fix: update Docker environment configuration

fix: update Docker environment configuration - Replace ENV with ARG for user credentials - Update Python virtual environment path to /opt/venv - Fix RETICULATE_PYTHON path configuration
davidycliao · Jan 12, 2025 · a47b172 · a47b172
1 parent dc6f523
commit a47b172
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diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml
@@ -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
diff --git a/Dockerfile b/Dockerfile
@@ -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 && \
@@ -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"]