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Likely to be abandoned attempt to make Dockerfile platform independent #19

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82 changes: 53 additions & 29 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,6 +1,9 @@
FROM obolibrary/odkfull:latest
FROM ubuntu:24.04

# Install git and dependencies
# Avoid apt cache issues
ENV DEBIAN_FRONTEND=noninteractive

# Install git and dependencies in one layer with proper cleanup
RUN apt-get update && apt-get install -y \
git \
build-essential \
Expand All @@ -12,26 +15,29 @@ RUN apt-get update && apt-get install -y \
curl \
liblzma-dev \
software-properties-common \
unzip \
ca-certificates \
--no-install-recommends \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
&& rm -rf /var/lib/apt/lists/* \
&& rm -rf /var/cache/apt/archives/*

# Set noninteractive installation
ENV DEBIAN_FRONTEND=noninteractive
ENV TZ=Etc/UTC

# Install Python 3.11 directly
RUN add-apt-repository ppa:deadsnakes/ppa && \
apt-get update && \
apt-get install -y python3.11 python3.11-venv python3.11-dev python3-pip tzdata && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*

# Set Python 3.11 as default
RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.11 1 && \
update-alternatives --set python3 /usr/bin/python3.11 && \
update-alternatives --install /usr/bin/python python /usr/bin/python3.11 1 && \
update-alternatives --set python /usr/bin/python3.11 && \
ln -sf /usr/bin/python3.11 /usr/local/bin/python
# Install bun.sh
RUN curl -fsSL https://bun.sh/install | bash -

# Install pyenv for Python version management
WORKDIR /root
RUN curl -sL https://github.com/pyenv/pyenv-installer/raw/master/bin/pyenv-installer | bash
ENV PYENV_ROOT="/root/.pyenv"
ENV PATH="${PYENV_ROOT}/bin:${PYENV_ROOT}/shims:${PATH}"

# Install Python 3.11 with pyenv
RUN pyenv install 3.11.4 && \
pyenv global 3.11.4

# Get the correct version of pip for Python 3.11
RUN curl -sS https://bootstrap.pypa.io/get-pip.py | python && \
pip install --upgrade pip

# Install Node.js using NVM
ENV NVM_DIR=/root/.nvm
Expand Down Expand Up @@ -59,15 +65,7 @@ RUN curl -fsSL https://get.pnpm.io/install.sh | bash -
# Install bun
RUN curl -fsSL https://bun.sh/install | bash -

# Clone and install cborg-code permanently using token
# Pass GH_TOKEN as a build arg: docker build --build-arg GH_TOKEN=your_token_here ...
ARG GH_TOKEN
RUN mkdir -p /tools/cborg && \
cd /tools/cborg && \
git clone https://${GH_TOKEN}@github.com/lbnl-science-it/cborg-code.git . && \
pnpm install && \
bun build src/entrypoints/cli.tsx --minify --outfile cli.mjs --target=node && \
pnpm link --global


# Pre-configure cborg-code with default settings
#RUN mkdir -p /root/.config/cborg-code && \
Expand All @@ -80,6 +78,13 @@ RUN curl -sS https://bootstrap.pypa.io/get-pip.py | python3.11 && \
# Install Python packages
RUN python3.11 -m pip install aurelian jinja2-cli "wrapt>=1.17.2"

# remove /tools/cborg/cborg-code if it exists
RUN rm -rf /tools/cborg/cborg-code

# Clone and install cborg-code permanently using token
# Pass GH_TOKEN as a build arg: docker build --build-arg GH_TOKEN=your_token_here ...


# #export LOGFIRE_SEND_TO_LOGFIRE=false
ENV LOGFIRE_SEND_TO_LOGFIRE=false

Expand All @@ -95,11 +100,29 @@ RUN cat /tmp/git-bashrc-config.sh >> ~/.bashrc
# Make sure git and bash-completion are installed
# RUN apt-get update && apt-get install -y bash-completion

RUN mkdir -p /tools

# make sure we have the latest obo-scripts
RUN cd /tools/ && rm -rf obo-scripts && git clone https://github.com/cmungall/obo-scripts

