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…ps://github.com/AllenNeuralDynamics/aind-data-schema into 1642-create-instrumentjson-generator-for-barseq
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* Allow specimen_id to be a list (#1770) * Allow specimen_id to be a list * Removed nonetype test * Fixed specimen names in test * Updated specimen_id description to clarify expectation during in-vivo sessions * Spread args over multi lines to avoid lint fail * docs: rebuild docs (#1771) * docs: minor fixes to acquisition.md * docs: remove bad directives and links * docs: improve description for AcquisitionSubjectDetails (#1772) * docs: improve description for AcquisitionSubjectDetails * docs: rebuild docs * fix: throw warnings when users include multiple identically named devices in the Instrument (#1773) * fix: allow both planar and regular sectioning in sectioning procedures (#1777) * fix: allow NHPSubject as subject_details option (#1778) * docs: auto-build docs on opening PR (#1760) * docs: auto-build docs on opening PR * update docs [skip actions] * docs: update contribution.md * update docs [skip actions] * chore: remove all unnecessary graphviz dependencies * update docs [skip actions] * update docs [skip actions] --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Handle lists of specimen IDs in procedures validator (#1783) * Handle lists of specimen IDs in procedures validator * Fix to properly handle individual str as well as lists of str * refactor: simplifying code a tiny bit --------- Co-authored-by: Dan Birman <danbirman@gmail.com> * Add ticket linking workflow (#1785) * Barseq blackbox acquisition (#1781) * First pass at minimal blackbox acquisition. Has file that generates acquisition for two subjects, plus json outputs * Added reference to output files * Added specimen IDs to barseq acquisitions * Removed readme file * Updating examples/barseq_acquisition.py docstring * Cleaned up comments in examples/barseq_acquisition.py * Set timestamps to pacific with offset * Changed experimenters to 'Barseq team' * Removed references to local paths, removed duplicate jsons * Added ExternalDataStream, made instrument optional, added test, updated example barseq * Updated example json outputs for barseq subjects * update docs [skip actions] * Linting fixes * Used DiscriminatedList * Clean up stream adding logic * Simplify barseq acquisition example * Removed jsons * clean up test and import properly * Add ExternalDataStream support to Metadata validators and test that no instrument warning is raised for external acquisitions. * Wording updates as suggested by Dan --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * 1792 quality control validator has a bug at line 307 where it fails to check metrics before doing metrics0 (#1793) * fix: validator would trigger on empty metrics * fix: do this upfront by bypassing the validator, adds a test * chore: delete CHANGELOG.md (#1799) * chore: delete CHANGELOG.md * update docs [skip actions] --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * refactor: replace root calls to logging with module-level loggers (#1800) * fix: issue with actions being skipped unnecessarily * refactor: replace root logger with local loggers * test: fixes to logger patches * docs: improve docstring (#1748) * docs: improve docstring * docs: update specimen ID * docs: clarify suffix * docs: better writing * update docs * fix: bad merge * update docs --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * refactor: only allow wrapped NonSurgeryInjections in Procedures.subject_procedures (#1802) * refactor: only allow Injections in Procedures.subject_procedures when wrapped with an InjectionProcedure * chore: add ethics_review_id/protocol_id * fix: only allow Injection, BrainInjection requires a full CS from Surgery * update docs [skip actions] * refactor: NonSurgicalInjection * update docs --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Add missing `tzdata` dependency (#1811) * Add git hash to Code model (#1813) * Add git hash to Code model * update docs * Increase hash length upper bound * Change property name and emit warning if hash and version are not defined * Refactor type alias * update docs * Break lines * Update tests to reflect longer hashes --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * feat: add barseq instrument (#1685) * feat: add barseq instrument * refactor: SlapPlane -> Slap2Plane * Revert "refactor: SlapPlane -> Slap2Plane" This reverts commit 6f193b8. * chore: lint * refactor: fix serialization code in example * fix: fix issues blocking build * chore: fix write function for instrument example * fix: specimen_ids validator correctly flattens lists (#1763) * feat: working on procedures_sectioning example * feat: continuing to develop chunk sections * chore: embed slide regions in python code * chore: lint * chore: docstrings * chore: lint * chore: remove full sectioning file --------- Co-authored-by: Doug Ollerenshaw <doug.ollerenshaw@alleninstitute.org> * chore: bump version * bump schema version [skip actions] * chore: bump metadata * bump schema version [skip actions] --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Doug Ollerenshaw <doug.ollerenshaw@alleninstitute.org> Co-authored-by: gouwens <ngouwens@gmail.com> Co-authored-by: Bruno Cruz <7049351+bruno-f-cruz@users.noreply.github.com>
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