Merge pull request #1737 from AllenNeuralDynamics/release-v2.5.0

Release v2.5.0

Author: dbirman

.github/workflows/update_docs.yml

@@ -62,9 +62,6 @@ jobs:
         run: |
           sudo apt install graphviz libgraphviz-dev -y
           python -m pip install -e .[dev] -e .[docs] --no-cache-dir
-      - name: Generate new rst files
-        run: |
-          sphinx-apidoc -o docs/source/ src
       - name: Commit changes
         uses: EndBug/add-and-commit@v9
         with:

CONTRIBUTING.md

@@ -179,6 +179,6 @@ When you are ready to open a pull request, please link any relevant issues and r
 - Manually increment the major/minor/patch versions of the core files as needed
 - Push the branch and open a PR into main
 - After this push, any last minute changes to the release-vX.Y.Z will have to done to via a PR
-- After review, use a merge commit to merge into main
-- Open a PR from main back into dev so they're synced again
+- After review, use a **merge commit** to merge into main, DO NOT SQUASH INTO MAIN
+- Open a PR from main back into dev so they're synced again, bypass the rules to use a **merge commit**, DO NOT SQUASH MAIN INTO DEV
 - Create a Github release with the corresponding tag, modify the auto-generated release notes to focus on the major changes that occurred

docs/source/acquisition.md

@@ -79,7 +79,8 @@ while the StimulusEpoch represents all stimuli being presented.
 |-------|------|-------------|
 | `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) |
-| `acquisition_start_time` | `datetime (timezone-aware)` | Acquisition start time  |
+| `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` | `Optional[pydantic_extra_types.timezone_name.TimeZoneName]` | Acquisition start timezone (Automatically populated by a validator based on acquisition_start_time.) |
 | `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) |
@@ -108,7 +109,7 @@ Details about the subject during an acquisition
 | `animal_weight_post` | `Optional[decimal.Decimal]` | Animal weight (g) (Animal weight after procedure) |
 | `weight_unit` | [MassUnit](aind_data_schema_models/units.md#massunit) | Weight unit  |
 | `anaesthesia` | Optional[[Anaesthetic](components/surgery_procedures.md#anaesthetic)] | Anaesthesia (Anaesthesia present during entire acquisition, use Manipulation for partial anaesthesia) |
-| `mouse_platform_name` | `str` | Mouse platform  |
+| `mouse_platform_name` | `str` | Mouse platform (The surface that the mouse is on during the acquisition) |
 | `reward_consumed_total` | `Optional[decimal.Decimal]` | Total reward consumed (mL)  |
 | `reward_consumed_unit` | Optional[[VolumeUnit](aind_data_schema_models/units.md#volumeunit)] | Reward consumed unit  |
 
@@ -126,7 +127,7 @@ same time.
 | `code` | Optional[List[[Code](components/identifiers.md#code)]] | Acquisition code  |
 | `notes` | `Optional[str]` | Notes  |
 | `active_devices` | `List[str]` | Active devices (Device names must match devices in the Instrument) |
-| `configurations` | List[[LightEmittingDiodeConfig](components/configs.md#lightemittingdiodeconfig) or [LaserConfig](components/configs.md#laserconfig) or [ManipulatorConfig](components/configs.md#manipulatorconfig) or [DetectorConfig](components/configs.md#detectorconfig) or [PatchCordConfig](components/configs.md#patchcordconfig) or [FiberAssemblyConfig](components/configs.md#fiberassemblyconfig) or [MRIScan](components/configs.md#mriscan) or [LickSpoutConfig](components/configs.md#lickspoutconfig) or [AirPuffConfig](components/configs.md#airpuffconfig) or [ImagingConfig](components/configs.md#imagingconfig) or [SlapPlane](components/configs.md#slapplane) or [SampleChamberConfig](components/configs.md#samplechamberconfig) or [ProbeConfig](components/configs.md#probeconfig) or [EphysAssemblyConfig](components/configs.md#ephysassemblyconfig) or [CatheterConfig](components/configs.md#catheterconfig)] | Device configurations (Configurations are parameters controlling active devices during this stream) |
+| `configurations` | List[[LightEmittingDiodeConfig](components/configs.md#lightemittingdiodeconfig) or [LaserConfig](components/configs.md#laserconfig) or [ManipulatorConfig](components/configs.md#manipulatorconfig) or [DetectorConfig](components/configs.md#detectorconfig) or [PatchCordConfig](components/configs.md#patchcordconfig) or [FiberAssemblyConfig](components/configs.md#fiberassemblyconfig) or [MISCameraConfig](components/configs.md#miscameraconfig) or [MRIScan](components/configs.md#mriscan) or [LickSpoutConfig](components/configs.md#lickspoutconfig) or [AirPuffConfig](components/configs.md#airpuffconfig) or [ImagingConfig](components/configs.md#imagingconfig) or [SlapPlane](components/configs.md#slapplane) or [SampleChamberConfig](components/configs.md#samplechamberconfig) or [ProbeConfig](components/configs.md#probeconfig) or [EphysAssemblyConfig](components/configs.md#ephysassemblyconfig) or [CatheterConfig](components/configs.md#catheterconfig)] | Device configurations (Configurations are parameters controlling active devices during this stream) |
 | `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)) |
 
 
@@ -149,7 +150,7 @@ Summary of a StimulusEpoch
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `output_parameters` | `dict` | Additional metrics  |
+| `output_parameters` | `Optional[dict]` | Additional metrics  |
 | `reward_consumed_during_epoch` | `Optional[decimal.Decimal]` | Reward consumed during training (uL)  |
 | `reward_consumed_unit` | Optional[[VolumeUnit](aind_data_schema_models/units.md#volumeunit)] | Reward consumed unit  |
 | `trials_total` | `Optional[int]` | Total trials  |

docs/source/aind_data_schema.components.rst

@@ -64,13 +64,14 @@ Origin positions for coordinate systems
 | `ORIGIN` | `Origin` |
 | `BREGMA` | `Bregma` |
 | `LAMBDA` | `Lambda` |
-| `C1` | `C1` |
-| `C2` | `C2` |
-| `C3` | `C3` |
-| `C4` | `C4` |
-| `C5` | `C5` |
-| `C6` | `C6` |
-| `C7` | `C7` |
+| `BETWEEN_C1_C2` | `Between_C1-C2` |
+| `BETWEEN_C2_C3` | `Between_C2-C3` |
+| `BETWEEN_C3_C4` | `Between_C3-C4` |
+| `BETWEEN_C4_C5` | `Between_C4-C5` |
+| `BETWEEN_C6_C7` | `Between_C6-C7` |
+| `BETWEEN_C7_C8` | `Between_C7-C8` |
+| `BETWEEN_C8_T1` | `Between_C8-T1` |
+| `BETWEEN_T1_T2` | `Between_T1-T2` |
 | `TIP` | `Tip` |
 | `FRONT_CENTER` | `Front_center` |
 | `ARENA_CENTER` | `Arena_center` |