Task/add GitHub actions

.github/workflows/_build-docker-action.yml

@@ -0,0 +1,50 @@
+name: 'Build Docker Image'
+on:
+  workflow_call:
+env:
+  REGISTRY: docker.io
+  IMAGE_NAME: aberger4/mouse-tracking
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Log in to Container Registry
+      if: github.event_name != 'pull_request'
+      uses: docker/login-action@v3
+      with:
+        registry: ${{ env.REGISTRY }}
+        username: aberger4
+        password: ${{ secrets.DOCKER_SECRET }}
+
+    - name: Extract metadata
+      id: meta
+      uses: docker/metadata-action@v5
+      with:
+        images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+        tags: |
+          type=ref,event=branch
+          type=ref,event=pr
+          type=semver,pattern={{version}}
+          type=semver,pattern={{major}}.{{minor}}
+          type=raw,value=latest,enable={{is_default_branch}}
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+
+    - name: Build and push Docker image
+      uses: docker/build-push-action@v5
+      with:
+        context: .
+        push: ${{ github.event_name != 'pull_request' }}
+        tags: ${{ steps.meta.outputs.tags }}
+        labels: ${{ steps.meta.outputs.labels }}
+        cache-from: type=gha
+        cache-to: type=gha,mode=max

.github/workflows/_format-lint-action.yml

@@ -0,0 +1,33 @@
+name: 'Lint Code Definition'
+on:
+  workflow_call:
+    inputs:
+      python-version:
+        description: 'Python version to set up'
+        required: false
+        default: '3.10'
+        type: string
+jobs:
+  format-lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ inputs.python-version }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          version: "latest"
+
+      - name: Install dependencies with uv
+        run: uv sync --only-group lint
+
+      - name: Run Ruff Linter
+        run: uv run --only-group lint ruff check src/ tests/
+
+      - name: Run Ruff Formatter
+        run: uv run --only-group lint ruff format --check src/ tests/

.github/workflows/_run-tests-action.yml

@@ -0,0 +1,38 @@
+name: 'Python Tests Definition'
+on:
+  workflow_call:
+    inputs:
+      python-version:
+        description: Python version to set up'
+        required: false
+        default: '3.10'
+        type: string
+      runner-os:
+        description: 'Runner OS'
+        required: false
+        default: 'ubuntu-latest'
+        type: string
+jobs:
+  run-tests:
+    runs-on: ${{ inputs.runner-os }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ inputs.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ inputs.python-version }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          version: "latest"
+
+      - name: Install dependencies with uv
+        run: uv sync --extra cpu
+
+      - name: Make Sure PyTorch is Installed
+        run: uv pip install torch==2.6.0 torchvision==0.21.0 torchaudio==2.6.0 --index-url https://download.pytorch.org/whl/cpu
+
+      - name: Test with pytest
+        run: uv run pytest tests

.github/workflows/pull-request.yml

@@ -0,0 +1,20 @@
+name: Pull Request Checks
+
+on:
+  pull_request:
+    branches: [ main, repository-reorganization ]
+
+jobs:
+  format-lint:
+    name: "Format and Lint"
+    uses: ./.github/workflows/_format-lint-action.yml
+
+  test:
+    name: "Run Tests"
+    needs: format-lint
+    uses: ./.github/workflows/_run-tests-action.yml
+
+  build:
+    name: "Build Docker Image"
+    needs: [format-lint, test]
+    uses: ./.github/workflows/_build-docker-action.yml

pyproject.toml

@@ -9,7 +9,7 @@ dependencies = [
   "scipy==1.11.4",
   "pandas==2.0.3",
   "opencv-python-headless==4.8.0.76",
-  "imageio==2.31.6",
+  "imageio[ffmpeg]==2.31.6",
   "pillow==9.4.0",
   "matplotlib==3.7.1",
   "typer>=0.12.4",
@@ -40,16 +40,33 @@ cpu = [
 
 
 # ---- uv configuration: point Torch family at cu126 index ----
+# ---- uv indexes ----
+[[tool.uv.index]]
+name = "pypi"
+url  = "https://pypi.org/simple"
+explicit = false
+
 [[tool.uv.index]]
 name = "pytorch-cu126"
 url  = "https://download.pytorch.org/whl/cu126"
 explicit = true
 
