chore: bump version numbers and re-generate examples

AllenNeuralDynamics · Jan 27, 2025 · f0bb384 · f0bb384
1 parent 7602294
commit f0bb384
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diff --git a/examples/aibs_smartspim_instrument.json b/examples/aibs_smartspim_instrument.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/inst.py",
-   "schema_version": "1.0.5",
+   "schema_version": "2.0.0",
    "instrument_id": "440_SmartSPIM2_20231004",
    "mouse_platform": null,
    "modification_date": "2023-10-04",

diff --git a/examples/aibs_smartspim_procedures.json b/examples/aibs_smartspim_procedures.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",
-   "schema_version": "1.2.6",
+   "schema_version": "2.0.0",
    "subject_id": "651286",
    "subject_procedures": [
       {

diff --git a/examples/aind_smartspim_instrument.json b/examples/aind_smartspim_instrument.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/inst.py",
-   "schema_version": "1.0.5",
+   "schema_version": "2.0.0",
    "instrument_id": "440_SmartSPIM1_20231004",
    "mouse_platform": null,
    "modification_date": "2023-10-04",

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/core/session.py",
-   "schema_version": "1.1.5",
+   "schema_version": "2.0.0",
    "protocol_id": [],
    "experimenters": [
       {

diff --git a/examples/data_description.json b/examples/data_description.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/data_description.py",
-   "schema_version": "1.0.5",
+   "schema_version": "2.0.0",
    "license": "CC-BY-4.0",
    "subject_id": "12345",
    "creation_time": "2022-02-21T16:30:01Z",

diff --git a/examples/ephys_instrument.json b/examples/ephys_instrument.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/inst.py",
-   "schema_version": "1.0.5",
+   "schema_version": "2.0.0",
    "instrument_id": "323_EPHYS1_20231003",
    "mouse_platform": {
       "device_type": "Disc",

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/core/session.py",
-   "schema_version": "1.1.5",
+   "schema_version": "2.0.0",
    "protocol_id": [],
    "experimenters": [
       {

diff --git a/examples/exaspim_acquisition.json b/examples/exaspim_acquisition.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/acquisition.py",
-   "schema_version": "1.0.6",
+   "schema_version": "2.0.0",
    "protocol_id": [],
    "experimenters": [
       {

diff --git a/examples/exaspim_instrument.json b/examples/exaspim_instrument.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/inst.py",
-   "schema_version": "1.0.5",
+   "schema_version": "2.0.0",
    "instrument_id": "440_exaSPIM1_20231004",
    "mouse_platform": null,
    "modification_date": "2023-10-04",

diff --git a/examples/fip_behavior_instrument.json b/examples/fip_behavior_instrument.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/inst.py",
-   "schema_version": "1.0.5",
+   "schema_version": "2.0.0",
    "instrument_id": "447_FIP-Behavior_20000101",
    "mouse_platform": {
       "device_type": "Tube",

diff --git a/examples/fip_ophys_instrument.json b/examples/fip_ophys_instrument.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/inst.py",
-   "schema_version": "1.0.5",
+   "schema_version": "2.0.0",
    "instrument_id": "428_FIP1_20231003",
    "mouse_platform": {
       "device_type": "Disc",

diff --git a/examples/mri_session.json b/examples/mri_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
-   "schema_version": "1.1.5",
+   "schema_version": "2.0.0",
    "protocol_id": [
       "dx.doi.org/10.57824/protocols.io.bh7kl4n6"
    ],

diff --git a/examples/multiplane_ophys_session.json b/examples/multiplane_ophys_session.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
-   "schema_version": "1.1.5",
+   "schema_version": "2.0.0",
    "protocol_id": [],
    "experimenters": [
       {

diff --git a/examples/ophys_procedures.json b/examples/ophys_procedures.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",
-   "schema_version": "1.2.6",
+   "schema_version": "2.0.0",
    "subject_id": "625100",
    "subject_procedures": [
       {

