual behavior
- return None rather than raise exception if no container id was returned from lims id for given ophys id
- Project caches no longer accept arbitrary keywords
- matplotloib.pyplot.hist parameter normed no longer supported

Added
- Users have an option to provide credentials for accessing the database either explicitly via public API or by setting up the environment variables

Changed
- Allow users to modify BehaviorDataSession and BehaviorOphysSession data

Bug Fixes
- morphology.apply_affine correctly rescales radii
- invalid extracellular electrophysiology spikes no longer show up as spikes at time -1
- (internal) When loading a behavior session, behavior and eye tracking video frame times are assessed from the correct lines