Merge branch 'main' of https://github.com/AllenNeuralDynamics/Aind.Be…

…havior.Services

README.md

@@ -4,12 +4,15 @@ A repository containing code for data acquisition and processing for AIND behavi
 
 ---
 
-## Deployment
+## Installation
 
-Install the [prerequisites](#prerequisites) mentioned below.
-From the root of the repository, run `./scripts/deploy.ps1` to bootstrap both python and bonsai environments.
+The python package can be installed from pypi using the following command:
 
----
+```bash
+pip install aind-behavior-services
+```
+
+However, to use all the tasks and hardware that this package supports, you should over over the [prerequisites](#prerequisites) and [deployment](#deployment) sections.
 
 ## Prerequisites
 
@@ -24,6 +27,13 @@ These should only need to be installed once on a fresh new system, and are not r
 
 ---
 
+## Deployment
+
+Install the [prerequisites](#prerequisites) mentioned below.
+From the root of the repository, run `./scripts/deploy.ps1` to bootstrap both python and bonsai environments.
+
+---
+
 ## Generating valid JSON input files
 
 One of the core principles of this repository is the strict adherence to [json-schemas](https://json-schema.org/). We use [Pydantic](https://pydantic.dev/) as a way to write and compile our schemas, but also to generate valid JSON input files. These files can be used by Bonsai (powered by [Bonsai.SGen](https://github.com/bonsai-rx/sgen) code generation tool) or to simply record metadata. Examples of how to interact with the library can be found in the `./examples` folder.
@@ -58,4 +68,56 @@ Where possible, adhere to [Semantic Versioning](https://semver.org/).
 
 ## Project dependency tree
 
-![Dependency tree](https://github.com/AllenNeuralDynamics/Aind.Behavior.Services/raw/main/assets/dependency_tree.drawio.svg)
+
+```mermaid
+classDiagram
+    class aind_behavior_curriculum {
+        +Task
+        +Curriculum
+    }
+
+    class aind_behavior_services {
+        +Task (Subclasses)
+        +Rig (maintains hardware library)
+        +Session
+        +Calibration (maintains device/calibration library)
+        +Deployment instructions
+        +Ecosystem documentation
+    }
+
+    class aind_behavior_experiment_launcher {
+        +Launch experiment
+        +Interfaces with external applications (e.g. Bonsai)
+        +Interfaces with aind-services
+    }
+
+    class aind_behavior_some_task {
+        +Concrete implementation of a task
+        +Rig (Subclasses for some task)
+        +Session
+        +Task Logic (Subclasses for some task)
+        +Maintains a task data-schema
+        +Saves data in standard format
+    }
+
+    class aind_behavior_some_task_analysis {
+        +Analysis code for some task
+    }
+
+    class aind_behavior_core_analysis {
+        +Data ingestion
+        +Data contract definition
+        +Core analysis primitives
+        +QC
+    }
+
+    aind_behavior_curriculum --|> aind_behavior_services : Subclasses Task
+    aind_behavior_services --|> aind_behavior_some_task 
+    aind_behavior_some_task --|> aind_behavior_some_task_analysis : Analysis
+    aind_behavior_core_analysis --|> aind_behavior_some_task_analysis : Imports core analysis methods
+    aind_behavior_some_task_analysis --|> aind_behavior_curriculum : Metrics[Task]
+    
+    aind_behavior_experiment_launcher --|> aind_behavior_some_task : Launches
+
+```
+

src/Extensions/AindBehaviorSession.cs

@@ -15,7 +15,7 @@ namespace AindBehaviorServices.AindBehaviorSession
     public partial class AindBehaviorSessionModel
     {
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.0";
+        private string _aindBehaviorServicesPkgVersion = "0.8.1";
 
         private string _version = "0.3.0";
 

src/Extensions/AindManipulatorCalibrationLogic.cs

@@ -17,7 +17,7 @@ public partial class CalibrationParameters
 
         private double? _rngSeed;
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.0";
+        private string _aindBehaviorServicesPkgVersion = "0.8.1";
 
         public CalibrationParameters()
         {

src/Extensions/AindManipulatorCalibrationRig.cs

@@ -897,7 +897,7 @@ public enum MotorOperationMode
     public partial class CalibrationRig
     {
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.0";
+        private string _aindBehaviorServicesPkgVersion = "0.8.1";
 
         private string _version = "0.1.0";
 

src/Extensions/LoadCellsCalibrationLogic.cs

@@ -17,7 +17,7 @@ public partial class CalibrationParameters
 
         private double? _rngSeed;
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.0";
+        private string _aindBehaviorServicesPkgVersion = "0.8.1";
 
         private System.Collections.Generic.List<int> _channels = new System.Collections.Generic.List<int>();
 

src/Extensions/LoadCellsCalibrationRig.cs

@@ -892,7 +892,7 @@ public override string ToString()
     public partial class CalibrationRig
     {
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.0";
+        private string _aindBehaviorServicesPkgVersion = "0.8.1";
 
