Merge pull request #266 from davidycliao/0.1.7

0.1.7

.github/workflows/docker-publish.yml

@@ -4,6 +4,8 @@ on:
     branches: [main, master]
   pull_request:
     branches: [main, master]
+
+
 jobs:
   R-CMD-check:
     runs-on: ubuntu-latest
@@ -17,49 +19,78 @@ jobs:
         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:
-      - uses: actions/checkout@v3
+      - 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: .
-          push: true
-          tags: |
-            ghcr.io/${{ github.repository_owner }}/flair-rstudio:latest
-          labels: |
-            org.opencontainers.image.title=flaiR-RStudio
-            org.opencontainers.image.version=0.0.7
+          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

Dockerfile

@@ -1,69 +1,67 @@
 FROM rocker/r-ver:latest
 
-# 系統更新和安裝安全性修補
-RUN apt-get update && \
-    apt-get upgrade -y && \
-    apt-get install -y --no-install-recommends \
+# Install system dependencies
+RUN apt-get update && apt-get install -y \
     python3-minimal \
     python3-pip \
     python3-venv \
-    python3-full \
-    libcurl4-openssl-dev \
     libssl-dev \
     gdebi-core \
     wget \
-    sudo && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/*
+    sudo \
+    curl
 
-# 安裝 RStudio Server
-RUN wget --progress=dot:giga https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2023.12.1-402-amd64.deb && \
+# Create rstudio user
+ENV USER=rstudio
+ENV 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
 
-# Python 虛擬環境設置
-RUN python3 -m venv /opt/venv
+# 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 && \
+    chown -R $USER:$USER /usr/local/lib/R/etc/Renviron.site && \
+    chmod 644 /usr/local/lib/R/etc/Renviron.site
 
-# R env
-RUN echo "RETICULATE_PYTHON=/opt/venv/bin/python" >> /usr/local/lib/R/etc/Renviron.site
-
-# 安裝更新的 Python 包
-RUN /opt/venv/bin/pip install --no-cache-dir --upgrade pip && \
-    /opt/venv/bin/pip install --no-cache-dir \
-    numpy>=1.26.4 \
-    scipy>=1.12.0 \
+# Install Python packages
+RUN /opt/venv/bin/pip install --no-cache-dir \
+    numpy==1.26.4 \
+    scipy==1.12.0 \
     transformers \
     torch \
     flair
 
-# 安裝 R 包
-RUN install2.r --error --deps TRUE \
-    reticulate \
-    remotes && \
+# 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)"
 
-# 使用者設置（使用 ARG 而不是 ENV 來處理敏感資訊）
-ARG USER=rstudio
-ARG PASSWORD=rstudio123
-RUN useradd -m $USER && \
-    echo "$USER:$PASSWORD" | chpasswd && \
-    adduser $USER sudo
+# Set working directory
+WORKDIR /home/$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
 
-# 設置權限
-RUN mkdir -p /home/$USER && \
-    chown -R $USER:$USER /home/$USER && \
-    chown -R $USER:$USER /opt/venv && \
-    chown -R $USER:$USER /usr/local/lib/R/etc/Renviron.site && \
-    chmod 644 /usr/local/lib/R/etc/Renviron.site
-
-# 清理
-RUN apt-get clean && \
-    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
+# Expose port
 EXPOSE 8787
 
+# Run service as rstudio user
+USER $USER
 CMD ["/usr/lib/rstudio-server/bin/rserver", "--server-daemonize=0"]
+

R/zzz.R

@@ -89,86 +89,113 @@
 #   }
 # }
 .onAttach <- function(...) {
-  # Check if running in Docker
-  Sys.unsetenv("RETICULATE_PYTHON")
+  # Docker 環境檢查及 Python 設置
   in_docker <- file.exists("/.dockerenv")
 
-  # Determine Python command
   if (in_docker) {
-    python_path <- "/opt/venv/bin/python"
+    # Docker 環境使用固定路徑
+    python_path <- "/opt/venv/bin/python3"
+    Sys.setenv(RETICULATE_PYTHON = python_path)
   } else {
+    # 非 Docker 環境
     python_cmd <- if (Sys.info()["sysname"] == "Windows") "python" else "python3"
     python_path <- Sys.which(python_cmd)
   }
 
-  # Check Python path
+  # 檢查 Python 路徑
   if (python_path == "") {
-    packageStartupMessage("Cannot locate Python executable. Ensure it's installed and in your system's PATH. flaiR functionality requiring Python will not be available.")
+    packageStartupMessage("Cannot locate Python executable. Ensure Python is installed and in PATH.")
     return(invisible(NULL))
   }
 
-  # Check Python version
+  # 檢查 Python 版本
   tryCatch({
-    python_version <- system(paste(python_path, "--version"), intern = TRUE)
-    if (!grepl("Python 3", python_version)) {
-      packageStartupMessage("Python 3 is required. flaiR functionality requiring Python will not be available.")
+    python_version <- system2(python_path, "--version", stdout = TRUE, stderr = TRUE)
+    if (!any(grepl("Python 3", python_version))) {
+      packageStartupMessage("Python 3 is required.")
       return(invisible(NULL))
     }
   }, error = function(e) {
-    packageStartupMessage(paste("Failed to get Python version. Error:", e$message))
+    packageStartupMessage(sprintf("Failed to check Python version: %s", e$message))
     return(invisible(NULL))
   })
 
