aind-data-schema 2.6.0__tar.gz → 2.8.0__tar.gz

aind_data_schema-2.8.0/.github/workflows/link-issues-by-milestone.yml

@@ -0,0 +1,56 @@
+name: Link issue to cross-repo milestone parent
+
+on:
+  issues:
+    types: [milestoned]
+
+jobs:
+  link:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Link to parent issue in aind-scientific-computing
+        uses: actions/github-script@v7
+        with:
+          github-token: ${{ secrets.SERVICE_TOKEN }}
+          script: |
+            const issue = context.payload.issue;
+            const milestone = issue.milestone;
+
+            if (!milestone) return;
+
+            const targetOwner = "AllenNeuralDynamics";
+            const targetRepo = "aind-scientific-computing";
+
+            const url = milestone.description;
+            const match = url?.match(/\/issues\/(\d+)$/);
+
+            if (!match) {
+              console.log(`Milestone description is not a roadmap URL: ${url}`);
+              return;
+            }
+
+            const parentNumber = parseInt(match[1]);
+
+            const { data: parent } = await github.rest.issues.get({
+              owner: targetOwner,
+              repo: targetRepo,
+              issue_number: parentNumber
+            });
+
+            if (!parent) {
+              console.log(`No issue found at ${url}`);
+              return;
+            }
+
+            await github.request("POST /repos/{owner}/{repo}/issues/{issue_number}/sub_issues", {
+              owner: targetOwner,
+              repo: targetRepo,
+              issue_number: parentNumber,
+              sub_issue_id: issue.id,
+              headers: {
+                "X-GitHub-Api-Version": "2022-11-28"
+              }
+            });
+
+            console.log(`Linked issue #${issue.number} as sub-issue of ${targetRepo}#${parentNumber}`);

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/.github/workflows/run_dev_tests.yml

@@ -38,7 +38,6 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        sudo apt install graphviz libgraphviz-dev -y
         python -m pip install -e .[dev] -e .[docs] --no-cache-dir
     - name: Run tests and coverage
       run: coverage run -m unittest discover && coverage report

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/.github/workflows/run_main_tests.yml

@@ -40,7 +40,6 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        sudo apt install graphviz libgraphviz-dev -y
         python -m pip install -e .[dev] -e .[docs] --no-cache-dir
     - name: Run tests and coverage
       run: coverage run -m unittest discover && coverage report

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/.github/workflows/tag_and_publish_main.yml

@@ -3,6 +3,7 @@ on:
   push:
     branches:
       - main
+  workflow_dispatch:
 
 jobs:
   tag_and_publish:

aind_data_schema-2.8.0/.github/workflows/update_dev_docs.yml

@@ -0,0 +1,34 @@
+name: Update docs for dev PR
+
+on:
+  pull_request:
+    branches:
+      - dev
+
+jobs:
+  update_docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.SERVICE_TOKEN }}
+          ref: ${{ github.head_ref }}
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.10'
+      - name: Install dependencies
+        run: |
+          python -m pip install -e .[dev] -e .[docs] --no-cache-dir
+      - name: Generate docs
+        run: |
+          python src/aind_data_schema/utils/docs/model_generator.py
+          python src/aind_data_schema/utils/docs/registries_generator.py
+          python src/aind_data_schema/utils/docs/doc_generator.py
+          sphinx-build -b html docs/source/ docs/build/html
+      - name: Commit changes
+        uses: EndBug/add-and-commit@v9
+        with:
+          default_author: github_actions
+          message: "update docs"
+          add: '["docs"]'

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/.github/workflows/update_docs.yml

@@ -60,7 +60,6 @@ jobs:
           python-version: '3.10'
       - name: Install dependencies
         run: |
-          sudo apt install graphviz libgraphviz-dev -y
           python -m pip install -e .[dev] -e .[docs] --no-cache-dir
       - name: Commit changes
         uses: EndBug/add-and-commit@v9

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/.gitignore

@@ -146,3 +146,4 @@ examples/*.json
 *.json
 docs/base/models/*
 .github/copilot-instructions.md
+uv.lock

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/CONTRIBUTING.md

@@ -39,7 +39,9 @@ Starting with the v2.0 release all changes must be accompanied by an [upgrader](
 
 ### Documentation
 
-**Note**: The core files (`docs/source/acquisition.md`, etc) are auto-generated from the base files in the folder `docs/base/core` with the model definitions appended. You must modify the **base** file or your changes will be overwritten when you run the documentation generators.
+Documentation is automatically built when you open a PR into the aind-data-schema repository. For **core files, please make sure that you modify the base file**, these are used to construct the source files: i.e. `docs/base/core/acquisition.md` will over-write any changes made to `docs/source/acquisition.md`. 
+
+#### Manually build documentation
 