         private string _version = "0.0.0";
 

src/Extensions/OlfactometerCalibrationLogic.cs

@@ -17,7 +17,7 @@ public partial class CalibrationParameters
 
         private double? _rngSeed;
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.0";
+        private string _aindBehaviorServicesPkgVersion = "0.8.1";
 
         private System.Collections.Generic.IDictionary<string, OlfactometerChannelConfig> _channelConfig;
 

src/Extensions/OlfactometerCalibrationRig.cs

@@ -979,7 +979,7 @@ public enum OlfactometerChannelType
     public partial class CalibrationRig
     {
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.0";
+        private string _aindBehaviorServicesPkgVersion = "0.8.1";
 
         private string _version = "0.0.0";
 

src/Extensions/TreadmillCalibrationLogic.cs

@@ -17,7 +17,7 @@ public partial class CalibrationParameters
 
         private double? _rngSeed;
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.0";
+        private string _aindBehaviorServicesPkgVersion = "0.8.1";
 
         public CalibrationParameters()
         {

src/Extensions/TreadmillCalibrationRig.cs

@@ -550,7 +550,7 @@ public override string ToString()
     public partial class CalibrationRig
     {
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.0";
+        private string _aindBehaviorServicesPkgVersion = "0.8.1";
 
         private string _version = "0.0.0";
 

src/Extensions/WaterValveCalibrationLogic.cs

@@ -17,7 +17,7 @@ public partial class CalibrationParameters
 
         private double? _rngSeed;
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.0";
+        private string _aindBehaviorServicesPkgVersion = "0.8.1";
 
         private System.Collections.Generic.List<double> _valveOpenTime = new System.Collections.Generic.List<double>();
 

src/Extensions/WaterValveCalibrationRig.cs

@@ -15,7 +15,7 @@ namespace AindBehaviorServices.WaterValveCalibrationRig
     public partial class CalibrationRig
     {
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.0";
+        private string _aindBehaviorServicesPkgVersion = "0.8.1";
 
         private string _version = "0.0.0";
 

src/aind_behavior_services/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.8.0"
+__version__ = "0.8.1"
 
 from .rig import AindBehaviorRigModel  # noqa: F401
 from .session import AindBehaviorSessionModel  # noqa: F401

src/aind_behavior_services/base.py

@@ -20,7 +20,7 @@ class SchemaVersionedModel(BaseModel):
     )
     version: str = Field(..., pattern=SEMVER_REGEX, description="schema version", title="Version", frozen=True)
 
-    @field_validator("aind_behavior_services_pkg_version", mode="before", check_fields=False)
+    @field_validator("aind_behavior_services_pkg_version", "version", mode="before", check_fields=False)
     @classmethod
     def coerce_version(cls, v: str, ctx) -> str:
         return coerce_schema_version(cls, v, ctx.field_name)
@@ -72,14 +72,11 @@ def coerce_schema_version(cls: type[SchemaVersionedModel], v: str, version_strin
     semver = Version.parse(v)
     if semver > _default_schema_version:
         raise ValueError(
-            f"Deserialized schema version ({semver}) \
-                is greater than the current version({_default_schema_version})."
+            f"Error deserializing versioned field {version_string} (v{semver} > v{_default_schema_version})"
         )
     elif semver < _default_schema_version:
         warnings.warn(
-            f"Deserialized schema version ({semver}) \
-                is less than the current version({_default_schema_version}). \
-                    Will attempt to coerce the conversion."
+            f"Coercing deserialized versioned field {version_string} (v{semver} < v{_default_schema_version})"
         )
         return str(_default_schema_version)
     else:

src/aind_behavior_services/rig/__init__.py

@@ -6,7 +6,7 @@
 
 from pydantic import BaseModel, Field, RootModel, field_validator
 
-from aind_behavior_services.base import SchemaVersionedModel, coerce_schema_version
+from aind_behavior_services.base import SchemaVersionedModel
 
 
 class Device(BaseModel):
@@ -275,8 +275,3 @@ class Screen(Device):
 class AindBehaviorRigModel(SchemaVersionedModel):
     computer_name: str = Field(default_factory=lambda: os.environ["COMPUTERNAME"], description="Computer name")
     rig_name: str = Field(..., description="Rig name")
-
-    @field_validator("version", mode="before")
-    @classmethod
-    def coerce_version(cls, v: str) -> str:
-        return coerce_schema_version(cls, v)

src/aind_behavior_services/session/__init__.py

@@ -2,10 +2,10 @@
 import datetime
 from typing import List, Literal, Optional, Self
 
-from pydantic import Field, field_validator, model_validator
+from pydantic import Field, model_validator
 
 import aind_behavior_services.utils
-from aind_behavior_services.base import SchemaVersionedModel, coerce_schema_version
+from aind_behavior_services.base import SchemaVersionedModel
 
