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install geometric dependencies before invalidating caches with source copy #224

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merged 6 commits into from
Oct 2, 2024
Merged

install geometric dependencies before invalidating caches with source copy #224

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install geometric dependencies before invalidating caches with source…
pstjohn Oct 1, 2024
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add requirements-cve to docker build
pstjohn Oct 1, 2024
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expand dockerignore
pstjohn Oct 1, 2024
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update requirements-cve
pstjohn Oct 2, 2024
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add jupyter server cve
pstjohn Oct 2, 2024
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add comment for jupyter-server
pstjohn Oct 2, 2024
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6 changes: 6 additions & 0 deletions Dockerfile
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Expand Up @@ -79,6 +79,12 @@ ENV UV_LINK_MODE=copy \
UV_PYTHON_DOWNLOADS=never \
UV_SYSTEM_PYTHON=true

# Install the bionemo-geomtric requirements ahead of copying over the rest of the repo, so that we can cache their
# installation. These involve building some torch extensions, so they can take a while to install.
RUN --mount=type=bind,source=./sub-packages/bionemo-geometric/requirements.txt,target=/requirements-pyg.txt \
--mount=type=cache,id=uv-cache,target=/root/.cache,sharing=locked \
uv pip install --no-build-isolation -r /requirements-pyg.txt

WORKDIR /workspace/bionemo2

# Install 3rd-party deps and bionemo submodules.
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3 changes: 2 additions & 1 deletion sub-packages/bionemo-geometric/pyproject.toml
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Expand Up @@ -14,7 +14,8 @@ classifiers = ["Private :: Do Not Upload", "Programming Language :: Python :: 3.
dynamic = ["version"]
dependencies = [
'bionemo-core',
# Version pins for the pip package. If updating these, also update the image pins in requirements.txt.
# Version pins for the pip package. If updating these, also update the image pins in requirements.txt. Ideally we
# should allow these dependencies to float in the package definition.
'torch-cluster==1.6.3',
'torch-geometric==2.5.0',
'torch-scatter==2.1.2',
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