 To generate the source files for the documentation and model class links, run:
 

{aind_data_schema-2.6.0/src/aind_data_schema.egg-info → aind_data_schema-2.8.0}/PKG-INFO

@@ -1,15 +1,16 @@
 Metadata-Version: 2.4
 Name: aind-data-schema
-Version: 2.6.0
+Version: 2.8.0
 Summary: A library that defines AIND data schema and validates JSON files.
 License: MIT
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: aind-data-schema-models<6,>=5.4.1
+Requires-Dist: aind-data-schema-models<6,>=5.7.1
 Requires-Dist: pydantic<2.12,>=2.7
 Requires-Dist: pydantic-extra-types
+Requires-Dist: tzdata
 Provides-Extra: dev
 Requires-Dist: aind_data_schema[linters]; extra == "dev"
 Requires-Dist: pydantic!=2.9.0,!=2.9.1,>=2.7; extra == "dev"

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/docs/base/core/acquisition.md

@@ -19,9 +19,9 @@ Because the start and stop times are independent for data streams and stimulus e
 
 ## Uniqueness
 
-You can uniquely identify acquisition sessions (and therefore a specific data asset) by their acquisition datetime (`Acquisition.acquisition_end_time`). In addition, the `Acquisition.acquisition_type` is an open `str` field where you can put conceptual information that groups similar acquisitions together. This should not be completely redundant with project names, modalities, stimulus names, or any other fields in the metadata.
+You can uniquely identify acquisition sessions (and therefore a specific data asset) by their acquisition datetime (`Acquisition.acquisition_start_time`). In addition, the `Acquisition.acquisition_type` is an open `str` field where you can put conceptual information that groups similar acquisitions together. This should not be completely redundant with project names, modalities, stimulus names, or any other fields in the metadata.
 
-For example, in the `"Brain Computer Interface"` project name, good acquisition types would be strings like: `"BCI: Single neuron stim"` and `"BCI: Group neuron stim"`. These phrases clearly identify what part of a project these acquisitions belong to, without being overly redundant with controlled fields in the metadata.
+For example, in the `"Brain Computer Interface"` project name, good acquisition types would be strings like: `"Single neuron stim"` and `"Group neuron stim"`. These phrases clearly identify what part of a project these acquisitions belong to, without being overly redundant with controlled fields in the metadata.
 
 ## Stimulus parameters
 

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/docs/base/core/quality_control.md

@@ -26,7 +26,7 @@ If you find yourself computing a value for something smaller than an entire moda
 
 `tags` are groups of descriptors that define how metrics are organized hierarchically, making it easier to visualize metrics. Good tag keys (groups) are things like "probe" and good tag values are things like "Probe A" or just "A".
 
-```{python}
+```python
 # For an electrophysiology metric
 tags = {
     "probe": "A",

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/docs/source/acquisition.md

@@ -19,9 +19,9 @@ Because the start and stop times are independent for data streams and stimulus e
 
 ## Uniqueness
 
-You can uniquely identify acquisition sessions (and therefore a specific data asset) by their acquisition datetime (`Acquisition.acquisition_end_time`). In addition, the `Acquisition.acquisition_type` is an open `str` field where you can put conceptual information that groups similar acquisitions together. This should not be completely redundant with project names, modalities, stimulus names, or any other fields in the metadata.
+You can uniquely identify acquisition sessions (and therefore a specific data asset) by their acquisition datetime (`Acquisition.acquisition_start_time`). In addition, the `Acquisition.acquisition_type` is an open `str` field where you can put conceptual information that groups similar acquisitions together. This should not be completely redundant with project names, modalities, stimulus names, or any other fields in the metadata.
 
-For example, in the `"Brain Computer Interface"` project name, good acquisition types would be strings like: `"BCI: Single neuron stim"` and `"BCI: Group neuron stim"`. These phrases clearly identify what part of a project these acquisitions belong to, without being overly redundant with controlled fields in the metadata.
+For example, in the `"Brain Computer Interface"` project name, good acquisition types would be strings like: `"Single neuron stim"` and `"Group neuron stim"`. These phrases clearly identify what part of a project these acquisitions belong to, without being overly redundant with controlled fields in the metadata.
 
