v2.8.1

This is a hotfix patch to pin the version of aind-data-schema-models. This avoids using a bad release that included breaking changes in a patch.

Full Changelog: v2.8.0...v2.8.1

v2.8.0

Important changes

A new Solution class is now available for in-house reagents.

Organization.X groups have been removed from all objects. There is no longer a need to maintain separate organization groups in aind-data-schema-models.

What's Changed

• feat: add Solution object, in-house reagents by @saskiad in #1825
• fix: add Reagent as an option for Acquisition.manipulations by @dbirman in #1797
• chore: build ISI instrument example by @dbirman in #1833
• feat: add name field to DataAsset (#1787) by @tmchartrand in #1836
• fix: dataprocess validator allow name or notes to specify Other by @tmchartrand in #1837
• refactor: remove all Organization.X groups by @dbirman in #1835
• fix: do not run data regex on names that are passed in by @dbirman in #1848
• Release v2.8.0 by @dbirman in #1850

Full Changelog: v2.7.1...v2.8.0

v2.7.1

Major changes:

• Multiple specimen_id can be passed into acquisition, and external acquisitions where we don't have instrument details can now be reported in the metadata
• Injections now have to be wrapped in a parent object, either a NonSurgeryInjection or a Surgery when included in procedures. This ensures that injections have dates attached to them.

What's Changed

• Allow specimen_id to be a list by @dougollerenshaw in #1770
• docs: improve description for AcquisitionSubjectDetails by @dbirman in #1772
• fix: throw warnings when users put identical Device.names by @dbirman in #1773
• fix: allow both planar and regular sectioning in sectioning procedures by @dbirman in #1777
• fix: allow NHPSubject as subject_details option by @dbirman in #1778
• docs: auto-build docs on opening PR by @dbirman in #1760
• Handle lists of specimen IDs in procedures validator by @gouwens in #1783
• Barseq blackbox acquisition by @dougollerenshaw in #1781
• 1792 quality control validator has a bug at line 307 where it fails to check metrics before doing metrics0 by @dbirman in #1793
• chore: delete CHANGELOG.md by @dbirman in #1799
• refactor: replace root calls to logging with module-level loggers by @dbirman in #1800
• docs: improve docstring by @dbirman in #1748
• refactor: only allow wrapped NonSurgeryInjections in Procedures.subject_procedures by @dbirman in #1802
• Add missing tzdata dependency by @bruno-f-cruz in #1811
• Add git hash to Code model by @bruno-f-cruz in #1813
• feat: add barseq instrument by @dbirman in #1685
• fix: specimen_ids validator correctly flattens lists by @dbirman in #1763

Full Changelog: v2.6.0...v2.7.0

v2.6.0

This minor release adds support for the slap2 microscope, along with some smaller fixes to some of the acquisition configuration files.

What's Changed

• nhp subject by @saskiad in #1738
• Added to validate.md to clarify which fields must match between inst and acq by @dougollerenshaw in #1757
• refactor: olfactometerchannel flow capacity by @dbirman in #1758
• fix: RPS -> LPS by @dbirman in #1759
• added crop to detector config by @saskiad in #1709
• fix: remove behavior modality requirement for a LickSpoutAssembly by @dbirman in #1765
• docs: clarify how specimen_id should be set by @dbirman in #1766
• Slap2 Metadata Updates by @dbirman in #1710

Full Changelog: v2.5.1...v2.6.0

v2.5.1

This quick hotfix repairs an issue introduced by the new acquisition_start_tz field that was causing all assets to fail validation after a roundtrip serialization/de-serialization.