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/core/session.py",
-   "schema_version": "1.1.5",
+   "schema_version": "2.0.0",
    "protocol_id": [],
    "experimenters": [
       {

diff --git a/examples/procedures.json b/examples/procedures.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",
-   "schema_version": "1.2.6",
+   "schema_version": "2.0.0",
    "subject_id": "625100",
    "subject_procedures": [
       {

diff --git a/examples/processing.json b/examples/processing.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/processing.py",
-   "schema_version": "1.1.6",
+   "schema_version": "2.0.0",
    "processing_pipeline": {
       "data_processes": [
          {

diff --git a/examples/quality_control.json b/examples/quality_control.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/quality_control.py",
-   "schema_version": "1.2.2",
+   "schema_version": "2.0.0",
    "evaluations": [
       {
          "modality": {

diff --git a/examples/subject.json b/examples/subject.json
@@ -1,6 +1,6 @@
 {
    "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/subject.py",
-   "schema_version": "1.0.3",
+   "schema_version": "2.0.0",
    "subject_id": "12345",
    "sex": "Male",
    "date_of_birth": "2022-11-22",

diff --git a/src/aind_data_schema/core/acquisition.py b/src/aind_data_schema/core/acquisition.py
@@ -46,7 +46,7 @@ class Acquisition(DataCoreModel):
 
     _DESCRIBED_BY_URL = DataCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/acquisition.py"
     describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
-    schema_version: SkipValidation[Literal["1.0.6"]] = Field(default="1.0.6")
+    schema_version: SkipValidation[Literal["2.0.0"]] = Field(default="2.0.0")
     protocol_id: List[str] = Field(default=[], title="Protocol ID", description="DOI for protocols.io")
     experimenters: List[Person] = Field(
         default=[],

diff --git a/src/aind_data_schema/core/data_description.py b/src/aind_data_schema/core/data_description.py
@@ -39,7 +39,7 @@ class DataDescription(DataCoreModel):
 
     _DESCRIBED_BY_URL = DataCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/data_description.py"
     describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
-    schema_version: SkipValidation[Literal["1.0.5"]] = Field(default="1.0.5")
+    schema_version: SkipValidation[Literal["2.0.0"]] = Field(default="2.0.0")
     license: Literal["CC-BY-4.0"] = Field(default="CC-BY-4.0", title="License")
 
     subject_id: str = Field(

diff --git a/src/aind_data_schema/core/instrument.py b/src/aind_data_schema/core/instrument.py
@@ -85,7 +85,7 @@ class Instrument(DataCoreModel):
     # metametadata
     _DESCRIBED_BY_URL = DataCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/inst.py"
     describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
-    schema_version: SkipValidation[Literal["1.0.5"]] = Field(default="1.0.5")
+    schema_version: SkipValidation[Literal["2.0.0"]] = Field(default="2.0.0")
 
     # instrument definition
     instrument_id: str = Field(

diff --git a/src/aind_data_schema/core/metadata.py b/src/aind_data_schema/core/metadata.py
@@ -68,7 +68,7 @@ class Metadata(DataCoreModel):
 
     _DESCRIBED_BY_URL = DataCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/metadata.py"
     describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
-    schema_version: SkipValidation[Literal["1.1.7"]] = Field(default="1.1.7")
+    schema_version: SkipValidation[Literal["2.0.0"]] = Field(default="2.0.0")
     id: UUID = Field(
         default_factory=uuid4,
         alias="_id",

diff --git a/src/aind_data_schema/core/model.py b/src/aind_data_schema/core/model.py
@@ -57,7 +57,7 @@ class Model(DataCoreModel):
 
     _DESCRIBED_BY_URL = DataCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/model.py"
     describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
-    schema_version: Literal["0.0.1"] = Field(default="0.0.1")
+    schema_version: Literal["2.0.0"] = Field(default="2.0.0")
 
     name: str = Field(..., title="Name")
     license: str = Field(..., title="License")

diff --git a/src/aind_data_schema/core/procedures.py b/src/aind_data_schema/core/procedures.py
@@ -708,7 +708,7 @@ class Procedures(DataCoreModel):
     _DESCRIBED_BY_URL = DataCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/procedures.py"
     describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
 