 ## Stimulus parameters
 
@@ -78,23 +78,23 @@ while the StimulusEpoch represents all stimuli being presented.
 | Field | Type | Title (Description) |
 |-------|------|-------------|
 | `subject_id` | `str` | Subject ID (Unique identifier for the subject) |
-| `specimen_id` | `Optional[str]` | Specimen ID (Specimen ID is required for in vitro imaging modalities) |
+| `specimen_id` | `str or List[str] or NoneType` | Specimen ID (Required for in vitro modalities. Standard format is {subject_id} with a _### suffix, as needed) |
 | `acquisition_start_time` | `datetime (timezone-aware)` | Acquisition start time (During validation, timezone information will be moved into the acquisition_start_tz field.) |
 | `acquisition_start_tz` | `int or pydantic_extra_types.timezone_name.TimeZoneName or NoneType` | 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.) |
 | `acquisition_end_time` | `datetime (timezone-aware)` | Acquisition end time  |
 | `experimenters` | `List[str]` | experimenter(s)  |
-| `protocol_id` | `Optional[List[str]]` | Protocol ID (DOI for protocols.io) |
 | `ethics_review_id` | `Optional[List[str]]` | Ethics review ID  |
-| `instrument_id` | `str` | Instrument ID (Should match the Instrument.instrument_id) |
+| `instrument_id` | `Optional[str]` | Instrument ID (Should match the Instrument.instrument_id. Required when instrument metadata is available.) |
 | `acquisition_type` | `str` | Acquisition type (Descriptive string detailing the type of acquisition, should be consistent across similar acquisitions for the same experiment.) |
 | `notes` | `Optional[str]` | Notes  |
 | `coordinate_system` | Optional[[CoordinateSystem](components/coordinates.md#coordinatesystem)] | Coordinate system (Origin and axis definitions for determining the configured position of devices during acquisition. Required when coordinates are provided within the Acquisition) |
 | `calibrations` | List[[Calibration](components/measurements.md#calibration) or [VolumeCalibration](components/measurements.md#volumecalibration) or [PowerCalibration](components/measurements.md#powercalibration)] | Calibrations (List of calibration measurements taken prior to acquisition.) |
 | `maintenance` | List[[Maintenance](components/measurements.md#maintenance)] | Maintenance (List of maintenance on instrument prior to acquisition.) |
-| `data_streams` | List[[DataStream](acquisition.md#datastream)] | Data streams (A data stream is a collection of devices that are acquiring data simultaneously. Each acquisition can include multiple streams. Streams should be split when configurations are changed.) |
+| `data_streams` | List[[DataStream](acquisition.md#datastream) or [ExternalDataStream](acquisition.md#externaldatastream)] | Data streams (A data stream is a collection of devices that are acquiring data simultaneously. Each acquisition can include multiple streams. Streams should be split when configurations are changed. Use ExternalDataStream for acquisitions where instrument metadata is unavailable.) |
 | `stimulus_epochs` | List[[StimulusEpoch](acquisition.md#stimulusepoch)] | Stimulus (A stimulus epoch captures all stimuli being presented during an acquisition. Epochs should be split when the purpose of the stimulus changes.) |
 | `manipulations` | List[[Manipulation](acquisition.md#manipulation)] | Manipulations (Procedures performed during the acquisition.) |
-| `subject_details` | Optional[[AcquisitionSubjectDetails](acquisition.md#acquisitionsubjectdetails)] | Subject details  |
+| `subject_details` | Optional[[AcquisitionSubjectDetails](acquisition.md#acquisitionsubjectdetails)] | Subject details (Required for in vivo acquisitions.) |
+| `protocol_id` | `Optional[List[str]]` | Protocol ID (DOI for protocols.io) |
 
 
 ## Model definitions
@@ -131,6 +131,18 @@ same time.
 | `connections` | List[[Connection](components/connections.md#connection)] | Connections (Connections are links between devices that are specific to this acquisition (i.e. not already defined in the Instrument)) |
 
 
+### ExternalDataStream
+
+A simplified data stream for acquisitions where instrument metadata is unavailable.
+
+| Field | Type | Title (Description) |
+|-------|------|-------------|
+| `stream_start_time` | `datetime (timezone-aware)` | Stream start time  |
+| `stream_end_time` | `datetime (timezone-aware)` | Stream stop time  |
+| `modalities` | List[[Modality](aind_data_schema_models/modalities.md#modality)] | Modalities (Modalities that are acquired in this stream) |
+| `notes` | `Optional[str]` | Notes  |
+
+
 ### Manipulation
 
 Description of procedures performed during an acquisition.
@@ -139,9 +151,10 @@ Description of procedures performed during an acquisition.
 |-------|------|-------------|
 | `start_time` | `datetime (timezone-aware)` | Manipulation start time (Must be between the acquisition start and end times) |
 | `end_time` | `datetime (timezone-aware)` | Manipulation end time (Must be between the acquisition start and end times) |
-| `procedures` | Optional[List[[Injection](components/injection_procedures.md#injection) or [BrainInjection](components/surgery_procedures.md#braininjection)]] | Procedures (Procedures performed during the manipulation) |
+| `procedures` | Optional[List[[Injection](components/injection_procedures.md#injection) or [BrainInjection](components/surgery_procedures.md#braininjection) or [Reagent](components/reagent.md#reagent)]] | Procedures (Procedures performed during the manipulation) |
 | `anaesthesia` | Optional[[Anaesthetic](components/surgery_procedures.md#anaesthetic)] | Anaesthesia  |
 | `notes` | `Optional[str]` | Notes  |
+| `protocol_id` | `Optional[List[str]]` | Protocol ID (DOI for protocols.io) |
 
