Update dependencies and add data contract

.config/dotnet-tools.json

@@ -3,7 +3,7 @@
   "isRoot": true,
   "tools": {
     "bonsai.sgen": {
-      "version": "0.4.0",
+      "version": "0.6.1",
       "commands": [
         "bonsai.sgen"
       ]

.gitignore

@@ -5,6 +5,7 @@ bin
 obj
 Packages
 Bonsai.exe.WebView2
+Bonsai/Settings/
 *.bin
 *.avi
 *.dll

bonsai/setup.ps1

@@ -15,7 +15,6 @@ if (!(Test-Path "./Bonsai.exe")) {
     Expand-Archive "temp.zip" -DestinationPath "." -Force
     Move-Item -Path "temp.config" "NuGet.config" -Force -ErrorAction SilentlyContinue
     Remove-Item -Path "temp.zip"
-    Remove-Item -Path "Bonsai32.exe"
 }
 & .\Bonsai.exe --no-editor
 Pop-Location

docs/json-schemas.rst

@@ -1,8 +1,18 @@
-json-schemas
+json-schema
 -------------
-.. toctree::
-   :maxdepth: 4
+The following json-schemas are used as the format definition of the input for this task. They are the result of the `Pydantic`` models defined in `src/aind_behavior_device_olfactometer`, and are also used to generate `src/Extensions/AindBehaviorDeviceOlfactometer.cs` via `Bonsai.Sgen`.
 
-   json-schemas.session
-   json-schemas.rig
-   json-schemas.task_logic
+`Download Schema <https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.Device.Olfactometer/main/src/DataSchemas/aind_behavior_device_olfactometer.json>`_
+
+Task Logic Schema
+~~~~~~~~~~~~~~~~~
+.. jsonschema:: https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.Device.Olfactometer/main/src/DataSchemas/aind_behavior_device_olfactometer.json#/$defs/OlfactometerCalibrationLogic
+   :lift_definitions:
+   :auto_reference:
+
+
+Rig Schema
+~~~~~~~~~~~~~~
+.. jsonschema:: https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.Device.Olfactometer/main/src/DataSchemas/aind_behavior_device_olfactometer.json#/$defs/OlfactometerCalibrationRig
+   :lift_definitions:
+   :auto_reference:

examples/clabe.yml

@@ -0,0 +1,6 @@
+# In order to get picked up, move this file to the root of the project or ./local
+
+data_dir: C:/Data
+
+default_behavior_picker:
+  config_library_dir: '\\allen\aind\scratch\AindBehavior.db\AindBehaviorDeviceOlfactometer'

examples/olfactometer.py

@@ -1,12 +1,14 @@
 import os
 
 from aind_behavior_services.base import get_commit_hash
+from aind_behavior_services.calibration import aind_manipulator as man
 from aind_behavior_services.calibration import olfactometer as olf
-from aind_behavior_services.rig import HarpAnalogInput, HarpWhiteRabbit
+from aind_behavior_services.rig.harp import HarpAnalogInput, HarpWhiteRabbit
 from aind_behavior_services.session import AindBehaviorSessionModel
 from aind_behavior_services.utils import utcnow
 
 from aind_behavior_device_olfactometer import rig, task_logic
+from aind_behavior_device_olfactometer.rig import AlicatFlowmeter
 
 channels_config = {
     olf.OlfactometerChannel.Channel0: olf.OlfactometerChannelConfig(
@@ -45,11 +47,28 @@
     commit_hash=get_commit_hash(),
 )
 
+manipulator_calibration = man.AindManipulatorCalibration(
+    output=man.AindManipulatorCalibrationOutput(),
+    input=man.AindManipulatorCalibrationInput(
+        full_step_to_mm=(man.ManipulatorPosition(x=0.010, y1=0.010, y2=0.010, z=0.010)),
+        axis_configuration=[
+            man.AxisConfiguration(axis=man.Axis.Y1, min_limit=-0.01, max_limit=25),
+            man.AxisConfiguration(axis=man.Axis.Y2, min_limit=-0.01, max_limit=25),
+            man.AxisConfiguration(axis=man.Axis.X, min_limit=-0.01, max_limit=25),
+            man.AxisConfiguration(axis=man.Axis.Z, min_limit=-0.01, max_limit=25),
+        ],
+        homing_order=[man.Axis.Y1, man.Axis.Y2, man.Axis.X, man.Axis.Z],
+        initial_position=man.ManipulatorPosition(y1=0, y2=0, x=0, z=0),
+    ),
+)
+
 _rig = rig.OlfactometerCalibrationRig(
     rig_name="OlfactometerRig",
-    harp_olfactometer=rig.HarpOlfactometer(port_name="COM10", calibration=calibration),
+    harp_olfactometer=olf.Olfactometer(port_name="COM10", calibration=calibration),
     harp_analog_input=HarpAnalogInput(port_name="COM8"),
     harp_clock_generator=HarpWhiteRabbit(port_name="COM9"),
+    harp_manipulator=man.AindManipulatorDevice(port_name="COM7", calibration=manipulator_calibration),
+    flowmeter=AlicatFlowmeter(port_name="COM6", device_id="A", pooling_period=0.2),
 )
 
 

pyproject.toml

@@ -18,7 +18,7 @@ classifiers = [
 ]
 
 dependencies = [
-  "aind_behavior_services>=0.10, <0.11",
+  "aind_behavior_services<0.13",
 ]
 
 [project.urls]
@@ -29,7 +29,7 @@ Changelog = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Device.Olfacto
 
 [project.optional-dependencies]
 
-launcher = ["aind_behavior_experiment_launcher[aind-services]>=0.3.0"]
+launcher = ["aind_clabe[aind-services]"]
 
 dev = ["aind_behavior_device_olfactometer[launcher]",
     "ruff",
@@ -47,7 +47,7 @@ docs = [
 ]
 
 analysis = [
-    "aind-behavior-core-analysis@git+https://github.com/AllenNeuralDynamics/Aind.Behavior.CoreAnalysis@051bc0c",
+    "contraqctor",
     "numpy",
     "pandas",
     "matplotlib",

scripts/deploy.cmd

@@ -0,0 +1 @@
+powershell -ExecutionPolicy Bypass -File .\scripts\deploy.ps1

scripts/deploy.ps1

@@ -0,0 +1,27 @@
+$scriptPath = $MyInvocation.MyCommand.Path
+$scriptDirectory = Split-Path -Parent $scriptPath
+Set-Location (Split-Path -Parent $scriptDirectory)
+Write-Output "Creating a Python  environment..."
+
+if (-not (Get-Command uv -ErrorAction SilentlyContinue)) {
+    throw "The 'uv' command was not found. See https://docs.astral.sh/uv/getting-started/installation/ for instructions."
+}
+
+if (Test-Path -Path ./.venv) {
+    Remove-Item ./.venv -Recurse -Force
+}
+&uv venv
+.\.venv\Scripts\Activate.ps1
+Write-Output "Synchronizing environment..."
+&uv sync --extra launcher
+Write-Output "Creating a Bonsai environment and installing packages..."
+if (Test-Path -Path "bonsai") {
+    Set-Location "bonsai"
+    .\setup.ps1
+} elseif (Test-Path -Path ".bonsai") {
+    Set-Location ".bonsai"
+    .\setup.ps1
+} else {
+    throw "Neither 'bonsai' nor '.bonsai' directory found."
+}
+Set-Location ..