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fix: update Docker environment configuration #286

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Jan 12, 2025
Merged

fix: update Docker environment configuration #286

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154 changes: 94 additions & 60 deletions .github/workflows/docker-publish.yml
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Original file line number Diff line number Diff line change
@@ -1,60 +1,94 @@
FROM rocker/r-ver:latest

# Install system dependencies
RUN apt-get update && apt-get install -y \
python3-minimal \
python3-pip \
python3-venv \
libssl-dev \
gdebi-core \
wget \
sudo \
curl

# Create rstudio user
ARG USER=rstudio
ARG PASSWORD=rstudio123
RUN useradd -m $USER && \
echo "$USER:$PASSWORD" | chpasswd && \
adduser $USER sudo && \
echo "$USER ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers

# Install RStudio Server
RUN wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2023.12.1-402-amd64.deb && \
gdebi -n rstudio-server-2023.12.1-402-amd64.deb && \
rm rstudio-server-*.deb

# Create and configure Python virtual environment
RUN python3 -m venv /opt/venv && \
chown -R $USER:$USER /opt/venv

ENV PATH="/opt/venv/bin:$PATH"
ENV RETICULATE_PYTHON="/opt/venv/bin/python"

# Setup R environment config
RUN mkdir -p /usr/local/lib/R/etc && \
echo "RETICULATE_PYTHON=/opt/venv/bin/python" >> /usr/local/lib/R/etc/Renviron.site && \
echo "options(reticulate.prompt = FALSE)" >> /usr/local/lib/R/etc/Rprofile.site

# Install Python packages
RUN /opt/venv/bin/pip install --no-cache-dir \
numpy==1.26.4 \
scipy==1.12.0 \
transformers \
torch \
flair

# Install R packages with proper setup
RUN R -e 'install.packages("reticulate", repos="https://cloud.r-project.org/", dependencies=TRUE)' && \
R -e 'if(require(reticulate)) { \
Sys.setenv(RETICULATE_PYTHON="/opt/venv/bin/python"); \
reticulate::use_python("/opt/venv/bin/python", required=TRUE); \
install.packages("remotes", repos="https://cloud.r-project.org/", dependencies=TRUE); \
remotes::install_github("davidycliao/flaiR", dependencies=TRUE) \
}'

WORKDIR /home/$USER
USER $USER
EXPOSE 8787

CMD ["/usr/lib/rstudio-server/bin/rserver", "--server-daemonize=0"]
name: flaiR-Docker
on:
push:
branches: [main, master]
pull_request:
branches: [main, master]


jobs:
R-CMD-check:
runs-on: ubuntu-latest
name: R-CMD-check
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes
steps:
- uses: actions/checkout@v3
- uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true
- uses: r-lib/actions/setup-pandoc@v2

- name: Setup Python
uses: actions/setup-python@v2
with:
python-version: '3.9'

- name: Install Python dependencies
run: |
python -m pip install --upgrade pip
pip install flair
- name: Install R dependencies
run: |
install.packages('remotes')
remotes::install_github("davidycliao/flaiR", force = TRUE)
shell: Rscript {0}

- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: rcmdcheck

docker:
needs: R-CMD-check
runs-on: ubuntu-latest
permissions:
contents: read
packages: write

steps:
- name: Checkout repository
uses: actions/checkout@v3

- name: Set up QEMU
uses: docker/setup-qemu-action@v2

- name: Log in to GitHub Container Registry
uses: docker/login-action@v2
with:
registry: ghcr.io
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}

- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
with:
buildkitd-flags: --debug

- name: Extract metadata for Docker
id: meta
uses: docker/metadata-action@v4
with:
images: ghcr.io/${{ github.repository_owner }}/flair-rstudio
tags: |
type=ref,event=branch
type=ref,event=pr
type=semver,pattern={{version}}
type=semver,pattern={{major}}.{{minor}}
type=sha
type=raw,value=latest,enable={{is_default_branch}}
- name: Build and push RStudio image
uses: docker/build-push-action@v4
with:
context: .
platforms: linux/amd64
push: ${{ github.event_name != 'pull_request' }}
tags: ${{ steps.meta.outputs.tags }}
labels: ${{ steps.meta.outputs.labels }}
build-args: |
DEFAULT_USER=rstudio
secrets: |
PASSWORD=${{ secrets.RSTUDIO_PASSWORD }}
cache-from: type=gha
cache-to: type=gha,mode=max
provenance: false
52 changes: 21 additions & 31 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -9,12 +9,11 @@ RUN apt-get update && apt-get install -y \
gdebi-core \
wget \
sudo \
curl \
virtualenv # 添加virtualenv
curl

