Merge pull request #580 from AllenNeuralDynamics/feat_smallthings

saskiad · web-flow · commit b293f0b1440b · 2023-11-02T10:06:05.000-07:00
Feat smallthings
diff --git a/examples/bergamo_ophys_session.json b/examples/bergamo_ophys_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/session.py",
-   "schema_version": "0.0.3",
+   "schema_version": "0.0.4",
    "experimenter_full_name": [
       "John Doe"
    ],
@@ -122,8 +122,8 @@
             "other_parameters": null,
             "notes": null
          },
-         "stimulus_start_time": "07:00:00",
-         "stimulus_end_time": "07:00:00"
+         "stimulus_start_time": "2022-07-12T07:00:00",
+         "stimulus_end_time": "2022-07-12T07:00:00"
       }
    ],
    "reward_delivery": null,
diff --git a/examples/bergamo_ophys_session.py b/examples/bergamo_ophys_session.py
@@ -7,7 +7,6 @@
 from aind_data_schema.stimulus import PhotoStimulation, PhotoStimulationGroup, StimulusEpoch
 
 t = datetime.datetime(2022, 7, 12, 7, 00, 00)
-t2 = datetime.time(7, 00, 00)
 
 s = Session(
     experimenter_full_name=["John Doe"],
@@ -83,8 +82,8 @@
                 ],
                 inter_trial_interval=10,
             ),
-            stimulus_start_time=t2,
-            stimulus_end_time=t2,
+            stimulus_start_time=t,
+            stimulus_end_time=t,
         )
     ],
 )
diff --git a/examples/ephys_rig.json b/examples/ephys_rig.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/rig.py",
-   "schema_version": "0.1.3",
+   "schema_version": "0.1.4",
    "rig_id": "323_EPHYS1",
    "modification_date": "2023-10-03",
    "modalities": [
diff --git a/examples/ephys_session.json b/examples/ephys_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/session.py",
-   "schema_version": "0.0.3",
+   "schema_version": "0.0.4",
    "experimenter_full_name": [
       "Jane Doe"
    ],
diff --git a/examples/fip_ophys_rig.json b/examples/fip_ophys_rig.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/rig.py",
-   "schema_version": "0.1.3",
+   "schema_version": "0.1.4",
    "rig_id": "428_FIP1_2",
    "modification_date": "2023-10-03",
    "modalities": [
diff --git a/examples/ophys_session.json b/examples/ophys_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/session.py",
-   "schema_version": "0.0.3",
+   "schema_version": "0.0.4",
    "experimenter_full_name": [
       "John Doe"
    ],
diff --git a/src/aind_data_schema/behavior/behavior_rig.py b/src/aind_data_schema/behavior/behavior_rig.py
@@ -24,9 +24,9 @@
 
 
 class BehaviorRig(AindCoreModel):
-    """Description of an behavior rig. This is being deprecated after 2023-11-01."""
+    """Description of an behavior rig. This is being deprecated after 2023-11-01. Use Rig class instead."""
 
-    schema_version: str = Field("0.1.17", description="schema version", title="Version", const=True)
+    schema_version: str = Field("0.1.18", description="schema version", title="Version", const=True)
 
     rig_id: str = Field(..., description="room_stim apparatus_version", title="Rig ID")
     mouse_platform: Annotated[
diff --git a/src/aind_data_schema/behavior/behavior_session.py b/src/aind_data_schema/behavior/behavior_session.py
@@ -52,10 +52,10 @@ def validate_other(cls, v):
 
 
 class BehaviorSession(AindCoreModel):
-    """Description of a behavior session. This is being deprecated after 2023-11-01."""
+    """Description of a behavior session. This is being deprecated after 2023-11-01. Use Session class instead."""
 
     schema_version: str = Field(
-        "0.0.10",
+        "0.0.11",
         description="Schema version",
         title="Schema Version",
         const=True,
diff --git a/src/aind_data_schema/device.py b/src/aind_data_schema/device.py
@@ -269,6 +269,7 @@ class CameraTarget(Enum):
     BOTTOM = "Bottom"
     EYE = "Eye"
     FACE_BOTTOM = "Face bottom"
+    FACE_FORWARD = "Face forward"
     FACE_SIDE = "Face side"
     SIDE = "Side"
     TONGUE = "Tongue"
diff --git a/src/aind_data_schema/ephys/ephys_rig.py b/src/aind_data_schema/ephys/ephys_rig.py
@@ -109,9 +109,9 @@ class EphysAssembly(AindModel):
 
 
 class EphysRig(AindCoreModel):
-    """Description of an ephys rig. This is being deprecated after 2023-11-01."""
+    """Description of an ephys rig. This is being deprecated after 2023-11-01. Use Rig class instead."""
 
-    schema_version: str = Field("0.7.16", description="schema version", title="Version", const=True)
+    schema_version: str = Field("0.7.17", description="schema version", title="Version", const=True)
     rig_id: str = Field(..., description="room_stim apparatus_version", title="Rig ID")
     ephys_assemblies: Optional[List[EphysAssembly]] = Field(None, title="Ephys probes", unique_items=True)
     stick_microscopes: Optional[List[StickMicroscopeAssembly]] = Field(None, title="Stick microscopes")
diff --git a/src/aind_data_schema/ephys/ephys_session.py b/src/aind_data_schema/ephys/ephys_session.py
@@ -126,9 +126,10 @@ class Stream(AindModel):
 
 
 class EphysSession(AindCoreModel):
-    """Description of an ephys recording session. This is being deprecated after 2023-11-01."""
+    """Description of an ephys recording session. This is being deprecated after 2023-11-01.
+    Use Session class instead."""
 