+# ---- uv per-package sources with markers ----
+# Use CUDA wheels only when installing the `gpu` extra AND on platforms that can use them.
+# Fall back to CPU wheels when installing the `cpu` extra.
 [tool.uv.sources]
-torch = { index = "pytorch-cu126" }
-torchvision = { index = "pytorch-cu126" }
-torchaudio = { index = "pytorch-cu126" }
-
+torch = [
+  { index = "pytorch-cu126", marker = "sys_platform == 'linux' and extra == 'gpu'" },
+  { index = "pypi", marker = "sys_platform == 'linux' and extra != 'gpu'" },
+]
+torchvision = [
+  { index = "pytorch-cu126", marker = "sys_platform == 'linux' and extra == 'gpu'" },
+  { index = "pypi", marker = "sys_platform == 'linux' and extra != 'gpu'" },
+]
+torchaudio = [
+  { index = "pytorch-cu126", marker = "sys_platform == 'linux' and extra == 'gpu'" },
+  { index = "pypi", marker = "sys_platform == 'linux' and extra != 'gpu'" },
+]
 
 [project.scripts]
 mouse-tracking-runtime = "mouse_tracking.cli.main:app"
@@ -98,8 +115,14 @@ addopts = "--benchmark-skip"
 
 [dependency-groups]
 dev = [
+  {include-group = "lint"},
+  {include-group = "test"}
+]
+test = [
     "pytest>=8.3.5",
     "pytest-benchmark>=5.1.0",
     "pytest-cov>=6.1.1",
+]
+lint = [
     "ruff>=0.11.2",
 ]

tests/cli/infer/test_arena_corner.py

@@ -255,7 +255,9 @@ def test_arena_corner_frame_options(self, mock_infer, num_frames, frame_interval
     def test_arena_corner_help_text(self):
         """Test that the command has proper help text."""
         # Arrange & Act
-        result = self.runner.invoke(app, ["arena-corner", "--help"])
+        result = self.runner.invoke(
+            app, ["arena-corner", "--help"], env={"TERM": "dumb"}
+        )
 
         # Assert
         assert result.exit_code == 0

tests/cli/infer/test_commands.py

@@ -111,7 +111,7 @@ def test_infer_commands_help_structure():
 
     # Act & Assert
     for command in commands:
-        result = runner.invoke(app, [command, "--help"])
+        result = runner.invoke(app, [command, "--help"], env={"TERM": "dumb"})
         assert result.exit_code == 0
         assert "Usage:" in result.stdout
         assert "--help" in result.stdout
@@ -252,7 +252,7 @@ def test_infer_command_help_format(command_name):
     runner = CliRunner()
 
     # Act
-    result = runner.invoke(app, [command_name, "--help"])
+    result = runner.invoke(app, [command_name, "--help"], env={"TERM": "dumb"})
 
     # Assert
     assert result.exit_code == 0

tests/cli/infer/test_fecal_boli.py

@@ -280,7 +280,7 @@ def test_fecal_boli_default_values(self, mock_infer):
     def test_fecal_boli_help_text(self):
         """Test that the fecal boli command has proper help text."""
         # Arrange & Act
-        result = self.runner.invoke(app, ["fecal-boli", "--help"])
+        result = self.runner.invoke(app, ["fecal-boli", "--help"], env={"TERM": "dumb"})
 
         # Assert
         assert result.exit_code == 0

tests/cli/infer/test_food_hopper.py

@@ -278,7 +278,9 @@ def test_food_hopper_default_values(self, mock_infer):
     def test_food_hopper_help_text(self):
         """Test that the food hopper command has proper help text."""
         # Arrange & Act
-        result = self.runner.invoke(app, ["food-hopper", "--help"])
+        result = self.runner.invoke(
+            app, ["food-hopper", "--help"], env={"TERM": "dumb"}
+        )
 
         # Assert
         assert result.exit_code == 0

tests/cli/infer/test_lixit.py

@@ -276,7 +276,7 @@ def test_lixit_default_values(self, mock_infer):
     def test_lixit_help_text(self):
         """Test that the lixit command has proper help text."""
         # Arrange & Act
-        result = self.runner.invoke(app, ["lixit", "--help"])
+        result = self.runner.invoke(app, ["lixit", "--help"], env={"TERM": "dumb"})
 