-    schema_version: SkipValidation[Literal["1.2.6"]] = Field(default="1.2.6")
+    schema_version: SkipValidation[Literal["2.0.0"]] = Field(default="2.0.0")
     subject_id: str = Field(
         ...,
         description="Unique identifier for the subject. If this is not a Allen LAS ID, indicate this in the Notes.",

diff --git a/src/aind_data_schema/core/processing.py b/src/aind_data_schema/core/processing.py
@@ -123,7 +123,7 @@ class Processing(DataCoreModel):
 
     _DESCRIBED_BY_URL: str = DataCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/processing.py"
     describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
-    schema_version: SkipValidation[Literal["1.1.6"]] = Field(default="1.1.6")
+    schema_version: SkipValidation[Literal["2.0.0"]] = Field(default="2.0.0")
 
     processing_pipeline: PipelineProcess = Field(
         ..., description="Pipeline used to process data", title="Processing Pipeline"

diff --git a/src/aind_data_schema/core/quality_control.py b/src/aind_data_schema/core/quality_control.py
@@ -199,7 +199,7 @@ class QualityControl(DataCoreModel):
 
     _DESCRIBED_BY_URL = DataCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/quality_control.py"
     describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
-    schema_version: SkipValidation[Literal["1.2.2"]] = Field(default="1.2.2")
+    schema_version: SkipValidation[Literal["2.0.0"]] = Field(default="2.0.0")
     evaluations: List[QCEvaluation] = Field(..., title="Evaluations")
     notes: Optional[str] = Field(default=None, title="Notes")
 

diff --git a/src/aind_data_schema/core/session.py b/src/aind_data_schema/core/session.py
@@ -546,7 +546,7 @@ class Session(DataCoreModel):
 
     _DESCRIBED_BY_URL = DataCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/session.py"
     describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
-    schema_version: SkipValidation[Literal["1.1.5"]] = Field(default="1.1.5")
+    schema_version: SkipValidation[Literal["2.0.0"]] = Field(default="2.0.0")
     protocol_id: List[str] = Field(default=[], title="Protocol ID", description="DOI for protocols.io")
     experimenters: List[Person] = Field(
         default=[],

diff --git a/src/aind_data_schema/core/subject.py b/src/aind_data_schema/core/subject.py
@@ -89,7 +89,7 @@ class Subject(DataCoreModel):
 
     _DESCRIBED_BY_URL = DataCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/subject.py"
     describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL})
-    schema_version: SkipValidation[Literal["1.0.3"]] = Field(default="1.0.3")
+    schema_version: SkipValidation[Literal["2.0.0"]] = Field(default="2.0.0")
     subject_id: str = Field(
         ...,
         description="Unique identifier for the subject. If this is not a Allen LAS ID, indicate this in the Notes.",

diff --git a/tests/test_inst_acq_compatibility.py b/tests/test_inst_acq_compatibility.py
@@ -59,7 +59,7 @@
 behavior_computer = "W10DT72941"
 ephys_computer = "W10DT72942"
 
-running_wheel = Disc(name="Running Wheel", radius=15)
+disc_mouse_platform = Disc(name="Running Wheel", radius=15)
 
 digital_out0 = DAQChannel(channel_name="DO0", device_name="Face Camera", channel_type="Digital Output")
 
@@ -246,8 +246,8 @@
         basestation,
         harp,
         microscope,
-        running_wheel,
     ],
+    mouse_platform=disc_mouse_platform,
     calibrations=[red_laser_calibration, blue_laser_calibration],
 )
 

diff --git a/tests/test_metadata.py b/tests/test_metadata.py
@@ -209,11 +209,12 @@ def test_validate_smartspim_metadata(self):
         surgery2 = Surgery.model_construct(procedures=[nano_inj])
         with self.assertRaises(ValidationError) as context:
             Metadata(
-                name="ecephys_655019_2023-04-03_18-17-09",
+                name="655019_2023-04-03T181709",
                 location="bucket",
                 data_description=DataDescription.model_construct(
                     creation_time=time(12, 12, 12),
                     modalities=[Modality.SPIM],
+                    subject_id="655019",
                 ),
                 subject=Subject.model_construct(),
                 procedures=Procedures.model_construct(subject_procedures=[surgery2]),