 
 ### PerformanceMetrics

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/docs/source/aind_data_schema_models/harp_types.md

@@ -10,18 +10,22 @@ Harp device types
 |------|------|------|
 | `ANALOGINPUT` | `AnalogInput` | `1236` |
 | `ARCHIMEDES` | `Archimedes` | `1136` |
+| `AUDIOSWITCH` | `AudioSwitch` | `1248` |
 | `BEHAVIOR` | `Behavior` | `1216` |
 | `CAMERACONTROLLER` | `CameraController` | `1168` |
 | `CAMERACONTROLLERGEN2` | `CameraControllerGen2` | `1170` |
 | `CLOCKSYNCHRONIZER` | `ClockSynchronizer` | `1152` |
+| `CURRENTDRIVER` | `CurrentDriver` | `1282` |
 | `CUTTLEFISH` | `cuTTLefish` | `1403` |
 | `CUTTLEFISHFIP` | `cuTTLefishFip` | `1407` |
+| `DELUXDRIVER` | `deLuxDriver` | `1410` |
 | `DRIVER12VOLTS` | `Driver12Volts` | `1072` |
 | `ENVIRONMENTSENSOR` | `EnvironmentSensor` | `1405` |
 | `FLYPAD` | `FlyPad` | `1200` |
 | `HOBGOBLIN` | `Hobgoblin` | `123` |
 | `IBL_BEHAVIOR_CONTROL` | `Ibl_behavior_control` | `2080` |
 | `INPUTEXPANDER` | `InputExpander` | `1106` |
+| `LASERDRIVERCONTROLLER` | `LaserDriverController` | `1298` |
 | `LEDCONTROLLER` | `LedController` | `1088` |
 | `LICKETYSPLIT` | `LicketySplit` | `1400` |
 | `LOADCELLS` | `LoadCells` | `1232` |
@@ -33,7 +37,7 @@ Harp device types
 | `POKE` | `Poke` | `1024` |
 | `PYCONTROLADAPTER` | `PyControlAdapter` | `1184` |
 | `RFIDREADER` | `RfidReader` | `2094` |
-| `RGBARRAY` | `RgbArray` | `1248` |
+| `RGBARRAY` | `RgbArray` | `1264` |
 | `SIMPLEANALOGGENERATOR` | `SimpleAnalogGenerator` | `1121` |
 | `SNIFFDETECTOR` | `SniffDetector` | `1401` |
 | `SOUNDCARD` | `SoundCard` | `1280` |

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/docs/source/aind_data_schema_models/organizations.md

