v1.8.0

v1.8.0

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 fix testing in AllenSDK

Bug Fixes

• Removal of old calls to mock return objects that no longer exist
• Moving from old test endpoint to production endpoint for testing

v1.7.0

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

v1.6.0: Merge pull request #1378 from AllenInstitute/rc/1.6.0

• added get_receptive_field alias() for _get_rf() in allensdk/brain_observatory/ecephys/stimulus_analysis/receptive_field_mapping.py
• Added required version to namespace and caches spec in ecephy nwb outputs in allensdk/brain_observatory/ecephys/nwb/AIBS_ecephys_namespace.yaml
• Added version for ophys behavior nwb output to allensdk/brain_observatory/nwb/AIBS_ophys_behavior_namespace.yaml
• Behavior and ECEphys project caches no longer accept arbitrary keywords to prevent confusion when user supplies incorrect kwargs to constructor.
• New ecephys notebook for optotagging tutorial.

v1.5.0

What's New - 1.5.0 (February 21, 2020)

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

v1.4.0

As of the 1.4.0 release:

• users of the ephys extractor can supply their own cutoff frequency for low-pass bessel filter.
• (internal feature) the ophys time sync module writes an output json describing its results.

v1.3.0

What's New - 1.3.0 (December 12, 2019)

The 1.3.0 release adds

• Improved Neuropixels data download performance by enabling asynchronous transfers. Users can now also specify a timeout and number of retries when downloading data.

and fixes

• Hanging downloads for Neuropixels NWB files
• Updated AllenSDK readme and contributing documentation

v1.2.0

What's New - 1.2.0 (November 21, 2019)

The 1.2.0 release adds

• (internal feature) A project cache for the Behavior Ophys project, with example notebook
• (internal feature) A major overhaul of the BehaviorOphysLimsApi
• (internal feature) Updates to the EcephysProjectLimsApi such that it returns data in the same format as the EcephyProjectWarehouseApi
• improved eye-tracking area calculation

and fixes

• several flaky tests
• regress tests which depend on scipy's ks_2samp
• (internal feature) duplicate caching on the Bevavior Ophys Lims Api

v1.1.1

The 1.1.1 release adds

• several new Visual Coding - Neuropixels example notebooks

and fixes

• a bug in which p_value_rf and on_screen_rf were swapped when accessed from an EcephysSession

v1.1.0

What's New - 1.1.0 (October 31, 2019)

The 1.1.0 release adds:

• an updated gaze mapping algorithm
• automatic retries for failed neuropixels NWB file downloads

and fixes:

• several failing nightly build tests
• warnings emitted due to use of deprecated h5py.Dataset.value