# Create rstudio user
ENV USER=rstudio
ENV PASSWORD=rstudio123
ARG USER=rstudio
ARG PASSWORD=rstudio123
RUN useradd -m $USER && \
echo "$USER:$PASSWORD" | chpasswd && \
adduser $USER sudo && \
Expand All @@ -25,46 +24,37 @@ RUN wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2023.12
gdebi -n rstudio-server-2023.12.1-402-amd64.deb && \
rm rstudio-server-*.deb

# 修改虚拟环境路径到用户目录
ENV VENV_PATH=/home/$USER/flair_env
RUN python3 -m venv $VENV_PATH && \
chown -R $USER:$USER $VENV_PATH
# Create and configure Python virtual environment
RUN python3 -m venv /opt/venv && \
chown -R $USER:$USER /opt/venv

# 更新环境变量
ENV PATH="$VENV_PATH/bin:$PATH"
ENV RETICULATE_PYTHON="$VENV_PATH/bin/python"
ENV PATH="/opt/venv/bin:$PATH"
ENV RETICULATE_PYTHON="/opt/venv/bin/python"

# Setup R environment config
RUN mkdir -p /usr/local/lib/R/etc && \
echo "RETICULATE_PYTHON=$VENV_PATH/bin/python" >> /usr/local/lib/R/etc/Renviron.site && \
chown -R $USER:$USER /usr/local/lib/R/etc/Renviron.site && \
chmod 644 /usr/local/lib/R/etc/Renviron.site
echo "RETICULATE_PYTHON=/opt/venv/bin/python" >> /usr/local/lib/R/etc/Renviron.site && \
echo "options(reticulate.prompt = FALSE)" >> /usr/local/lib/R/etc/Rprofile.site

# Install Python packages in the virtual environment
RUN $VENV_PATH/bin/pip install --no-cache-dir \
# Install Python packages
RUN /opt/venv/bin/pip install --no-cache-dir \
numpy==1.26.4 \
scipy==1.12.0 \
transformers \
torch \
flair

# Install R packages
RUN R -e "install.packages('reticulate', repos='https://cloud.r-project.org/', dependencies=TRUE)" && \
R -e "install.packages('remotes', repos='https://cloud.r-project.org/', dependencies=TRUE)" && \
R -e "options(timeout=600); Sys.setenv(RETICULATE_PYTHON='$VENV_PATH/bin/python'); library(reticulate); use_virtualenv('$VENV_PATH', required = TRUE); remotes::install_github('davidycliao/flaiR', dependencies=TRUE)"
# Install R packages with proper setup
RUN R -e 'install.packages("reticulate", repos="https://cloud.r-project.org/", dependencies=TRUE)' && \
R -e 'if(require(reticulate)) { \
Sys.setenv(RETICULATE_PYTHON="/opt/venv/bin/python"); \
reticulate::use_python("/opt/venv/bin/python", required=TRUE); \
install.packages("remotes", repos="https://cloud.r-project.org/", dependencies=TRUE); \
remotes::install_github("davidycliao/flaiR", dependencies=TRUE) \
}'

# Set working directory
WORKDIR /home/$USER
RUN chown -R $USER:$USER /home/$USER

# Add healthcheck
HEALTHCHECK --interval=30s --timeout=10s --start-period=5s --retries=3 \
CMD curl -f http://localhost:8787/ || exit 1

# Expose port
USER $USER
EXPOSE 8787

# Run service as rstudio user
USER $USER
CMD ["/usr/lib/rstudio-server/bin/rserver", "--server-daemonize=0"]
CMD ["/usr/lib/rstudio-server/bin/rserver", "--server-daemonize=0"]
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