@@ -22,6 +22,7 @@ Organization
 | `ASUS` | `None` | `ASUS` | `Research Organization Registry (ROR)` | `00bxkz165` |
 | `BASLER` | `None` | `Basler` | `None` | `None` |
 | `BCM` | `BCM` | `Baylor College of Medicine` | `Research Organization Registry (ROR)` | `02pttbw34` |
+| `BROADCOM` | `None` | `Broadcom` | `Research Organization Registry (ROR)` | `035gt5s03` |
 | `BRUKER` | `None` | `Bruker` | `Research Organization Registry (ROR)` | `04r739x86` |
 | `BU` | `BU` | `Boston University` | `Research Organization Registry (ROR)` | `05qwgg493` |
 | `CAJAL` | `Cajal` | `Cajal Neuroscience` | `Research Organization Registry (ROR)` | `05pdc0q70` |
@@ -47,6 +48,7 @@ Organization
 | `EDMUND_OPTICS` | `None` | `Edmund Optics` | `Research Organization Registry (ROR)` | `01j1gwp17` |
 | `EMORY` | `Emory` | `Emory University` | `Research Organization Registry (ROR)` | `03czfpz43` |
 | `EURESYS` | `None` | `Euresys` | `None` | `None` |
+| `EXCELITAS_TECHNOLOGIES` | `None` | `Excelitas Technologies` | `Research Organization Registry (ROR)` | `01tpbbf75` |
 | `FILTER_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `FLIR` | `FLIR` | `Teledyne FLIR` | `Research Organization Registry (ROR)` | `01j1gwp17` |
 | `FUJINON` | `None` | `Fujinon` | `None` | `None` |
@@ -66,6 +68,7 @@ Organization
 | `JENOPTIK` | `None` | `Jenoptik` | `Research Organization Registry (ROR)` | `05g7t5c49` |
 | `JHU` | `JHU` | `Johns Hopkins University` | `Research Organization Registry (ROR)` | `00za53h95` |
 | `JULABO` | `None` | `Julabo` | `None` | `None` |
+| `KENT_SCIENTIFIC_CORPORATION` | `None` | `Kent Scientific Corporation` | `Research Organization Registry (ROR)` | `03xkj6a08` |
 | `KOWA` | `None` | `Kowa` | `Research Organization Registry (ROR)` | `03zbwg482` |
 | `LASER_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `LASOS` | `LASOS` | `LASOS Lasertechnik` | `None` | `None` |
@@ -86,6 +89,7 @@ Organization
 | `MIT_BCS` | `MIT-BCS` | `MIT Department of Brain and Cognitive Sciences` | `None` | `None` |
 | `MJFF` | `MJFF` | `Michael J. Fox Foundation for Parkinson's Research` | `Research Organization Registry (ROR)` | `03arq3225` |
 | `MKS_NEWPORT` | `None` | `MKS Newport` | `Research Organization Registry (ROR)` | `00k17f049` |
+| `MOLECULAR_INSTRUMENTS` | `None` | `Molecular Instruments` | `None` | `None` |
 | `MONITOR_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `MPI` | `MPI` | `MPI` | `None` | `None` |
 | `NATIONAL_INSTRUMENTS` | `None` | `National Instruments` | `Research Organization Registry (ROR)` | `026exqw73` |
@@ -103,6 +107,7 @@ Organization
 | `OLYMPUS` | `None` | `Olympus` | `Research Organization Registry (ROR)` | `02vcdte90` |
 | `OPTOTUNE` | `None` | `Optotune` | `None` | `None` |
 | `OTHER` | `None` | `Other` | `None` | `None` |
+| `OXFORD_INSTRUMENTS` | `None` | `Oxford Instruments` | `Research Organization Registry (ROR)` | `01age2z78` |
 | `OXXIUS` | `None` | `Oxxius` | `None` | `None` |
 | `PLACID_INDUSTRIES` | `None` | `Placid Industries` | `None` | `None` |
 | `PRIZMATIX` | `None` | `Prizmatix` | `None` | `None` |
@@ -111,6 +116,7 @@ Organization
 | `RESEARCH_INSTITUTIONS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `SAME_SKY` | `None` | `Same Sky` | `None` | `None` |
 | `SCHNEIDER_KREUZNACH` | `None` | `Schneider-Kreuznach` | `None` | `None` |
+| `SCIENTIFICA` | `None` | `Scientifica` | `Research Organization Registry (ROR)` | `00z72df47` |
 | `SECOND_ORDER_EFFECTS` | `None` | `Second Order Effects` | `None` | `None` |
 | `SEMROCK` | `None` | `Semrock` | `None` | `None` |
 | `SICGEN` | `None` | `SICGEN` | `None` | `None` |
@@ -136,5 +142,6 @@ Organization
 | `UPENN` | `UPENN` | `University of Pennsylvania` | `Research Organization Registry (ROR)` | `00b30xv10` |
 | `VIEWORKS` | `None` | `Vieworks` | `None` | `None` |
 | `VORTRAN` | `None` | `Vortran` | `None` | `None` |
+| `WPI` | `WPI` | `World Precision Intstruments` | `Research Organization Registry (ROR)` | `03st5df34` |
 
 

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/docs/source/aind_data_schema_models/process_names.md

@@ -17,6 +17,7 @@ Process names
 | `EPHYS_VISUALIZATION` | `Ephys visualization` |
 | `FIDUCIAL_SEGMENTATION` | `Fiducial segmentation` |
 | `FILE_FORMAT_CONVERSION` | `File format conversion` |
+| `FIX_COLOR_RANGE` | `Fix color range` |
 | `FLUORESCENCE_EVENT_DETECTION` | `Fluorescence event detection` |
 | `IMAGE_ATLAS_ALIGNMENT` | `Image atlas alignment` |
 | `IMAGE_BACKGROUND_SUBTRACTION` | `Image background subtraction` |
@@ -28,6 +29,7 @@ Process names
 | `IMAGE_FLAT_FIELD_CORRECTION` | `Image flat-field correction` |
 | `IMAGE_IMPORTING` | `Image importing` |
 | `IMAGE_MIP_VISUALIZATION` | `Image mip visualization` |
+| `IMAGE_MULTISCALING` | `Image multiscaling` |
 | `IMAGE_RADIAL_CORRECTION` | `Image radial correction` |
 | `IMAGE_SPOT_DETECTION` | `Image spot detection` |
 | `IMAGE_SPOT_SPECTRAL_UNMIXING` | `Image spot spectral unmixing` |
@@ -35,6 +37,7 @@ Process names
 | `IMAGE_TILE_ALIGNMENT` | `Image tile alignment` |
 | `IMAGE_TILE_FUSING` | `Image tile fusing` |
 | `IMAGE_TILE_PROJECTION` | `Image tile projection` |
+| `MANUAL_CURATION` | `Manual curation` |
 | `MODEL_EVALUATION` | `Model evaluation` |
 | `MODEL_TRAINING` | `Model training` |
 | `NEURON_SKELETON_PROCESSING` | `Neuron skeleton processing` |

