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Release v2.9.0 - #1873
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Release v2.9.0#1873
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* added joystick config * update docs * add description * update docs * lint --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* add FluorescentReagent * update docs * whitespace * update docs * specimen procedures * update docs * lint --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* refactor: rework coordinates * update docs * refactor: replace Scale with Rectangle/Circle * fix: extrinsic/intrinsic -> global/local * fix: simplify * test: repair tests * update docs * chore: lint * update docs * chore: lint * fix: repair outputs to match coordinate definitions * update docs * chore: lint * chore: lint * chore: lint * docs: small tweaks to the coordinate system viewer * feat: allow the use of EMAPA structures as origins * update docs * chore: lint * refactor: frame->reference_frame, better descriptions * update docs * refactor: migrate to global_ local_ prefixes * update docs * test/fix: fix tests, clarify title/descriptions * update docs * test: missing test * chore: lint * chore: lint * refactor: fix generator in docs * refactor: rename reference_frame field * update docs * docs: improve docstrings * chore: lint * update docs * test: rename --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* chore: dependency changes * update docs --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
(1) PR adds a function in `schema_tree.py` that generates a stylized
schema tree, looks like this basically:
- **Acquisition** — Description of data acquisition metadata including
streams, stimuli, and experimental setup.
- `protocol_id` (Optional[LIST OF: str]) — Protocol ID: DOI for
protocols.io
- `subject_id` (str, required) — Subject ID: Unique identifier for the
subject
- `specimen_id` (Optional[ONE OF: str, LIST OF: str]) — Specimen ID:
Required for in vitro modalities. Standard format is {subject_id} with a
_### suffix, as needed
- `acquisition_start_time` (AwareDatetime, required) — Acquisition start
time: During validation, timezone information will be moved into the
acquisition_start_tz field.
- `acquisition_start_tz` (Optional[ONE OF: int, TimeZoneName]) —
Acquisition start timezone: Automatically populated by a validator based
on acquisition_start_time. Will be a TimeZoneName (IANA name) when the
datetime uses a ZoneInfo timezone, or an integer UTC offset in hours for
fixed-offset timezones. Use ZoneInfo (from the zoneinfo standard
library) to preserve the named timezone.
But it keeps going for the entire schema. This will be used for the
appendix in the data-schema paper, as well as for the aind-data-mcp.
(2) Using the new schema tree the code now adds a new section to the
docs with an interactive diagram, see preview:
https://aind-data-schema--1864.org.readthedocs.build/en/1864/
---------
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Adds a new DeviceImplant to support thermistor wire implants, and adds an example showing how to use it. Molex is not an available manufacturer, we'll have to add it separately (we can do that before merging, if we want). --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Add FoodRestriction class --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
closes #1867 by using Path instance methods that are compatible with other Path-like objects, rather than stdlib functions that aren't. retains compatibility with path strings even though the type annotations don't support that usage.
This PR adds a new function `Metadata.from_metadata` that simplifies the process of generating derived asset metadata. It implements four rules (see the docs page) that control how metadata is inherited. Added some new functionality: - Data description names now default to the DataRegex.ANALYZED pattern when from_metadata is called with multiple Metadata objects - Clarified what process name we expect - Made the docs a bit more clear about how inheritance works
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📚 Documentation preview 📚: https://aind-data-schema--1873.org.readthedocs.build/en/1873/