-  # Version check functions
+  # 檢查 PyTorch 版本
   check_torch_version <- function() {
-    torch_version_command <- paste(python_path, "-c \"import torch; print(torch.__version__)\"")
-    result <- system(torch_version_command, intern = TRUE)
-    if (length(result) == 0 || result[1] == "ERROR" || is.na(result[1])) {
-      return(list(paste("PyTorch", paste0("\033[31m", "\u2717", "\033[39m"), sep = " "), FALSE))
-    }
-    return(list(paste("PyTorch", paste0("\033[32m", "\u2713", "\033[39m"), result[1], sep = " "), TRUE, result[1]))
+    tryCatch({
+      cmd <- sprintf("%s -c 'import torch; print(torch.__version__)'", python_path)
+      result <- system(cmd, intern = TRUE)
+      if (length(result) > 0 && !is.na(result[1])) {
+        return(list(
+          status = paste("PyTorch", "\u2713", result[1]),
+          success = TRUE,
+          version = result[1]
+        ))
+      }
+    }, error = function(e) NULL)
+    return(list(status = paste("PyTorch", "\u2717"), success = FALSE))
   }
 
+  # 檢查 Flair 版本
   check_flair_version <- function() {
-    flair_version_command <- paste(python_path, "-c \"import flair; print(flair.__version__)\"")
-    result <- system(flair_version_command, intern = TRUE)
-    if (length(result) == 0 || result[1] == "ERROR" || is.na(result[1])) {
-      return(list(paste("flair", paste0("\033[31m", "\u2717", "\033[39m"), sep = " "), FALSE))
-    }
-    return(list(paste("flair", paste0("\033[32m", "\u2713", "\033[39m"), result[1], sep = " "), TRUE, result[1]))
+    tryCatch({
+      cmd <- sprintf("%s -c 'import flair; print(flair.__version__)'", python_path)
+      result <- system(cmd, intern = TRUE)
+      if (length(result) > 0 && !is.na(result[1])) {
+        return(list(
+          status = paste("Flair", "\u2713", result[1]),
+          success = TRUE,
+          version = result[1]
+        ))
+      }
+    }, error = function(e) NULL)
+    return(list(status = paste("Flair", "\u2717"), success = FALSE))
   }
 
-  flair_version <- check_flair_version()
-  torch_version <- check_torch_version()
+  # 執行版本檢查
+  flair_check <- check_flair_version()
+  torch_check <- check_torch_version()
 
-  if (isFALSE(flair_version[[2]])) {
-    packageStartupMessage(sprintf(" Flair %-50s", paste0("is installing from Python")))
+  # 如果 Flair 未安裝，嘗試安裝
+  if (!flair_check$success) {
+    packageStartupMessage("Installing Flair and dependencies...")
 
-    # Docker-specific installation commands
-    if (in_docker) {
-      commands <- c(
-        paste(python_path, "-m pip install --no-cache-dir numpy==1.26.4"),
-        paste(python_path, "-m pip install --no-cache-dir torch"),
-        paste(python_path, "-m pip install --no-cache-dir flair"),
-        paste(python_path, "-m pip install --no-cache-dir scipy==1.12.0")
+    # 安裝命令
+    install_commands <- if (in_docker) {
+      c(
+        sprintf("%s -m pip install --no-cache-dir numpy==1.26.4", python_path),
+        sprintf("%s -m pip install --no-cache-dir torch", python_path),
+        sprintf("%s -m pip install --no-cache-dir flair", python_path),
+        sprintf("%s -m pip install --no-cache-dir scipy==1.12.0", python_path)
       )
     } else {
-      commands <- c(
-        paste(python_path, "-m pip install --upgrade pip"),
-        paste(python_path, "-m pip install torch"),
-        paste(python_path, "-m pip install flair"),
-        paste(python_path, "-m pip install scipy==1.12.0")
+      c(
+        sprintf("%s -m pip install --upgrade pip", python_path),
+        sprintf("%s -m pip install torch", python_path),
+        sprintf("%s -m pip install flair", python_path),
+        sprintf("%s -m pip install scipy==1.12.0", python_path)
       )
     }
 
-    command_statuses <- vapply(commands, system, FUN.VALUE = integer(1))
+    # 執行安裝
+    install_status <- vapply(install_commands, function(cmd) {
+      tryCatch({
+        system(cmd)
+        TRUE
+      }, error = function(e) FALSE)
+    }, logical(1))
 
-    flair_check_again <- check_flair_version()
-    if (isFALSE(flair_check_again[[2]])) {
-      packageStartupMessage("Failed to install Flair. {flaiR} requires Flair NLP. Please ensure Flair NLP is installed in Python manually.")
+    # 重新檢查安裝
+    flair_check <- check_flair_version()
+    if (!flair_check$success) {
+      packageStartupMessage("Failed to install Flair. Please install manually.")
+      return(invisible(NULL))
     }
-  } else {
-    packageStartupMessage(sprintf("\033[1m\033[34mflaiR\033[39m\033[22m: \033[1m\033[33mAn R Wrapper for Accessing Flair NLP\033[39m\033[22m %-5s",
-                                  paste("\033[1m\033[33m", flair_version[[3]], "\033[39m\033[22m", sep = "")))
   }
+
+  # 顯示啟動訊息
+  packageStartupMessage(sprintf(
+    "flaiR: An R Wrapper for Accessing Flair NLP %s",
+    if (flair_check$success) flair_check$version else ""
+  ))
 }