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release v2.3.1 (#1659)
* bump main (#1645) * chore: hotfix v2.0.1 * bump schema version [skip actions] * chore: bump version * bump schema version [skip actions] * fix: adds check if dependency_graph is None (#1576) * fix: adds check if dependency_graph is None * build: version bump to 2.0.3 * chore: set a ceiling on pydantic to avoid errors with model_validators * chore: increment patch version * hotfix: move the subject_details validator out of Acquisition and into Metadata * chore: bump version * tests: fix test that included specimen_id but doesn't need it * chore: upgrade versions * bump schema version [skip actions] * chore: bump minor versions * bump schema version [skip actions] * bump schema version [skip actions] * chore: bump minor versions * bump schema version [skip actions] --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: jtyoung84 <104453205+jtyoung84@users.noreply.github.com> * refactor: allow passing strings to default_grouping, also build docs (#1648) * refactor: allow un-tupled string to make life easier * docs: update * fix: actually allow str | * tests: fix tests, and properly handle input data that looks like new data * docs: improve how allow_tag_failures is explained * chore: lint * fix: overenthusiastic defensiveness * added protocol to calibrations (#1652) * added protocol * docs: build docs for protocl addition --------- Co-authored-by: Dan Birman <danbirman@gmail.com> * fix: repair QualityControl.default_grouping merge for new list[str | tuple[str, ...]] type (#1655) * fix: fix bad functionality in how default_grouping was being merged * chore: lint * tests: simplify and add docstrings * refactor: make headframe_part_number Optional[] (#1654) * optional * docs * fix: populate source_data properly (#1656) * chore: bump versions * bump schema version [skip actions] * bump schema version [skip actions] * chore: fix workflow issues and prevent adsm 5 from importing * bump schema version [skip actions] * updates diagrams [skip actions] --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: jtyoung84 <104453205+jtyoung84@users.noreply.github.com> Co-authored-by: Saskia de Vries <saskiad@users.noreply.github.com>
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‎.github/workflows/update_docs.yml‎

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- uses: actions/checkout@v3
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with:
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token: ${{ secrets.SERVICE_TOKEN }}
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ref: ${{ github.ref }}
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- name: Pull latest changes
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run: git pull origin ${{ github.ref_name }}
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- name: Set up Python 3.10
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uses: actions/setup-python@v2
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with:

‎docs/base/core/quality_control.md‎

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}
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```
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Use the `QualityControl.default_grouping` list to define how users should organize a visualization by default. In almost all cases *modality should be the top-level grouping*. For example, building on the example above you might group by: `[["modality"], ["probe", "video"], ["shank"]]` to get a tree split by modality first (which naturally splits ephys and behavior-videos tags into two groups), then by which probe or video a metric belongs to, and finally only for probes the individual shanks are split into groups.
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Use the `QualityControl.default_grouping` list to define how users should organize a visualization by default. In almost all cases *modality should be the top-level grouping*. For example, building on the example above you might group by: `["modality", ("probe", "video"), "shank"]` to get a tree split by modality first (which naturally splits ephys and behavior-videos tags into two groups), then by which probe or video a metric belongs to, and finally only for probes the individual shanks are split into groups.
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### QualityControl.evaluate_status()
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You can evaluate the state of a set of metrics filtered by any combination of modalities, stages, and tags on a specific date (by default, today). When evaluating the [Status](#status) of a group of metrics the following rules apply:
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First, any metric that is failing and also has a matching tag *value* in the `QualityControl.allow_tag_failures` list is set to pass. This allows you to specify that certain metrics are not critical to a data asset.
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First, any metric that has a tag *value* in the `QualityControl.allow_tag_failures` list is ignored. This allows you to specify that certain metrics are not critical to a data asset.
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Then, given the status of all the metrics in the group:
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Then, given the status of all the remaining metrics in the group:
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1. If any metric is still failing, the evaluation fails
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2. If any metric is pending and the rest pass the evaluation is pending

‎docs/source/aind_data_schema.components.rst‎

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aind\_data\_schema.components package
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=====================================
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Submodules
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----------
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aind\_data\_schema.components.configs module
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--------------------------------------------
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.. automodule:: aind_data_schema.components.configs
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:members:
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:undoc-members:
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:show-inheritance:
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aind\_data\_schema.components.connections module
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------------------------------------------------
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.. automodule:: aind_data_schema.components.connections
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:members:
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:undoc-members:
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:show-inheritance:
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aind\_data\_schema.components.coordinates module
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------------------------------------------------
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.. automodule:: aind_data_schema.components.coordinates
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:members:
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:undoc-members:
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:show-inheritance:
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aind\_data\_schema.components.devices module
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--------------------------------------------
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.. automodule:: aind_data_schema.components.devices
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:members:
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:undoc-members:
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:show-inheritance:
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aind\_data\_schema.components.identifiers module
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------------------------------------------------
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.. automodule:: aind_data_schema.components.identifiers
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:members:
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:undoc-members:
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:show-inheritance:
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aind\_data\_schema.components.injection\_procedures module
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----------------------------------------------------------
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.. automodule:: aind_data_schema.components.injection_procedures
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:members:
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:undoc-members:
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:show-inheritance:
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aind\_data\_schema.components.measurements module
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-------------------------------------------------
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.. automodule:: aind_data_schema.components.measurements
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:members:
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:undoc-members:
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:show-inheritance:
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aind\_data\_schema.components.reagent module
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--------------------------------------------
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.. automodule:: aind_data_schema.components.reagent
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:members:
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:undoc-members:
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:show-inheritance:
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aind\_data\_schema.components.specimen\_procedures module
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---------------------------------------------------------
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.. automodule:: aind_data_schema.components.specimen_procedures
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:members:
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:undoc-members:
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:show-inheritance:
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aind\_data\_schema.components.stimulus module
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---------------------------------------------
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.. automodule:: aind_data_schema.components.stimulus
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:members:
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:undoc-members:
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:show-inheritance:
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aind\_data\_schema.components.subject\_procedures module
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--------------------------------------------------------
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.. automodule:: aind_data_schema.components.subject_procedures
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:members:
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:undoc-members:
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:show-inheritance:
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aind\_data\_schema.components.subjects module
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---------------------------------------------
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.. automodule:: aind_data_schema.components.subjects
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:undoc-members:
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aind\_data\_schema.components.surgery\_procedures module
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--------------------------------------------------------
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.. automodule:: aind_data_schema.components.surgery_procedures
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:undoc-members:
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aind\_data\_schema.components.wrappers module
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---------------------------------------------
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.. automodule:: aind_data_schema.components.wrappers
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:members:
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:undoc-members:
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Module contents
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---------------
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:show-inheritance:

