mirror of
https://github.com/KosinskiLab/AlphaPulldown.git
synced 2026-06-04 14:14:24 +08:00
fff63051b4
* Harden MMseqs species ID resolution fallback * Reorganize tests for CPU coverage CI * New * Fix function coverage checker def-line false positives * Expand unit coverage for helper and backend manager utilities * New. * New. * Expand unit coverage for template and post-processing helpers * Expand unit coverage for objects.py edge cases * Publish HTML coverage reports via GitHub Pages * Add CPU unit coverage for AlphaFold3 backend helpers * Reorganize tests and expand backend coverage * Reset shared test flags between cases * Expand AF3 prepare_input unit coverage * Cover AF3 and truemultimer feature creation * Test AF3 multimer MSA translation paths * Cover AF3 duplicate-residue multimer fallback * Cover AF2 resume and postprocess edge paths * Cover AF3 template mmCIF preparation * Test small script entry points * Expand workflow and ModelCIF test coverage * Add backend extras and install guide * Clarify AF3 backend installation path * Stabilize cluster GPU test runners * Document AF3 CMake SQLite hints * Simplify backend installation guide * Align AF3 install with working cluster env * Backfill typing dataclass_transform for AF2 * Pin TensorFlow for cluster installs * Fallback AF2 relax when CUDA OpenMM is unavailable * Raise AF3 default minimum bucket size * Simplify backend cluster installation guide * Fix AF3 wrapper JSON output isolation * Fix AF3 JSON wrapper outputs and MMseqs ID parsing * Fix CI entrypoint stub and Python 3.8 typing * Document release readiness test gates
83 lines
2.9 KiB
Docker
83 lines
2.9 KiB
Docker
# syntax=docker/dockerfile:1.4
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ARG CUDA=12.2.2
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FROM nvidia/cuda:${CUDA}-cudnn8-runtime-ubuntu20.04
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ARG CUDA
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SHELL ["/bin/bash","-o","pipefail","-c"]
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# Trim docs/locales to shrink APT-installed footprint
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RUN set -eux; \
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echo 'path-exclude=/usr/share/man/*' > /etc/dpkg/dpkg.cfg.d/01_nodoc; \
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echo 'path-exclude=/usr/share/doc/*' >> /etc/dpkg/dpkg.cfg.d/01_nodoc; \
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echo 'path-exclude=/usr/share/locale/*' >> /etc/dpkg/dpkg.cfg.d/01_nodoc; \
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echo 'path-include=/usr/share/locale/en*' >> /etc/dpkg/dpkg.cfg.d/01_nodoc; \
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printf 'Acquire::Languages "none";\n' > /etc/apt/apt.conf.d/99no-languages
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# Only minimal runtime deps to bootstrap micromamba; no upgrade, no dev toolchain
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RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
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--mount=type=cache,target=/var/lib/apt,sharing=locked \
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set -eux; \
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apt-get update; \
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DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
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ca-certificates curl bzip2 tzdata openssh-client; \
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rm -rf /var/lib/apt/lists/*
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# Micromamba bootstrap (smaller than Miniforge)
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ENV MAMBA_ROOT_PREFIX=/opt/conda
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RUN set -eux; \
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mkdir -p "$MAMBA_ROOT_PREFIX"; \
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curl -k -L https://micro.mamba.pm/api/micromamba/linux-64/latest \
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| tar -xj -C /usr/local/bin --strip-components=1 bin/micromamba
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ENV PATH="/opt/conda/bin:${PATH}"
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ENV LD_LIBRARY_PATH="/opt/conda/lib:${LD_LIBRARY_PATH}"
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RUN set -eux; \
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micromamba install -y -r "/opt/conda" -n base \
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-c conda-forge -c bioconda \
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python=3.11 \
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kalign2 \
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modelcif \
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hmmer \
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hhsuite \
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"numpy<2" \
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"openmm>=8.2" \
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"pdbfixer>=1.10" \
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pip \
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git \
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&& micromamba clean -a -y
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#RUN micromamba run -n base python -m pip install --no-cache-dir "openmm==8.1.1"
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RUN python -m pip install --no-cache-dir "setuptools<82" # setuptools>82 breaks pdbfixer at relaxation
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# Clone from repo
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RUN mkdir -p /root/.ssh && chmod 700 /root/.ssh
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RUN ssh-keyscan github.com >> /root/.ssh/known_hosts
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RUN git clone --recurse-submodules https://github.com/KosinskiLab/AlphaPulldown.git
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WORKDIR AlphaPulldown
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#DEBUG
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#WORKDIR /AlphaPulldown
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#COPY . /AlphaPulldown
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RUN pip install --no-build-isolation .
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RUN pip3 install --upgrade pip --no-cache-dir \
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&& pip3 install --upgrade --no-cache-dir \
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"jax[cuda12]"==0.5.3
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# Strip Python caches to reduce layer size
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RUN find /opt/conda -type d -name "__pycache__" -prune -exec rm -rf {} + \
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&& find /opt/conda -type f -name "*.pyc" -delete \
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&& find /AlphaPulldown -type d -name "__pycache__" -prune -exec rm -rf {} + \
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&& find /AlphaPulldown -type f -name "*.pyc" -delete
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# Clean out APT bootstrap tools (curl/bzip2) to shave a bit more
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RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
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--mount=type=cache,target=/var/lib/apt,sharing=locked \
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set -eux; \
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apt-get purge -y curl bzip2 || true; \
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apt-get autoremove -y; \
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apt-get clean; \
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rm -rf /var/lib/apt/lists/* /root/.cache
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#ENTRYPOINT ["bash"]
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