Restore uv for system-wide dependency installation

Dockerfile

@@ -6,23 +6,15 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     curl \
     && rm -rf /var/lib/apt/lists/*
 
-# Install uv for fast Python environment management
-RUN pip install --no-cache-dir uv
-
 # Create working directory
 WORKDIR /workspace
 
 # Copy dependency lists first to leverage Docker layer caching
 COPY requirements.txt /workspace/requirements.txt
 
-# Create a virtual environment and install Python dependencies
-RUN uv venv /opt/venv \
-    && . /opt/venv/bin/activate \
-    && uv pip install -r /workspace/requirements.txt
-
-# Ensure the virtual environment is used by default
-ENV VIRTUAL_ENV=/opt/venv
-ENV PATH="/opt/venv/bin:$PATH"
+# Install uv and use it to install Python dependencies system-wide
+RUN pip install --no-cache-dir uv \
+    && uv pip install --system -r /workspace/requirements.txt
 
 # Copy the rest of the repository into the container
 COPY . /workspace

Makefile

@@ -2,36 +2,36 @@
 
 # Run the unit test suite
 test:
-	pytest -q
+        pytest -q
 
 # Check style with ruff
 lint:
-	ruff check src tests
+        ruff check src tests
 
 # Format code with ruff
 format:
-	ruff format src tests
+        ruff format src tests
 
 # Build the Docker image
 build:
-	docker compose build
+        docker compose build
 
 # Bring up the research container
 up:
-	docker compose up
+        docker compose up
 
 # Tear down the research container
 down:
-	docker compose down --remove-orphans
+        docker compose down --remove-orphans
 
 # Open a shell inside the container
 shell:
-	docker compose run --rm research bash
+        docker compose run --rm --user "$$(id -u):$$(id -g)" research bash
 
 # Run the default experiment runner
 run:
-	docker compose run --rm research python -m molmole_research.runner
+        docker compose run --rm --user "$$(id -u):$$(id -g)" research python -m molmole_research.runner
 
 # Download the MolMole dataset into the data/ directory
 download:
-	docker compose run --rm research python -m molmole_research.downloader --dataset doxa-friend/MolMole_Patent300 --out data/images
+        docker compose run --rm --user "$$(id -u):$$(id -g)" research python -m molmole_research.downloader --dataset doxa-friend/MolMole_Patent300 --out data/images