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Keeping v2 up to date #1123
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Keeping v2 up to date #1123
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* docs: adding draft QC docs * docs: adding more qc docs * feat: add myst_parser and qc to index * refactor: replace .rst file with .md * docs: adding information about reference URLs * docs: separating portal information into an AIND section * docs: cleaning up documentation for qc * docs: more cleanup on qc docs * docs: small updates to docs based on discussion about credentials * docs: updating qc docs based on discussion * docs: cleaning up docs and clarifying in a few spots
* feat: adding optional ResourceUsage to DataProcess * tests: adding example * refactor: adding ResourceTimestamped * chore: remove timeunit * tests: adding tests * fix: missing Field() * chore: lint * chore: lint * tests: examples * chore: lint * refactor: date->datetime and usage_unit * chore: update processing example * chore: lint * fix: datetime -> AwareDatetime * refactor: rename memory to system_memory * chore: lint * tests: force timezones to utc for CI * fix: timezone issue for tests * refactor: remove MemoryValue and add validators for Optional unit fields * refactor: remove file_io * chore: lint * chore: lint * refactor: remove file_io * refactor: clean up validators into a single root validator * chore: lint * tests: fix examples, also allow float memory sizes * tests: update example file * chore: lint
…sed on metric states (#1074) * refactor: changing references -> reference * feat: add an overall evaluator name * feat: adding QCStatus and lists of status for versioning * chore: lint * tests: updating tests for QCStatus * feat: add QCStatus list to metrics * feat: adding a function to automate setting the evaluation_status field Coverage not at 100% yet Also replaced date with datetime in QCStatus * test: test coverage for overall_status * test: add coverage for properties * refactor: date -> datetime * chore: lint * doc: missing docstrings * tests: remove unnecessary test * feat: auto-set status when never previously evaluated, and tests * fix: fixing an issue with private attributes You can't do what I wanted (hide the _evaluation_status list) because pydantic doesn't serialize the field. So we have to keep the history exposed but we'll have to encourage people not to access it directly * chore: example and lint * fix: removing default_factory, trying to allow timestamp pass through * test: fixing examples test timestamp issue * chore: lint * refactor: datetime -> AwareDatetime and remove default * tests: add a test that confirms that order is preserved * fix: missing timezones for example * feat: add option to allow failures in metrics * feat: add a convenience function to get metrics that are failing * tests: update qc.json example * feat: ensure metric_status_history not empty with validator * chore: docstring * test: improving examples * chore: lint * feat: add asset_id field to qc * tests: fix examples * tests: fix examples * docs: extended desc for allowing failed metrics * feat: removing prefixes to clean up fields * feat: remove property prefixes * chore: lint * chore/tests: lint and fix examples * tests: fix refactor issues in tests * docs: fix typo * chore: unused import snuck in? * fix: allow none to return from failed_metrics * ci: fix for python 3.8 failures * fix: remove the confusing "Automated" evaluator * tests: fix qc example * refactor: removing redundant status_history from QualityControl and QCEvaluation * fix: forgot to remove redundant fields * tests: fix examples
* build: updates version number * feat: adds qc schema json * fix: updates schema version check to handle new core schemas * ci: adds service account token to github actions * bump schema version [skip actions] * fix: updates broken github action * bump schema version [skip actions] * build: increments version to 1.0.0 * build: sets core metadata schema to v1.0.0 * chore: version bump * bump schema version [skip actions] * chore: version bump for schemas (#1094) * chore: version bump for schemas * tests: example updates * bump schema version [skip actions] --------- Co-authored-by: Jon Young <104453205+jtyoung84@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
…xpected modalities (#1084) * feat/refactor: add validator for required/excluded files Also refactors CORE_FILES into a separate variable * refactor: remove redundant validators * fix: properly handle modalit*ies* list, fixing tests * chore: lint * tests: adding excluded file test * feat: adding support for multi-modal records Prioritize required > optional > excluded for files * fix: partial fix for modalities with underscores * fix: fixing underscore issues and adding test coverage * tests: fixing underscore test * tests: Value->ValidationError * fix: modality.abbreviation tracked correctly Added modality into requirement_dict to track it for throwing errors * chore: lint * chore: lint
example file generated in the root folder by accident
* chore: add default= to schema_version * chore: add default= for URL
…1106) * feat: adding provenance * chore: lint * feat: adding multi-asset stage and typo * chore: examples * refactor: adding validator and renaming tests are still todo * tests: adding tests, minor fixes * tests: examples and line length * fix: multi_session->multi_asset * fix: session suffix to asset * fix: typo * fix: more typos
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