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/docs/source/aind_data_schema_models/specimen_procedure_types.md

@@ -25,6 +25,5 @@ Specimen procedures
 | `SOAK` | `Soak` |
 | `STORAGE` | `Storage` |
 | `STRIPPING` | `Stripping` |
-| `TAMOXIFEN_INDUCTION` | `Tamoxifen induction` |
 
 

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/docs/source/components/configs.md

@@ -476,7 +476,6 @@ Configuration of a SLAP2 imaging plane (all imaging ROIs of a specific acquisiti
 | `specimen_id` | `Optional[str]` | Specimen ID (Unique index identifying the cell being imaged: <subject_id>_###) |
 | `fov_index` | `Optional[int]` | Field of view index (For FOVs that are imaged multiple times, assign a shared index to each instance of the FOV) |
 | `structure_types` | Optional[List[[NeuronStructure](#neuronstructure)]] | Structure type  |
-| `target_name` | `Optional[str]` | Name of imaged target  |
 | `y_dilations` | `List[int]` | Unique Y dilations  |
 | `y_dilations_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Dilation unit  |
 | `frame_rates` | `List[float]` | Unique frame rates  |

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/docs/source/components/devices.md

@@ -57,7 +57,7 @@ Camera Detector
 | Field | Type | Title (Description) |
 |-------|------|-------------|
 | `detector_type` | [DetectorType](../aind_data_schema_models/devices.md#detectortype) |   |
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `data_interface` | [DataInterface](../aind_data_schema_models/devices.md#datainterface) | Data interface  |
 | `cooling` | [Cooling](../aind_data_schema_models/devices.md#cooling) | Cooling  |
 | `frame_rate` | `Optional[decimal.Decimal]` | Frame rate (Hz) (Frame rate being used) |
@@ -192,7 +192,7 @@ Data acquisition device containing multiple I/O channels
 | Field | Type | Title (Description) |
 |-------|------|-------------|
 | `data_interface` | [DataInterface](../aind_data_schema_models/devices.md#datainterface) | Type of connection to PC  |
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `channels` | List[[DAQChannel](#daqchannel)] | DAQ channels  |
 | `firmware_version` | `Optional[str]` | Firmware version  |
 | `hardware_version` | `Optional[str]` | Hardware version  |
@@ -210,7 +210,7 @@ Description of a generic detector
 | Field | Type | Title (Description) |
 |-------|------|-------------|
 | `detector_type` | [DetectorType](../aind_data_schema_models/devices.md#detectortype) | Detector Type  |
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `data_interface` | [DataInterface](../aind_data_schema_models/devices.md#datainterface) | Data interface  |
 | `cooling` | [Cooling](../aind_data_schema_models/devices.md#cooling) | Cooling  |
 | `frame_rate` | `Optional[decimal.Decimal]` | Frame rate (Hz) (Frame rate being used) |
@@ -417,7 +417,7 @@ Filter used in a light path
 | Field | Type | Title (Description) |
 |-------|------|-------------|
 | `filter_type` | [FilterType](../aind_data_schema_models/devices.md#filtertype) | Type of filter  |
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `cut_off_wavelength` | `Optional[int]` | Cut-off wavelength (nm)  |
 | `cut_on_wavelength` | `Optional[int]` | Cut-on wavelength (nm)  |
 | `center_wavelength` | `int or List[int] or NoneType` | Center wavelength (nm) (Single wavelength or list of wavelengths for MULTIBAND or MULTI_NOTCH filters) |
@@ -435,7 +435,7 @@ DAQ that uses the Harp protocol for synchronization and data transmission
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `harp_device_type` | [HarpDeviceType](../aind_data_schema_models/harp_types.md#harpdevicetype) | Type of Harp device  |
 | `core_version` | `Optional[str]` | Core version  |
 | `tag_version` | `Optional[str]` | Tag version  |
@@ -476,7 +476,7 @@ Laser module with a specific wavelength (may be a sub-component of a larger asse
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `wavelength` | `int` | Wavelength (nm)  |
 | `wavelength_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Wavelength unit  |
 | `coupling` | Optional[[Coupling](../aind_data_schema_models/devices.md#coupling)] | Coupling  |
@@ -508,7 +508,7 @@ Lens
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `name` | `str` | Device name  |
 | `serial_number` | `Optional[str]` | Serial number  |
 | `model` | `Optional[str]` | Model  |
@@ -564,7 +564,7 @@ Description of a Light Emitting Diode (LED) device
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `wavelength` | `int` | Wavelength (nm)  |
 | `wavelength_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Wavelength unit  |
 | `bandwidth` | `Optional[int]` | Bandwidth (FWHM)  |
@@ -582,7 +582,7 @@ Manipulator used on a dome module
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `name` | `str` | Device name  |
 | `serial_number` | `Optional[str]` | Serial number  |
 | `model` | `Optional[str]` | Model  |
@@ -610,7 +610,7 @@ Description of visual display for visual stimuli
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `refresh_rate` | `int` | Refresh rate (Hz)  |
 | `width` | `int` | Width (pixels)  |
 | `height` | `int` | Height (pixels)  |
@@ -732,7 +732,7 @@ Description of an olfactometer for odor stimuli
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `harp_device_type` | [HarpDeviceType](../aind_data_schema_models/harp_types.md#harpdevicetype) | Type of Harp device  |
 | `channels` | List[[OlfactometerChannel](#olfactometerchannel)] |   |
 | `core_version` | `Optional[str]` | Core version  |
@@ -888,7 +888,7 @@ Description of a speaker for auditory stimuli
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `name` | `str` | Device name  |
 | `serial_number` | `Optional[str]` | Serial number  |
 | `model` | `Optional[str]` | Model  |

