Update to Ubuntu 24.04 / CUDA 12.6.3 base image and use Python 3.12

PiperOrigin-RevId: 765229057
Change-Id: I7b1c8234fd1b067e62e308116d603f0e3d375972

dev-requirements.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.11
+# This file is autogenerated by pip-compile with Python 3.12
 # by the following command:
 #
 #    pip-compile --extra=dev --generate-hashes --output-file=dev-requirements.txt pyproject.toml

docker/Dockerfile

@@ -8,23 +8,20 @@
 # if received directly from Google. Use is subject to terms of use available at
 # https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md
 
-FROM nvidia/cuda:12.6.0-base-ubuntu22.04
+FROM nvidia/cuda:12.6.3-base-ubuntu24.04
 
 # Some RUN statements are combined together to make Docker build run faster.
-# Get latest package listing, install software-properties-common, git, wget,
-# compilers and libraries.
-# git is required for pyproject.toml toolchain's use of CMakeLists.txt.
-# gcc, g++, make are required for compiling hmmer and AlphaFold 3 libaries.
-# zlib is a required dependency of AlphaFold 3.
-RUN apt-get update --quiet \
-    && apt-get install --yes --quiet software-properties-common \
+# Get latest package listing, install python, git, wget, compilers and libs.
+# * git is required for pyproject.toml toolchain's use of CMakeLists.txt.
+# * 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
 
-# Get apt repository of specific Python versions. Then install Python. Tell APT
-# this isn't an interactive TTY to avoid timezone prompt when installing.
-RUN add-apt-repository ppa:deadsnakes/ppa \
-    && DEBIAN_FRONTEND=noninteractive apt-get install --yes --quiet python3.11 python3-pip python3.11-venv python3.11-dev
-RUN python3.11 -m venv /alphafold3_venv
+# 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
@@ -36,7 +33,7 @@ RUN pip3 install --no-cache-dir --upgrade pip
 # using `apt-get install hmmer` instead of bulding it from source, but we want
 # to have control over the exact version of HMMER. Also note that eddylab.org
 # unfortunately doesn't support HTTPS and the tar file published on GitHub is
-# is explicitly not recommended to be used for building from source.
+# explicitly not recommended to be used for building from source.
 RUN mkdir /hmmer_build /hmmer ; \
     wget http://eddylab.org/software/hmmer/hmmer-3.4.tar.gz --directory-prefix /hmmer_build ; \
     (cd /hmmer_build && echo "ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3 hmmer-3.4.tar.gz" | sha256sum --check) && \
@@ -52,8 +49,10 @@ RUN mkdir /hmmer_build /hmmer ; \
 COPY . /app/alphafold
 WORKDIR /app/alphafold
 
-# Install the Python dependencies AlphaFold 3 needs.
-RUN pip3 install --no-cache-dir -r dev-requirements.txt \
+# 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

requirements.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.11
+# This file is autogenerated by pip-compile with Python 3.12
 # by the following command:
 #
 #    pip-compile --generate-hashes