Modernize setup, switch to Python 3.12, and migrate to uv

PiperOrigin-RevId: 856564478
Change-Id: I31af1c170846fb787235dfc03b3a6da0464f51be

.github/workflows/ci.yaml

@@ -1,7 +1,6 @@
 name: Continuous Integration
 
 on:
-  # Trigger the workflow on push or pull request, only on the main branch.
   push:
     branches:
       - main
@@ -18,21 +17,28 @@ jobs:
       matrix:
         include:
           - name-prefix: "all tests"
-            python-version: '3.11'
+            python-version: '3.12'
             os: ubuntu-latest
+
     steps:
     - uses: actions/checkout@v6
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v6
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v7
       with:
-        python-version: ${{ matrix.python-version }}
+        enable-cache: true
+        cache-dependency-glob: "uv.lock"
+
+    - name: Set up Python ${{ matrix.python-version }}
+      run: uv python install ${{ matrix.python-version }}
+
     - name: Install dependencies
-      run: |
-        sudo apt-get install -y hmmer
-        pip install --upgrade pip
-        pip install -r dev-requirements.txt
-        pip install --no-deps .
-        build_data
+      run: sudo apt-get install -y hmmer
+
+    - name: Install Python dependencies
+      run: uv sync --frozen --all-groups
+
+    - name: Build data
+      run: uv run build_data
+
     - name: Run CPU-only tests
-      run: |
-        python run_alphafold_data_test.py
+      run: uv run python run_alphafold_data_test.py

docker/Dockerfile

@@ -16,17 +16,21 @@ FROM nvidia/cuda:12.6.3-base-ubuntu24.04
 # * gcc, g++, make are required for compiling HMMER and AlphaFold 3 libaries.
 # * zlib is a required dependency of AlphaFold 3.
 RUN DEBIAN_FRONTEND=noninteractive \
-    apt-get update --quiet \
-    && apt-get install --yes --quiet python3.12 python3-pip python3.12-venv python3.12-dev \
-    && apt-get install --yes --quiet git wget gcc g++ make zlib1g-dev zstd
+apt-get update --quiet \
+&& apt-get install --yes --quiet python3.12 python3.12-dev \
+&& apt-get install --yes --quiet git wget gcc g++ make zlib1g-dev zstd
+
+# Install uv from the official repository. The version is pinned for
+# reproducibility.
+COPY --from=ghcr.io/astral-sh/uv:0.9.24 /uv /uvx /bin/
+
+# UV_COMPILE_BYTECODE=1 speeds up future container starts.
+# UV_PROJECT_ENVIRONMENT explicitly sets the virtual environment location.
+ENV UV_COMPILE_BYTECODE=1
+ENV UV_PROJECT_ENVIRONMENT=/alphafold3_venv
+RUN uv venv $UV_PROJECT_ENVIRONMENT
 
-# The base image uses Python 3.12. For local installation use 3.11 or greater.
-RUN python3 -m venv /alphafold3_venv
 ENV PATH="/hmmer/bin:/alphafold3_venv/bin:$PATH"
-# Update pip to the latest version. Not necessary in Docker, but good to do when
-# this is used as a recipe for local installation since we rely on new pip
-# features for secure installs.
-RUN pip3 install --no-cache-dir --upgrade pip
 
 # Install HMMER. Do so before copying the source code, so that docker can cache
 # the image layer containing HMMER. Alternatively, you could also install it
@@ -58,13 +62,18 @@ RUN (cd /hmmer_build/hmmer-3.4 && ./configure --prefix /hmmer) ; \
 COPY . /app/alphafold
 WORKDIR /app/alphafold
 
-# Install setuptools (removed in Python 3.12) which some libraries still need.
-# Then install the Python dependencies of AlphaFold 3.
-RUN pip3 install --no-cache-dir setuptools \
-    && pip3 install --no-cache-dir -r dev-requirements.txt \
-    && pip3 install --no-cache-dir --no-deps .
-# Build chemical components database (this binary was installed by pip).
-RUN build_data
+# Install the exact dependency tree using uv and cache the build artifacts.
+# --frozen: do not update the lockfile during build.
+# --all-groups: install development/test dependencies defined in pyproject.toml.
+# --no-editable: install as a static package.
+# If using this as a recipe for local installation and you want to modify
+# AlphaFold 3 code and change its dependencies, remove the --frozen and
+# --no-editable flags.
+RUN --mount=type=cache,target=/root/.cache/uv \
+    uv sync --frozen --all-groups --no-editable
+
+# Build chemical components database (this binary was installed by uv sync).
+RUN uv run build_data
 
 # To work around a known XLA issue causing the compilation time to greatly
 # increase, the following environment variable setting XLA flags must be enabled
@@ -77,4 +86,4 @@ ENV XLA_FLAGS="--xla_gpu_enable_triton_gemm=false"
 ENV XLA_PYTHON_CLIENT_PREALLOCATE=true
 ENV XLA_CLIENT_MEM_FRACTION=0.95
 
-CMD ["python3", "run_alphafold.py"]
+CMD ["uv", "run", "python3", "run_alphafold.py"]

pyproject.toml

@@ -11,7 +11,7 @@ build-backend = "scikit_build_core.build"
 [project]
 name = "alphafold3"
 version = "3.0.1"
-requires-python = ">=3.11"
+requires-python = ">=3.12"
 readme = "README.md"
 license = {file = "LICENSE"}
 dependencies = [
@@ -27,8 +27,13 @@ dependencies = [
     "zstandard",
 ]
 
-[project.optional-dependencies]
-test = ["pytest>=6.0"]
+[dependency-groups]
+dev = [
+    "pytest>=6.0",
+]
+
+[tool.uv]
+package = true
 
 [tool.scikit-build]
 wheel.exclude = [