Merge pull request #125 from AllenNeuralDynamics/cdci-uv-as-package-m…

…anager

Add support of uv package manager

.github/workflows/ci.yml

@@ -4,30 +4,40 @@ on:
   pull_request:
     branches:
       - main
+  push:
+    branches:
+      - main
 
 jobs:
   linters:
     runs-on: windows-latest
+    name: Lint ${{ matrix.python-version }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.11', '3.12', '3.13']
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v3
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v3
         with:
-          python-version: "3.11"
+          enable-cache: true
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
       - name: Install dependencies
-        run: |
-          python -m pip install -e .[linters] --no-cache-dir
+        run: uv sync --extra dev
       - name: Run ruff format
-        run: ruff format . --config .\pyproject.toml
+        run: uv run ruff format . --config .\pyproject.toml
       - name: Run ruff check
-        run: ruff check . --config .\pyproject.toml
+        run: uv run ruff check . --config .\pyproject.toml
       - name: Run codespell
-        run : codespell .
+        run : uv run codespell .
 
   tests:
     runs-on: windows-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Setup .NET Core SDK
         uses: actions/[email protected]
@@ -39,18 +49,18 @@ jobs:
         working-directory: bonsai
         run: .\Setup.ps1
 
-      - name: Set up Python
-        uses: actions/setup-python@v3
+      - uses: astral-sh/setup-uv@v3
         with:
-          python-version: '3.11'
+          enable-cache: true
+      - name: Set up Python
+        run: uv python install
 
       - name: Install dependencies
-        run: |
-          python -m pip install -e . --no-cache-dir
+        run: uv sync --extra dev
       - name: Run tests
-        run: python -m unittest
+        run: uv run -m unittest
       - name: Regenerate schemas
-        run: regenerate
+        run: uv run regenerate
       - name: Check for uncommitted changes
         run: |
           git config --global core.safecrlf false

.python-versions

@@ -0,0 +1,3 @@
+3.11
+3.12
+3.13

pyproject.toml

@@ -33,7 +33,7 @@ Changelog = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Services/relea
 
 [project.optional-dependencies]
 
-linters = [
+dev = [
     'ruff',
     'codespell'
 ]
@@ -73,5 +73,5 @@ mccabe = { max-complexity = 14 }
 pydocstyle = { convention = 'google' }
 
 [tool.codespell]
-skip = '.git,*.pdf,*.svg,./bonsai,*.bonsai,./docs/_build'
+skip = '.git,*.pdf,*.svg,./bonsai,*.bonsai,./docs/_build,uv.lock'
 ignore-words-list = 'nd'

scripts/install_dependencies.ps1

@@ -12,6 +12,7 @@ winget install -e --id Nvidia.GeForceExperience -v 3.26.0.160 @autoaccept
 winget install -e --id Nvidia.CUDA -v 11.3 @autoaccept
 winget install -e --id Notepad++.Notepad++ @autoaccept
 winget install --id=Microsoft.DotNet.SDK.8  -e @autoaccept
+winget install --id=astral-sh.uv  -e @autoaccept
 
 ## Install dotnet tools
 

src/Extensions/AindBehaviorSession.cs

@@ -15,7 +15,7 @@ namespace AindBehaviorServices.AindBehaviorSession
     public partial class AindBehaviorSessionModel
     {
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.7";
+        private string _aindBehaviorServicesPkgVersion = "0.8.8";
 
         private string _version = "0.3.0";
 

src/Extensions/AindManipulatorCalibrationLogic.cs

@@ -17,7 +17,7 @@ public partial class CalibrationParameters
 
         private double? _rngSeed;
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.7";
+        private string _aindBehaviorServicesPkgVersion = "0.8.8";
 
         public CalibrationParameters()
         {

src/Extensions/AindManipulatorCalibrationRig.cs

@@ -897,7 +897,7 @@ public enum MotorOperationMode
     public partial class CalibrationRig
     {
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.7";
+        private string _aindBehaviorServicesPkgVersion = "0.8.8";
 
         private string _version = "0.1.0";
 