-    schema_version: str = Field("0.4.12", description="schema version", title="Version", const=True)
+    schema_version: str = Field("0.4.13", description="schema version", title="Version", const=True)
     experimenter_full_name: List[str] = Field(
         ...,
         description="First and last name of the experimenter(s).",
diff --git a/src/aind_data_schema/metadata.py b/src/aind_data_schema/metadata.py
@@ -37,7 +37,7 @@ class Metadata(AindCoreModel):
     """The records in the Data Asset Collection needs to contain certain fields
     to easily query and index the data."""
 
-    schema_version: str = Field("0.0.3", description="schema version", title="Version", const=True)
+    schema_version: str = Field("0.0.4", description="schema version", title="Version", const=True)
 
     id: UUID = Field(
         default_factory=uuid4,
diff --git a/src/aind_data_schema/ophys/ophys_rig.py b/src/aind_data_schema/ophys/ophys_rig.py
@@ -86,10 +86,10 @@ class Patch(Device):
 
 
 class OphysRig(AindCoreModel):
-    """Description of an optical physiology rig. This is being deprecated after 2023-11-01."""
+    """Description of an optical physiology rig. This is being deprecated after 2023-11-01. Use Rig class instead."""
 
     schema_version: str = Field(
-        "0.7.6",
+        "0.7.7",
         description="schema version",
         title="Schema Version",
         const=True,
diff --git a/src/aind_data_schema/ophys/ophys_session.py b/src/aind_data_schema/ophys/ophys_session.py
@@ -85,10 +85,10 @@ class Camera(AindModel):
 
 
 class OphysSession(AindCoreModel):
-    """Description of an ophys session"""
+    """Description of an ophys session. This is being deprecated after 2023-11-01. Use Session class instead."""
 
     schema_version: str = Field(
-        "0.2.11",
+        "0.2.12",
         description="schema version",
         title="Schema Version",
         const=True,
diff --git a/src/aind_data_schema/rig.py b/src/aind_data_schema/rig.py
@@ -45,7 +45,7 @@
 class Rig(AindCoreModel):
     """Description of a rig"""
 
-    schema_version: str = Field("0.1.3", description="schema version", title="Version", const=True)
+    schema_version: str = Field("0.1.4", description="schema version", title="Version", const=True)
     rig_id: str = Field(..., description="room_stim apparatus_version", title="Rig ID")
     modification_date: date = Field(..., title="Date of modification")
     modalities: List[Modality] = Field(..., title="Modalities", unique_items=True)
diff --git a/src/aind_data_schema/session.py b/src/aind_data_schema/session.py
@@ -267,7 +267,7 @@ class Session(AindCoreModel):
     """Description of a physiology and/or behavior session"""
 
     schema_version: str = Field(
-        "0.0.3",
+        "0.0.4",
         description="schema version",
         title="Schema Version",
         const=True,
diff --git a/src/aind_data_schema/stimulus.py b/src/aind_data_schema/stimulus.py
@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from datetime import time
+from datetime import datetime
 from decimal import Decimal
 from enum import Enum
 from typing import Any, Dict, List, Optional, Union
@@ -160,12 +160,12 @@ class StimulusEpoch(AindModel):
         Union[OptoStimulation, VisualStimulation, BehaviorStimulation, PhotoStimulation],
         Field(..., title="Stimulus", discriminator="stimulus_type"),
     ]
-    stimulus_start_time: time = Field(
+    stimulus_start_time: datetime = Field(
         ...,
         title="Stimulus start time",
         description="When a specific stimulus begins. This might be the same as the session start time.",
     )
-    stimulus_end_time: time = Field(
+    stimulus_end_time: datetime = Field(
         ...,
         title="Stimulus end time",
         description="When a specific stimulus ends. This might be the same as the session end time.",
diff --git a/tests/test_behavior.py b/tests/test_behavior.py
@@ -66,8 +66,8 @@ def test_constructors(self):
                         trials_finished=343,
                         trials_rewarded=146,
                     ),
-                    stimulus_start_time=now.time(),
-                    stimulus_end_time=now.time(),
+                    stimulus_start_time=now,
+                    stimulus_end_time=now,
                 )
             ],
         )

Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/rig.py",`
`3`		`- "schema_version": "0.1.3",`
	`3`	`+ "schema_version": "0.1.4",`
`4`	`4`	`"rig_id": "323_EPHYS1",`
`5`	`5`	`"modification_date": "2023-10-03",`
`6`	`6`	`"modalities": [`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/session.py",`
`3`		`- "schema_version": "0.0.3",`
	`3`	`+ "schema_version": "0.0.4",`
`4`	`4`	`"experimenter_full_name": [`
`5`	`5`	`"Jane Doe"`
`6`	`6`	`],`