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/docs/source/components/identifiers.md

@@ -11,6 +11,7 @@ Code or script identifier
 | `url` | `str` | Code URL (URL to code repository) |
 | `name` | `Optional[str]` | Name  |
 | `version` | `Optional[str]` | Code version  |
+| `commit_hash` | `Optional[str]` | Commit hash (Commit hash of the code.) |
 | `container` | Optional[[Container](#container)] | Container  |
 | `run_script` | `Optional[pathlib.Path]` | Run script (Path to run script) |
 | `language` | `Optional[str]` | Programming language (Programming language used) |
@@ -49,7 +50,8 @@ Description of a single data asset
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `url` | `str` | Asset location (URL pointing to the data asset) |
+| `name` | `Optional[str]` | Asset name (Name of the data asset) |
+| `url` | `Optional[str]` | Asset location (URL pointing to the data asset) |
 
 
 ### Database

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/docs/source/components/measurements.md

@@ -10,7 +10,6 @@ Generic calibration class
 |-------|------|-------------|
 | `calibration_date` | `datetime (timezone-aware)` | Date and time of calibration  |
 | `description` | `str` | Description (Brief description of what is being calibrated) |
-| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `measured_at` | `Optional[str]` | Measurement location  |
 | `input` | `List[float or str]` | Inputs (Calibration input) |
 | `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) or {TorqueUnit} | Input unit  |
@@ -19,6 +18,7 @@ Generic calibration class
 | `output_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) or {TorqueUnit} | Output unit  |
 | `fit` | Optional[[CalibrationFit](#calibrationfit)] | Fit (Fit equation for the calibration data used during data acquisition) |
 | `notes` | `Optional[str]` | Notes  |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `device_name` | `str` | Device name (Must match a device defined in the instrument.json) |
 
 
@@ -51,9 +51,9 @@ Generic maintenance class
 |-------|------|-------------|
 | `maintenance_date` | `datetime (timezone-aware)` | Date and time of maintenance  |
 | `description` | `str` | Description (Description on maintenance procedure) |
-| `protocol_id` | `Optional[str]` | Protocol ID  |
 | `reagents` | Optional[List[[Reagent](reagent.md#reagent)]] | Reagents  |
 | `notes` | `Optional[str]` | Notes  |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `device_name` | `str` | Device name (Must match a device defined in the instrument.json) |
 
 
@@ -69,11 +69,11 @@ Calibration of a device that outputs power based on input strength
 | `output_unit` | [PowerUnit](../aind_data_schema_models/units.md#powerunit) | Output unit  |
 | `description` | `"Power measured for various power or percentage input strengths"` |   |
 | `calibration_date` | `datetime (timezone-aware)` | Date and time of calibration  |
-| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `measured_at` | `Optional[str]` | Measurement location  |
 | `repeats` | `Optional[int]` | Number of repeats (If each input was repeated multiple times, provide the number of repeats) |
 | `fit` | Optional[[CalibrationFit](#calibrationfit)] | Fit (Fit equation for the calibration data used during data acquisition) |
 | `notes` | `Optional[str]` | Notes  |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `device_name` | `str` | Device name (Must match a device defined in the instrument.json) |
 