What's Changed

• Removed reference to metadata app in instrument.md by @dougollerenshaw in #1742
• added IcEphysAssembly by @saskiad in #1739
• hotfix: repair acquisition_start_tz by @dbirman in #1752

Full Changelog: v2.5.0...v2.5.1

v2.5.0

What's Changed

• docs: clarify DataDescription.name, re-build all docs (without API) by @dbirman in #1691
• refactor: allow instrument_id to merge in alphabetical order by @dbirman in #1705
• docs: small update to clarify docs by @dbirman in #1706
• feat: allow PlanarSectioning to accept Atlas coordinate systems by @dbirman in #1694
• updated examples by @saskiad in #1708
• refactor: fix examples generator to properly hide generated .json test files by @dbirman in #1716
• refactor: remove requirement that all specimen_id fields match by @dbirman in #1717
• refactor: pull TZ information out of acquisition_start_time by @dbirman in #1714
• docs: improve QCMetric.description description and build docs by @dbirman in #1719
• fix: recursive_get_all_names should only get names from DataModel objects by @dbirman in #1722
• feat: Section and Sectioning by @dbirman in #1695
• fix: forgot to implement Acquisition.instrument_id merge by @dbirman in #1720
• feat: add MISCameraConfig by @dbirman in #1718
• feat: refactor MRIScan to reflect BIDS standards by @dbirman in #1734
• docs: better description and example for mouse_platform_name by @dbirman in #1736

Full Changelog: v2.4.0...v2.5.0

v2.4.0

The main change in v2.4.0 is that we now link to aind-data-schema-models v5, where the slap modality has been replaced by slap2. Other small changes have been made to support the new quality control tags format and to simplify functionality in several places in the schema.

When using GenericModel subclasses you no longer need to call .model_dump()

What's Changed

• refactor: allow passing strings to default_grouping, also build docs by @dbirman in #1648
• added protocol to calibrations by @saskiad in #1652
• fix: repair QualityControl.default_grouping merge for new list[str | tuple[str, ...]] type by @dbirman in #1655
• refactor: make headframe_part_number Optional[] by @saskiad in #1654
• fix: populate source_data properly by @dbirman in #1656
• fix: properly handle None dependency_graph during merge by @dbirman in #1657
• chore: bump to aind-data-schema-models 5, replace slap->slap2 by @dbirman in #1665
• Feat 1562 unitfix by @saskiad in #1662
• fix: reduce requirement for SLAP2 to just ImagingConfig by @dbirman in #1671
• refactor: allow instrument_id to be included in device.name fields by @dbirman in #1663
• add GenericModelType to fix serialization by @tmchartrand in #1672
• fix: small regression introduced in #1672 by @bruno-f-cruz in #1676
• fix: for backward compatibility, add defaults to _unit fields for contrast/brightness using a validator by @dbirman in #1677
• feat: compute group:value pairs for tag status by @dbirman in #1673

Full Changelog: v2.3.2...v2.4.0

v2.3.2

What's Changed

This patch release includes some small hotfixes, including limiting the version of aind-data-schema-models to <5. Version 2.3.0 is broken due to having no ceiling on that dependency, please use this release instead or manually limit aind-data-schema-models to <5.

Full Changelog: v2.3.0...v2.3.2

v2.3.0

Important change: we modified the QualityControl.tags field in a way that is "sort-of-backward-compatible". Please read the README and see the post on Teams for more information about the new approach. Old assets will need to be migrated to function properly in the new system.

What's Changed

• Fix minor typos in acquisition docs by @rly in #1633
• refactor: deprecate breeding_group and clear field by @dbirman in #1640
• feat: re-organize quality control tags as dictionary by @dbirman in #1643
• release v2.3.0 by @dbirman in #1644

New Contributors

• @rly made their first contribution in #1633

Full Changelog: v2.2.0...v2.3.0

v2.2.0

What's Changed

• feat: adding Manipulation during acquisition by @dbirman in #1607
• docs: update docs for external registries by @dbirman in #1610
• docs: improvements to coordinate system docs by @dbirman in #1606
• fix: modify instrument merge by @dbirman in #1619
• fix: allow acquisition/procedures with None coordinate_system to merge by @dbirman in #1628
• feat: filename_suffix to do what suffix should have done by @dbirman in #1631
• Allow for partial instrument/acquisition compatibility checks without constructing Metadata object by @dbirman in #1623
• feat: DataStream.add and Acquistion._merge_data_stream_lists by @dbirman in #1634

Full Changelog: v2.1.0...v2.2.0