‎docs/source/aind_data_schema.core.rst‎

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aind\_data\_schema.core package
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===============================
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Submodules
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----------
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aind\_data\_schema.core.acquisition module
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------------------------------------------
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.. automodule:: aind_data_schema.core.acquisition
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:members:
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aind\_data\_schema.core.data\_description module
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------------------------------------------------
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.. automodule:: aind_data_schema.core.data_description
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:undoc-members:
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aind\_data\_schema.core.instrument module
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-----------------------------------------
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.. automodule:: aind_data_schema.core.instrument
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:undoc-members:
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:show-inheritance:
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aind\_data\_schema.core.metadata module
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---------------------------------------
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.. automodule:: aind_data_schema.core.metadata
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:undoc-members:
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aind\_data\_schema.core.model module
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------------------------------------
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.. automodule:: aind_data_schema.core.model
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:undoc-members:
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aind\_data\_schema.core.procedures module
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-----------------------------------------
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:members:
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:undoc-members:
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:show-inheritance:
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aind\_data\_schema.core.processing module
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-----------------------------------------
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:members:
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:undoc-members:
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:show-inheritance:
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aind\_data\_schema.core.quality\_control module
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-----------------------------------------------
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:members:
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:undoc-members:
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aind\_data\_schema.core.subject module
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--------------------------------------
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Module contents
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:undoc-members:
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:show-inheritance:

‎docs/source/aind_data_schema.rst‎

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aind\_data\_schema package
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==========================
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Subpackages
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-----------
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.. toctree::
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:maxdepth: 4
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aind_data_schema.components
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aind_data_schema.core
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aind_data_schema.utils
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----------
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aind\_data\_schema.base module
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------------------------------
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.. automodule:: aind_data_schema.base
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:members:
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:undoc-members:
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:show-inheritance:
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Module contents
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---------------
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.. automodule:: aind_data_schema
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:members:
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:undoc-members:
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:show-inheritance:

‎docs/source/aind_data_schema.utils.rst‎

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aind\_data\_schema.utils package
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================================
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----------
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aind\_data\_schema.utils.compatibility\_check module
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----------------------------------------------------
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:members:
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:undoc-members:
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aind\_data\_schema.utils.examples\_generator module
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---------------------------------------------------
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:members:
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:undoc-members:
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aind\_data\_schema.utils.exceptions module
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aind\_data\_schema.utils.json\_writer module
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--------------------------------------------
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:undoc-members:
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aind\_data\_schema.utils.merge module
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-------------------------------------
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:members:
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:undoc-members:
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:show-inheritance:
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aind\_data\_schema.utils.schema\_version\_bump module
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-----------------------------------------------------
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.. automodule:: aind_data_schema.utils.schema_version_bump
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:members:
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:undoc-members:
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aind\_data\_schema.utils.validators module
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:undoc-members:
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Module contents
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:show-inheritance:

‎docs/source/components/measurements.md‎

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|-------|------|-------------|
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| `calibration_date` | `datetime (timezone-aware)` | Date and time of calibration |
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| `description` | `str` | Description (Brief description of what is being calibrated) |
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| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
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| `measured_at` | `Optional[str]` | Measurement location |
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| `input` | `List[float or str]` | Inputs (Calibration input) |
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| `input_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) or [MassUnit](../aind_data_schema_models/units.md#massunit) or [FrequencyUnit](../aind_data_schema_models/units.md#frequencyunit) or [SpeedUnit](../aind_data_schema_models/units.md#speedunit) or [VolumeUnit](../aind_data_schema_models/units.md#volumeunit) or [AngleUnit](../aind_data_schema_models/units.md#angleunit) or [TimeUnit](../aind_data_schema_models/units.md#timeunit) or [PowerUnit](../aind_data_schema_models/units.md#powerunit) or [CurrentUnit](../aind_data_schema_models/units.md#currentunit) or [ConcentrationUnit](../aind_data_schema_models/units.md#concentrationunit) or [TemperatureUnit](../aind_data_schema_models/units.md#temperatureunit) or [SoundIntensityUnit](../aind_data_schema_models/units.md#soundintensityunit) or [VoltageUnit](../aind_data_schema_models/units.md#voltageunit) or [MemoryUnit](../aind_data_schema_models/units.md#memoryunit) or [UnitlessUnit](../aind_data_schema_models/units.md#unitlessunit) or [MagneticFieldUnit](../aind_data_schema_models/units.md#magneticfieldunit) or [PressureUnit](../aind_data_schema_models/units.md#pressureunit) | Input unit |
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‎docs/source/components/subjects.md‎

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‎docs/source/components/surgery_procedures.md‎

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| `well_type` | `Optional[str]` | Well type |

‎docs/source/modules.rst‎

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src
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===
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.. toctree::
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aind_data_schema

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