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Re-pin numpy<2 after jax install in alphafold2 dockerfile #622

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Merged
DimaMolod merged 1 commit into from
Jun 8, 2026
Merged

Re-pin numpy<2 after jax install in alphafold2 dockerfile #622

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8 changes: 8 additions & 0 deletions docker/alphafold2.dockerfile
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Expand Up @@ -64,6 +64,14 @@ RUN pip3 install --upgrade pip --no-cache-dir \
&& pip3 install --upgrade --no-cache-dir \
"jax[cuda12]"==0.5.3

# `pip install --upgrade "jax[cuda12]"==0.5.3` above drags in numpy 2.x, which makes
# AlphaFold multimer fail at runtime: alphafold/data/msa_pairing.py does
# `np.sum(x for x in feats)` and numpy>=2 raises
# `TypeError: Calling np.sum(generator) is deprecated`. The numpy<2 pins earlier in
# this file (conda + pyproject) run BEFORE the jax upgrade so they do not stick; re-pin
# numpy<2 as the LAST dependency step. jax 0.5.3 runs fine with numpy 1.26.x.
RUN pip install --no-cache-dir "numpy<2"

# Strip Python caches to reduce layer size
RUN find /opt/conda -type d -name "__pycache__" -prune -exec rm -rf {} + \
&& find /opt/conda -type f -name "*.pyc" -delete \
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