v0.4.0-rc1

What's Changed

• Refactor logging to follow latest harp standard by @bruno-f-cruz in #239
• Implement ffmpeg logging by @bruno-f-cruz in #240
• Adopt new launcher to automatically perform animal <-> task association by @bruno-f-cruz in #241
• Add docs by @bruno-f-cruz in #243
• Update Behavior.Services to 0.7.0 by @bruno-f-cruz in #245
• Implement display color adjustment by @bruno-f-cruz in #248
• Implement patch flanking sites by @bruno-f-cruz in #253
• Implement treadmill brake control by @bruno-f-cruz in #254
• Add bonsai deserialization tests by @bruno-f-cruz in #255
• Fix typo by @bruno-f-cruz in #258
• Bruno-f-cruz/issue257 by @bruno-f-cruz in #259
• Feat-add-repeater-to-rig-schema by @bruno-f-cruz in #261
• Add AindManipulator to workflow by @bruno-f-cruz in #262
• Update to latest core dependencies by @bruno-f-cruz in #268
• Adding CI github action for ruff linting and unit testing by @bruno-f-cruz in #273
• Update index.rst to include home and source code by @bruno-f-cruz in #276
• Account for treadmill potential aperiodic sampling rate by @bruno-f-cruz in #275
• [Release] v0.4.0 by @bruno-f-cruz in #242

Full Changelog: v0.3.0...v0.4.0

Additional details:

• Updates Bonsai to 2.8.5
• Adds breaking changes to the TaskLogic, Rig, and Session schemas. Make sure that these are updated to the most recent version. See the ./examples/examples.py
• Adds a way to configure a small database-like document to drive associations between subjects and task logic (closes #237 )
• Refactors workflow to use logging by modality (closes #234)
• Refactors workflow to adopt the new schemas from https://github.com/AllenNeuralDynamics/Aind.Behavior.Services/releases/tag/0.7.11
• Refactors workflow to use the latest harp logging standard (closes #136 and #233 ) and removes now unused legacy operators
• Implements ffmpeg-powered video encoding (closes #235 )
• Implements new camera control and logging (procedurally generated)
• Align video logging format with latest AIND behavior agreed upon standards
• Docs deployment
• Moves several operators to Aind.Core package
• Add infrastructure necessary for data-mapper
• Removes legacy scripting python folder from the root of the repository. Remove corresponding Analysis requirements from project.toml
• Adds an online QC routine that checks if the difference between frame times reported by the camera matches the one reported by the triggers. Essentially implements an online quality check for dropped frames, non-exposed frames and, in some cases, trigger misalignment. Note, this warning will likely be triggered during the session if the synchronization bug is triggered. (closes #224)
• Patches are now bilaterally flanked by two inter-patch regions InterPatch and PostPatch
• Deprecates Aind.Core.Design UI elements in favor of Bonsai.GUI (closes #216)
• Deprecates Bonsai.Visualizer plotting in favor of Bonsai.GUI (closes #216 )
• Drops support for the old treadmill reading (using the behavior board) and now only supports the new Harp Treadmill developed in-house. (closes #207)
• Adds support for each site defining its own treadmill break value.
• Add support for null reward specification logic in reward sites
• Adds support for the new AIND manipulator (closes #249)
• New tests for bonsai schema deserializers
• Adds clock generator repeater to the workflow (closes #250)
• Updates definition of TransitionMatrix and InitialState. The initial state is now an array that is used to draw the first state from a set of probabilities. (Closes #272 )