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Update .onAttach to prevent reticulate prompt #284

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merged 7 commits into from
Jan 12, 2025
Merged

Update .onAttach to prevent reticulate prompt #284

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7ee0cb5
fix: standardize flair environment path setup
davidycliao Jan 12, 2025
819f63d
fix: standardize flair environment path setup
davidycliao Jan 12, 2025
904861f
fix: standardize flair environment path setup
davidycliao Jan 12, 2025
862a394
Update Dockerfile to use user-specific virtual environment path
davidycliao Jan 12, 2025
5441faa
Add Docker environment detection and support
davidycliao Jan 12, 2025
c3dc9d2
Add Docker environment detection and support
davidycliao Jan 12, 2025
b96fca9
Update .onAttach to prevent reticulate prompt
davidycliao Jan 12, 2025
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25 changes: 13 additions & 12 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@ RUN apt-get update && apt-get install -y \
gdebi-core \
wget \
sudo \
curl
curl \
virtualenv # 添加virtualenv

# Create rstudio user
# default accout 'rstudio'; password: rstudio123
ENV USER=rstudio
ENV PASSWORD=rstudio123
RUN useradd -m $USER && \
Expand All @@ -25,21 +25,23 @@ 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

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

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

# Install Python packages
RUN /opt/venv/bin/pip install --no-cache-dir \
# Install Python packages in the virtual environment
RUN $VENV_PATH/bin/pip install --no-cache-dir \
numpy==1.26.4 \
scipy==1.12.0 \
transformers \
Expand All @@ -49,7 +51,7 @@ RUN /opt/venv/bin/pip install --no-cache-dir \
# Install R packages
RUN R -e "install.packages('reticulate', repos='https://cloud.r-project.org/', dependencies=TRUE)" && \
R -e "install.packages('remotes', repos='https://cloud.r-project.org/', dependencies=TRUE)" && \
R -e "remotes::install_github('davidycliao/flaiR', dependencies=TRUE)"
R -e "options(timeout=600); Sys.setenv(RETICULATE_PYTHON='$VENV_PATH/bin/python'); library(reticulate); use_virtualenv('$VENV_PATH', required = TRUE); remotes::install_github('davidycliao/flaiR', dependencies=TRUE)"

# Set working directory
WORKDIR /home/$USER
Expand All @@ -65,4 +67,3 @@ EXPOSE 8787
# Run service as rstudio user
USER $USER
CMD ["/usr/lib/rstudio-server/bin/rserver", "--server-daemonize=0"]

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