ENV PATH=$PATH:/tools/obo-scripts/

# Clone repository with GitHub token using BuildKit secrets
# This requires Docker BuildKit to be enabled
RUN --mount=type=secret,id=gh_token \
mkdir -p /tools/cborg && \
cd /tools/cborg && \
GH_TOKEN=$(cat /run/secrets/gh_token) && \
echo "Using token to clone repository..." && \
git clone https://oauth2:${GH_TOKEN}@github.com/lbnl-science-it/cborg-code.git . && \
echo "Installing dependencies with pnpm..." && \
pnpm install && \
echo "Building with bun..." && \
bun build src/entrypoints/cli.tsx --minify --outfile cli.mjs --target=node && \
echo "Linking package globally..." && \
pnpm link --global && \
rm -rf /tools/cborg/.git

# Copy entrypoint script
COPY bin/entrypoint.sh /usr/local/bin/entrypoint.sh

Expand All @@ -109,5 +132,6 @@ ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
# Set working directory
WORKDIR /work


# Default command
CMD ["bash"]
71 changes: 62 additions & 9 deletions Makefile
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Original file line number Diff line number Diff line change
@@ -1,35 +1,88 @@
.PHONY: build push
.PHONY: build push setup-buildx build-multiarch push-multiarch run test test-repos

IMAGE_NAME = odk-ai
TAG = latest
PLATFORMS = linux/amd64,linux/arm64

#BUILD_OPTS = --no-cache
BUILD_OPTS =

build:
# Check for GH_TOKEN
check-token:
@if [ -z "$$GH_TOKEN" ]; then \
echo "ERROR: GH_TOKEN environment variable is not set"; \
echo "Please set it with: export GH_TOKEN=your_github_token"; \
echo "You can create a token at https://github.com/settings/tokens"; \
exit 1; \
fi

# Setup buildx for multi-architecture builds
setup-buildx:
docker buildx create --name multiarch-builder --use || true
docker buildx inspect --bootstrap

# Original single-architecture build
build: check-token
docker build $(BUILD_OPTS) --build-arg GH_TOKEN=$(GH_TOKEN) -t cmungall/$(IMAGE_NAME):$(TAG) .

# Push the single-architecture image
push: build
docker tag $(IMAGE_NAME):$(TAG) cmungall/$(IMAGE_NAME):$(TAG)
docker push cmungall/$(IMAGE_NAME):$(TAG)

# Multi-architecture build using buildx
build-multiarch: check-token setup-buildx
# Note: For local use, build only for the current architecture
docker system prune -f || true
docker buildx build $(BUILD_OPTS) \
--platform linux/amd64 \
--secret id=gh_token,env=GH_TOKEN \
-t cmungall/$(IMAGE_NAME):$(TAG) \
--load \
.


# Build individual platform images with proper disk space management
build-amd64: check-token setup-buildx
# Ensure we have enough disk space for the build
docker system prune -f || true
docker buildx build $(BUILD_OPTS) \
--platform linux/amd64 \
--secret id=gh_token,env=GH_TOKEN \
-t cmungall/$(IMAGE_NAME):amd64 \
--load \
.

build-arm64: check-token setup-buildx
# Ensure we have enough disk space for the build
docker system prune -f || true
docker buildx build $(BUILD_OPTS) \
--platform linux/arm64 \
--secret id=gh_token,env=GH_TOKEN \
-t cmungall/$(IMAGE_NAME):arm64 \
--load \
.

# Push multi-architecture images
push-multiarch: check-token setup-buildx
# Ensure we have enough disk space for the build
docker system prune -f || true
docker buildx build $(BUILD_OPTS) \
--platform $(PLATFORMS) \
--secret id=gh_token,env=GH_TOKEN \
-t cmungall/$(IMAGE_NAME):$(TAG) \
--push \
.

# Run the container
run:
docker run -it --rm $(IMAGE_NAME):$(TAG)
docker run -it --rm cmungall/$(IMAGE_NAME):$(TAG)

# Test in a scratch directory
test:
cd scratch && docker run -v $PWD:/work -e ANTHROPIC_API_KEY=$$ANTHROPIC_API_KEY -it --rm odk-ai:latest bash
cd scratch && docker run -v $${PWD}:/work -e ANTHROPIC_API_KEY=$$ANTHROPIC_API_KEY -it --rm cmungall/$(IMAGE_NAME):$(TAG) bash

# e.g. test-repos/obophenotype/uberon
# git clone https://github.com/obophenotype/uberon
test-repos/%:
cd test-repos && git clone https://github.com/$*




cd test-repos && git clone https://github.com/$*