Reconcile dependencies with colab and add dockerfile

Dockerfile

@@ -0,0 +1,37 @@
+FROM us-docker.pkg.dev/colab-images/public/runtime:release-colab_20240626-060133_RC01
+
+# Install uv
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv
+
+# Verify existing packages (optional, for debugging)
+RUN python -m pip list
+
+# Set working directory
+WORKDIR /app
+
+# Configure uv to use system Python and packages
+ENV UV_SYSTEM_PYTHON=1
+ENV UV_PYTHON=/usr/local/bin/python
+
+# Copy dependency files first (better layer caching)
+COPY pyproject.toml .
+COPY uv.lock* .
+COPY README.md .
+
+# Install dependencies while respecting system packages
+RUN uv pip install --system -r pyproject.toml
+
+# Copy application code
+COPY src .
+
+# If you need to install your package in development mode
+RUN uv pip install --system -e .
+
+# Set Python to unbuffered mode
+ENV PYTHONUNBUFFERED=1
+
+# Reset the entrypoint to nothing
+ENTRYPOINT []
+
+# Entrypoint
+CMD ["mouse-tracking-runtime"]

pyproject.toml

@@ -5,36 +5,40 @@ description = "Runtime environment for mouse tracking experiments"
 requires-python = ">=3.10,<3.11"
 packages = ["src/mouse_tracking"]
 dependencies = [
-    "absl-py>=2.3.0",
-    "click==8.1.8",
-    "contourpy==1.3.2",
+    # Core scientific computing - exact versions from container
+    "numpy==1.25.2",
+    "scipy==1.11.4",
+    "pandas==2.0.3",
+    # Computer vision and image processing
+    "opencv-python==4.8.0.76",
+    "imageio==2.31.6",
+    "pillow==9.4.0",
+    # Plotting and visualization
+    "matplotlib==3.7.1",
+    "contourpy==1.2.1",
     "cycler==0.12.1",
-    "fonttools==4.57.0",
-    "h5py==3.13.0",
-    "imageio>=2.37.0",
-    "kiwisolver==1.4.8",
-    "matplotlib==3.10.1",
-    "mypy-extensions==1.0.0",
-    "networkx==3.4.2",
-    "numpy>=1.26.0,<2.0.0",
-    "opencv-python==4.11.0.86",
-    "packaging==24.2",
-    "pandas==2.2.3",
-    "pathspec==0.12.1",
-    "pillow==11.2.1",
-    "platformdirs==4.3.7",
-    "pydantic>=2.11.7",
+    "fonttools==4.53.0",
+    "kiwisolver==1.4.5",
+    # Machine learning frameworks - flexible versions to use pre-installed
+    "tensorflow>=2.15.0,<2.16.0",
+    "torch>=2.3.0,<2.4.0",
+    # Utilities and CLI
+    "click==8.1.7",
+    "typer>=0.12.4",
+    "absl-py==1.4.0",
+    # Data validation
+    "pydantic==2.7.4",
+    # Standard library extensions
+    "networkx==3.3",
+    "packaging==24.1",
+    "platformdirs==4.2.2",
+    "pyparsing==3.1.2",
+    "python-dateutil==2.8.2",
+    "pytz==2023.4",
+    "six==1.16.0",
+    "tzdata==2024.1",
+    "h5py==3.9.0",
     "pydantic-settings>=2.10.1",
-    "pyparsing==3.2.3",
-    "python-dateutil==2.9.0.post0",
-    "pytz==2025.1",
-    "scipy==1.15.2",
-    "six==1.17.0",
-    "tensorflow>=2.15",
-    "torch>=2.0.1",
-    "typer>=0.16.0",
-    "tzdata==2025.1",
-    "yacs>=0.1.8",
 ]
 
 [project.scripts]
@@ -77,9 +81,13 @@ convention = "google"
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401"]  # Unused imports in __init__ files
 
+[tool.pytest.ini_options]
+addopts = "--benchmark-skip"
+
 [dependency-groups]
 dev = [
     "pytest>=8.3.5",
+    "pytest-benchmark>=5.1.0",
     "pytest-cov>=6.1.1",
     "ruff>=0.11.2",
 ]