         # Assert
         assert result.exit_code == 0

tests/cli/infer/test_multi_identity.py

@@ -204,7 +204,9 @@ def test_multi_identity_default_values(self, mock_infer):
     def test_multi_identity_help_text(self):
         """Test that the multi-identity command has proper help text."""
         # Arrange & Act
-        result = self.runner.invoke(app, ["multi-identity", "--help"])
+        result = self.runner.invoke(
+            app, ["multi-identity", "--help"], env={"TERM": "dumb"}
+        )
 
         # Assert
         assert result.exit_code == 0

tests/cli/infer/test_multi_pose.py

@@ -319,7 +319,7 @@ def test_multi_pose_default_values(self, mock_infer):
     def test_multi_pose_help_text(self):
         """Test that the multi-pose command has proper help text."""
         # Arrange & Act
-        result = self.runner.invoke(app, ["multi-pose", "--help"])
+        result = self.runner.invoke(app, ["multi-pose", "--help"], env={"TERM": "dumb"})
 
         # Assert
         assert result.exit_code == 0

tests/cli/infer/test_multi_segmentation.py

@@ -244,7 +244,9 @@ def test_multi_segmentation_default_values(self, mock_infer):
     def test_multi_segmentation_help_text(self):
         """Test that the multi-segmentation command has proper help text."""
         # Arrange & Act
-        result = self.runner.invoke(app, ["multi-segmentation", "--help"])
+        result = self.runner.invoke(
+            app, ["multi-segmentation", "--help"], env={"TERM": "dumb"}
+        )
 
         # Assert
         assert result.exit_code == 0

tests/cli/infer/test_single_pose.py

@@ -294,7 +294,9 @@ def test_single_pose_default_values(self, mock_infer):
     def test_single_pose_help_text(self):
         """Test that the single-pose command has proper help text."""
         # Arrange & Act
-        result = self.runner.invoke(app, ["single-pose", "--help"])
+        result = self.runner.invoke(
+            app, ["single-pose", "--help"], env={"TERM": "dumb"}
+        )
 
         # Assert
         assert result.exit_code == 0

tests/cli/infer/test_single_segmentation.py

@@ -244,7 +244,9 @@ def test_single_segmentation_default_values(self, mock_infer):
     def test_single_segmentation_help_text(self):
         """Test that the single-segmentation command has proper help text."""
         # Arrange & Act
-        result = self.runner.invoke(app, ["single-segmentation", "--help"])
+        result = self.runner.invoke(
+            app, ["single-segmentation", "--help"], env={"TERM": "dumb"}
+        )
 
         # Assert
         assert result.exit_code == 0

tests/cli/qa/test_commands.py

@@ -111,7 +111,11 @@ def test_qa_single_pose_execution_with_mock_file():
         pose_file = Path(tmp_file.name)
 
     # Mock the inspect_pose_v6 function to avoid actual file processing
-    with patch("mouse_tracking.cli.qa.inspect_pose_v6") as mock_inspect:
+    # and mock to_csv to avoid creating real CSV files
+    with (
+        patch("mouse_tracking.cli.qa.inspect_pose_v6") as mock_inspect,
+        patch("pandas.DataFrame.to_csv") as mock_to_csv,
+    ):
         mock_inspect.return_value = {"metric1": 0.5, "metric2": 0.8}
 
         # Act
@@ -120,6 +124,7 @@ def test_qa_single_pose_execution_with_mock_file():
         # Assert
         assert result.exit_code == 0
         mock_inspect.assert_called_once()
+        mock_to_csv.assert_called_once()
 
     # Cleanup
     if pose_file.exists():
@@ -277,7 +282,7 @@ def test_qa_command_help_format(command_name):
     runner = CliRunner()
 
     # Act
-    result = runner.invoke(app, [command_name, "--help"])
+    result = runner.invoke(app, [command_name, "--help"], env={"TERM": "dumb"})
 
     # Assert
     assert result.exit_code == 0