 
@@ -90,10 +90,10 @@ Calibration of a liquid delivery device based on solenoid/valve opening times
 | `output_unit` | [VolumeUnit](../aind_data_schema_models/units.md#volumeunit) | Output unit  |
 | `description` | `"Volume measured for various solenoid opening times"` |   |
 | `calibration_date` | `datetime (timezone-aware)` | Date and time of calibration  |
-| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `measured_at` | `Optional[str]` | Measurement location  |
 | `fit` | Optional[[CalibrationFit](#calibrationfit)] | Fit (Fit equation for the calibration data used during data acquisition) |
 | `notes` | `Optional[str]` | Notes  |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `device_name` | `str` | Device name (Must match a device defined in the instrument.json) |
 
 

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/docs/source/components/reagent.md

@@ -115,3 +115,13 @@ Description of a small molecule probe
 | `mass_unit` | [MassUnit](../aind_data_schema_models/units.md#massunit) | Mass unit  |
 
 
+### Solution
+
+Description of a solution made in house. Should match a solution named in protocol.
+
+| Field | Type | Title (Description) |
+|-------|------|-------------|
+| `name` | `str` | Name  |
+| `lot_number` | `Optional[str]` | Lot number  |
+
+

{aind_data_schema-2.6.0 → aind_data_schema-2.8.0}/docs/source/components/specimen_procedures.md

@@ -41,7 +41,7 @@ Description of a single planar section of brain tissue
 | `thickness` | `Optional[float]` | Slice thickness  |
 | `thickness_unit` | Optional[[SizeUnit](../aind_data_schema_models/units.md#sizeunit)] | Slice thickness unit  |
 | `partial_slice` | Optional[List[[AnatomicalRelative](../aind_data_schema_models/coordinates.md#anatomicalrelative)]] | Partial slice (If sectioning does not include the entire slice, indicate which part of the slice is retained.) |
-| `output_specimen_id` | `str` | Specimen ID  |
+| `output_specimen_id` | `str` | Specimen ID (Output IDs should generally follow the format {input_specimen_id}_###) |
 | `targeted_structure` | Optional[[BrainAtlas](../aind_data_schema_models/brain_atlas.md#ccfv3)] | Targeted structure  |
 | `includes_surrounding_tissue` | `Optional[bool]` | Includes surrounding tissue (Whether the section includes additional tissue surrounding the targeted structure.) |
 
@@ -63,7 +63,7 @@ Description of a single section of brain tissue. Slices should use PlanarSection
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `output_specimen_id` | `str` | Specimen ID  |
+| `output_specimen_id` | `str` | Specimen ID (Output IDs should generally follow the format {input_specimen_id}_###) |
 | `targeted_structure` | Optional[[BrainAtlas](../aind_data_schema_models/brain_atlas.md#ccfv3)] | Targeted structure  |
 | `includes_surrounding_tissue` | `Optional[bool]` | Includes surrounding tissue (Whether the section includes additional tissue surrounding the targeted structure.) |
 | <del>`coordinate_system_name`</del> | `Optional[str]` | **[DEPRECATED]** Use PlanarSection instead. Coordinate system name  |
@@ -106,9 +106,9 @@ Description of surgical or other procedure performed on a specimen
 | `start_date` | `datetime.date` | Start date  |
 | `end_date` | `datetime.date` | End date  |
 | `experimenters` | `List[str]` | experimenter(s)  |
-| `protocol_id` | `Optional[List[str]]` | Protocol ID (DOI for protocols.io) |
 | `protocol_parameters` | `Optional[Dict[str, str]]` | Protocol parameters (Parameters defined in the protocol and their value during this procedure) |
-| `procedure_details` | List[[HCRSeries](#hcrseries) or [FluorescentStain](reagent.md#fluorescentstain) or [Sectioning](#sectioning) or [PlanarSectioning](#planarsectioning) or [ProbeReagent](reagent.md#probereagent) or [Reagent](reagent.md#reagent) or [GeneProbeSet](reagent.md#geneprobeset)] | Procedure details (Details of the procedures, including reagents and sectioning information.) |
+| `procedure_details` | List[[HCRSeries](#hcrseries) or [FluorescentStain](reagent.md#fluorescentstain) or [Sectioning](#sectioning) or [PlanarSectioning](#planarsectioning) or [ProbeReagent](reagent.md#probereagent) or [Reagent](reagent.md#reagent) or [GeneProbeSet](reagent.md#geneprobeset) or [Solution](reagent.md#solution)] | Procedure details (Details of the procedures, including reagents and sectioning information.) |
 | `notes` | `Optional[str]` | Notes  |
+| `protocol_id` | `Optional[List[str]]` | Protocol ID (DOI for protocols.io) |