 __version__ = "0.3.0"
 
@@ -28,11 +28,6 @@ class AindBehaviorSessionModel(SchemaVersionedModel):
     allow_dirty_repo: bool = Field(default=False, description="Allow running from a dirty repository")
     skip_hardware_validation: bool = Field(default=False, description="Skip hardware validation")
 
-    @field_validator("version", mode="before")
-    @classmethod
-    def coerce_version(cls, v: str, ctx) -> str:
-        return coerce_schema_version(cls, v)
-
     @model_validator(mode="after")
     def generate_session_name_default(self) -> Self:
         if self.session_name is None:

src/aind_behavior_services/task_logic/__init__.py

@@ -19,11 +19,12 @@ def coerce_version(cls, v: str, ctx) -> str:
         return coerce_schema_version(cls, v, ctx.field_name)
 
 
+# This class should be inherited from but do not add extra parameters. Instead, add them to TaskParameters
 class AindBehaviorTaskLogicModel(curriculum_task.Task):
     task_parameters: TaskParameters = Field(..., description="Parameters of the task logic", validate_default=True)
     version: str = Field(..., pattern=curriculum_task.SEMVER_REGEX, description="task schema version")
 
-    @field_validator("version", mode="before")
+    @field_validator("version", mode="before", check_fields=False)
     @classmethod
     def coerce_version(cls, v: str) -> str:
         return coerce_schema_version(cls, v)

src/schemas/aind_behavior_data_types.json

@@ -162,7 +162,7 @@
   },
   "properties": {
     "aind_behavior_services_pkg_version": {
-      "default": "0.8.0",
+      "default": "0.8.1",
       "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
       "title": "aind_behavior_services package version",
       "type": "string"

src/schemas/aind_behavior_session.json

@@ -1,7 +1,7 @@
 {
   "properties": {
     "aind_behavior_services_pkg_version": {
-      "default": "0.8.0",
+      "default": "0.8.1",
       "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
       "title": "aind_behavior_services package version",
       "type": "string"

src/schemas/aind_behavior_subject_database.json

@@ -17,7 +17,7 @@
   },
   "properties": {
     "aind_behavior_services_pkg_version": {
-      "default": "0.8.0",
+      "default": "0.8.1",
       "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
       "title": "aind_behavior_services package version",
       "type": "string"

src/schemas/aind_manipulator_calibration_logic.json

@@ -17,7 +17,7 @@
           "title": "Rng Seed"
         },
         "aind_behavior_services_pkg_version": {
-          "default": "0.8.0",
+          "default": "0.8.1",
           "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
           "title": "aind_behavior_services package version",
           "type": "string"

src/schemas/aind_manipulator_calibration_rig.json

@@ -351,7 +351,7 @@
   },
   "properties": {
     "aind_behavior_services_pkg_version": {
-      "default": "0.8.0",
+      "default": "0.8.1",
       "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
       "title": "aind_behavior_services package version",
       "type": "string"

src/schemas/load_cells_calibration_logic.json

@@ -17,7 +17,7 @@
           "title": "Rng Seed"
         },
         "aind_behavior_services_pkg_version": {
-          "default": "0.8.0",
+          "default": "0.8.1",
           "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
           "title": "aind_behavior_services package version",
           "type": "string"

src/schemas/load_cells_calibration_rig.json

@@ -280,7 +280,7 @@
   },
   "properties": {
     "aind_behavior_services_pkg_version": {
-      "default": "0.8.0",
+      "default": "0.8.1",
       "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
       "title": "aind_behavior_services package version",
       "type": "string"

src/schemas/olfactometer_calibration_logic.json

@@ -17,7 +17,7 @@
           "title": "Rng Seed"
         },
         "aind_behavior_services_pkg_version": {
-          "default": "0.8.0",
+          "default": "0.8.1",
           "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
           "title": "aind_behavior_services package version",
           "type": "string"

src/schemas/olfactometer_calibration_rig.json

@@ -339,7 +339,7 @@
   },
   "properties": {
     "aind_behavior_services_pkg_version": {
-      "default": "0.8.0",
+      "default": "0.8.1",
       "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
       "title": "aind_behavior_services package version",
       "type": "string"

src/schemas/treadmill_calibration_logic.json

@@ -17,7 +17,7 @@
           "title": "Rng Seed"
         },
         "aind_behavior_services_pkg_version": {
-          "default": "0.8.0",
+          "default": "0.8.1",
           "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
           "title": "aind_behavior_services package version",
           "type": "string"
@@ -45,7 +45,7 @@
       "$ref": "#/definitions/CalibrationParameters",
       "default": {
         "rng_seed": null,
-        "aind_behavior_services_pkg_version": "0.8.0"
+        "aind_behavior_services_pkg_version": "0.8.1"
       },
       "title": "Task parameters"
     },

src/schemas/treadmill_calibration_rig.json

@@ -175,7 +175,7 @@
   },
   "properties": {
     "aind_behavior_services_pkg_version": {
-      "default": "0.8.0",
+      "default": "0.8.1",
       "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
       "title": "aind_behavior_services package version",
       "type": "string"