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Add BridgeStan to user code Docker image #480

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Add BridgeStan to user code Docker image #480

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5f62efe
Bump user code Python versions
simeoncarstens Jul 15, 2023
c0ecfab
Add BrideStan to user code Docker image
simeoncarstens Jul 15, 2023
0e8d877
Add comments about Python version bumps
simeoncarstens Jul 20, 2023
987331a
Download `stanc` compiler at image build time
simeoncarstens Jul 20, 2023
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6 changes: 5 additions & 1 deletion app/user_code_server/pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,11 @@ packages = [ { include = 'chainsail' } ]
chainsail-user-code-server = 'chainsail.user_code_server:run'

[tool.poetry.dependencies]
python = "^3.8"
# Other Python applications / libraries in this project have Python 3.8 as a
# minimal requirement, but here we need Python 3.9 because that's the lower Python
# version bound for BridgeStan. Else Poetry would not be able to resolve dependencies
# when installing BridgeStan.
python = "^3.9"
numpy = "*"
chainsail-common = { path = "../../lib/common", develop = true }
chainsail-grpc = { path = "../../lib/grpc", develop = true }
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16 changes: 14 additions & 2 deletions docker/user-code/Dockerfile
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@@ -1,7 +1,10 @@
##############################################################################
# BASE
##############################################################################
FROM python:3.8.7-slim as base

# We use Python 3.10 (in contrast to Python 3.8 elsewhere in this project), because
# BridgeStan needs at least Python 3.9.
FROM python:3.10-slim as base

# Set up required directories
RUN mkdir -p /app/deps && mkdir -p /run/sshd
Expand Down Expand Up @@ -42,6 +45,15 @@ RUN cd /app/app/user_code_server && \
poetry run pip install --upgrade pip && \
poetry install --no-dev

# Install BridgeStan
ARG BRIDGESTAN_PATH=/app/deps/bridgestan
RUN git clone --recurse-submodules --shallow-submodules --branch v2.1.1 --single-branch https://github.com/roualdes/bridgestan.git $BRIDGESTAN_PATH
RUN cd /app/app/user_code_server && poetry add $BRIDGESTAN_PATH/python/
## BridgeStan requires the Stan compiler. If not available, it gets automatically downloaded
## when first compiling a model, but why do this at runtime if we can do it at image build time
RUN mkdir $BRIDGESTAN_PATH/bin
RUN wget -O $BRIDGESTAN_PATH/bin/stanc https://github.com/stan-dev/stanc3/releases/download/v2.32.1/linux-stanc
RUN chmod 777 $BRIDGESTAN_PATH/bin/stanc

##############################################################################
# FINAL
Expand All @@ -62,7 +74,7 @@ RUN chmod 555 /app/entrypoint.sh
# Adding the app venv bin to the front of path so it is the default pip, etc.
ENV PATH=/app/app/user_code_server/.venv/bin:$PATH
RUN pip install scipy==1.9.1 numpy==1.23.2 pymc==4.1.7 requests==2.28.1 chainsail-helpers==0.1.4

ENV BRIDGESTAN=/app/deps/bridgestan
WORKDIR /probability

ENV USER_CODE_SERVER_PORT=50052
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