src/Extensions/LoadCellsCalibrationLogic.cs

@@ -17,7 +17,7 @@ public partial class CalibrationParameters
 
         private double? _rngSeed;
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.7";
+        private string _aindBehaviorServicesPkgVersion = "0.8.8";
 
         private System.Collections.Generic.List<int> _channels = new System.Collections.Generic.List<int>();
 

src/Extensions/LoadCellsCalibrationRig.cs

@@ -910,7 +910,7 @@ public override string ToString()
     public partial class CalibrationRig
     {
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.7";
+        private string _aindBehaviorServicesPkgVersion = "0.8.8";
 
         private string _version = "0.0.0";
 

src/Extensions/OlfactometerCalibrationLogic.cs

@@ -17,7 +17,7 @@ public partial class CalibrationParameters
 
         private double? _rngSeed;
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.7";
+        private string _aindBehaviorServicesPkgVersion = "0.8.8";
 
         private System.Collections.Generic.IDictionary<string, OlfactometerChannelConfig> _channelConfig;
 

src/Extensions/OlfactometerCalibrationRig.cs

@@ -1087,7 +1087,7 @@ public enum OlfactometerChannelType
     public partial class CalibrationRig
     {
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.7";
+        private string _aindBehaviorServicesPkgVersion = "0.8.8";
 
         private string _version = "0.0.0";
 

src/Extensions/TreadmillCalibrationLogic.cs

@@ -17,7 +17,7 @@ public partial class CalibrationParameters
 
         private double? _rngSeed;
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.7";
+        private string _aindBehaviorServicesPkgVersion = "0.8.8";
 
         public CalibrationParameters()
         {

src/Extensions/TreadmillCalibrationRig.cs

@@ -550,7 +550,7 @@ public override string ToString()
     public partial class CalibrationRig
     {
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.7";
+        private string _aindBehaviorServicesPkgVersion = "0.8.8";
 
         private string _version = "0.0.0";
 

src/Extensions/WaterValveCalibrationLogic.cs

@@ -17,7 +17,7 @@ public partial class CalibrationParameters
 
         private double? _rngSeed;
 
-        private string _aindBehaviorServicesPkgVersion = "0.8.7";
+        private string _aindBehaviorServicesPkgVersion = "0.8.8";
 
         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 = "0.8.7";
+        private string _aindBehaviorServicesPkgVersion = "0.8.8";
 
         private string _version = "0.0.0";
 

src/schemas/aind_behavior_data_types.json

@@ -162,7 +162,7 @@
   },
   "properties": {
     "aind_behavior_services_pkg_version": {
-      "default": "0.8.7",
+      "default": "0.8.8",
       "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": "0.8.7",
+      "default": "0.8.8",
       "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": "0.8.7",
+      "default": "0.8.8",
       "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": "0.8.7",
+          "default": "0.8.8",
           "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": "0.8.7",
+      "default": "0.8.8",
       "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": "0.8.7",
+          "default": "0.8.8",
           "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

@@ -292,7 +292,7 @@
   },
   "properties": {
     "aind_behavior_services_pkg_version": {
-      "default": "0.8.7",
+      "default": "0.8.8",
       "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": "0.8.7",
+          "default": "0.8.8",
           "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

@@ -376,7 +376,7 @@
   },
   "properties": {
     "aind_behavior_services_pkg_version": {
-      "default": "0.8.7",
+      "default": "0.8.8",
       "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": "0.8.7",
+          "default": "0.8.8",
           "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": "0.8.7"
+        "aind_behavior_services_pkg_version": "0.8.8"
       },
       "title": "Task parameters"
     },

src/schemas/treadmill_calibration_rig.json

@@ -175,7 +175,7 @@
   },
   "properties": {
     "aind_behavior_services_pkg_version": {
-      "default": "0.8.7",
+      "default": "0.8.8",
       "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/water_valve_calibration_logic.json

@@ -17,7 +17,7 @@
           "title": "Rng Seed"
         },
         "aind_behavior_services_pkg_version": {
-          "default": "0.8.7",
+          "default": "0.8.8",
           "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/water_valve_calibration_rig.json

@@ -1,7 +1,7 @@
 {
   "properties": {
     "aind_behavior_services_pkg_version": {
-      "default": "0.8.7",
+      "default": "0.8.8",
       "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"