Merge pull request #277 from davidycliao/0.1.7

0.1.7
davidycliao · Jan 6, 2025 · 395fc51 · 395fc51
2 parents ce72144 + 22ccd58
commit 395fc51
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diff --git a/Dockerfile b/Dockerfile
@@ -12,6 +12,7 @@ RUN apt-get update && apt-get install -y \
     curl
 
 # Create rstudio user
+# default accout 'rstudio'; password: rstudio123
 ENV USER=rstudio
 ENV PASSWORD=rstudio123
 RUN useradd -m $USER && \

diff --git a/R/zzz.R b/R/zzz.R
@@ -19,42 +19,105 @@
 #' @importFrom reticulate py_module_available
 #' @importFrom reticulate py_install
 #' @keywords internal
+# .onAttach <- function(...) {
+#   # Determine Python command
+#   python_cmd <- if (Sys.info()["sysname"] == "Windows") "python" else "python3"
+#   python_path <- Sys.which(python_cmd)
+#
+#   # Check Python path
+#   if (python_path == "") {
+#     packageStartupMessage(paste("Cannot locate the", python_cmd, "executable. Ensure it's installed and in your system's PATH. flaiR functionality requiring Python will not be available."))
+#     return(invisible(NULL))  # Exit .onAttach without stopping package loading
+#   }
+#
+#   # Check Python versio Try to get Python version
+#   tryCatch({
+#     python_version <- system(paste(python_path, "--version"), intern = TRUE)
+#     if (!grepl("Python 3", python_version)) {
+#       packageStartupMessage("Python 3 is required, but a different version was found. Please install Python 3. flaiR functionality requiring Python will not be available.")
+#       return(invisible(NULL))  # Exit .onAttach without stopping package loading
+#     }
+#   }, error = function(e) {
+#     packageStartupMessage(paste("Failed to get Python version with path:", python_path, "Error:", e$message, ". flaiR functionality requiring Python will not be available."))
+#     return(invisible(NULL))   # Exit .onAttach without stopping package loading
+#   })
+#
+#   # Check if PyTorch is installed
+#   check_torch_version <- function() {
+#     # torch_version_command <- paste(python_path, "-c 'import torch; print(torch.__version__)'")
+#     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 flair version
+#     return(list(paste("PyTorch", paste0("\033[32m", "\u2713", "\033[39m") ,result[1], sep = " "), TRUE, result[1]))
+#   }
+#
+#   # Check if flair is installed
+  # check_flair_version <- function() {
+  #   # flair_version_command <- paste(python_path, "-c 'import flair; print(flair.__version__)'")
+  #   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 flair version
+  #   return(list(paste("flair", paste0("\033[32m", "\u2713", "\033[39m"),result[1], sep = " "), TRUE, result[1]))
+  # }
+
+#   flair_version <- check_flair_version()
+#   torch_version <- check_torch_version()
+#
+#   if (isFALSE(flair_version[[2]])) {
+#     packageStartupMessage(sprintf(" Flair %-50s", paste0("is installing from Python")))
+#
+#     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")
+#     )
+#     command_statuses <- vapply(commands, system, FUN.VALUE = integer(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.")
+#     }
+#   } 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 = "")))
+#   }
+# }
+
+
+
 .onAttach <- function(...) {
-  # Determine Python command
-  python_cmd <- if (Sys.info()["sysname"] == "Windows") "python" else "python3"
-  python_path <- Sys.which(python_cmd)
-
-  # Check Python path
-  if (python_path == "") {
-    packageStartupMessage(paste("Cannot locate the", python_cmd, "executable. Ensure it's installed and in your system's PATH. flaiR functionality requiring Python will not be available."))
-    return(invisible(NULL))  # Exit .onAttach without stopping package loading
-  }
+  # 总是先清除环境变量，避免冲突
+  Sys.unsetenv("RETICULATE_PYTHON")
 
-  # Check Python versio Try to get Python version
+  # 使用 reticulate 的 py_discover_config 来检测 Python
   tryCatch({
-    python_version <- system(paste(python_path, "--version"), intern = TRUE)
-    if (!grepl("Python 3", python_version)) {
-      packageStartupMessage("Python 3 is required, but a different version was found. Please install Python 3. flaiR functionality requiring Python will not be available.")
-      return(invisible(NULL))  # Exit .onAttach without stopping package loading
-    }
+    python_config <- reticulate::py_discover_config()
+    python_path <- python_config$python
   }, error = function(e) {
-    packageStartupMessage(paste("Failed to get Python version with path:", python_path, "Error:", e$message, ". flaiR functionality requiring Python will not be available."))
-    return(invisible(NULL))   # Exit .onAttach without stopping package loading
+    # 如果 py_discover_config 失败，尝试找系统 Python
+    python_cmd <- if (Sys.info()["sysname"] == "Windows") "python" else "python3"
+    python_path <- Sys.which(python_cmd)
   })
 
-  # Check if PyTorch is installed
-  check_torch_version <- function() {
-    # torch_version_command <- paste(python_path, "-c 'import torch; print(torch.__version__)'")
-    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 flair version
-    return(list(paste("PyTorch", paste0("\033[32m", "\u2713", "\033[39m") ,result[1], sep = " "), TRUE, result[1]))
+  # 检查 Python 路径
+  if (!file.exists(python_path)) {
+    packageStartupMessage("Cannot locate Python. Please ensure Python 3 is installed.")
+    return(invisible(NULL))
   }
 
-  # Check if flair is installed
+  # 设置 Python 路径并检查版本（全部静默执行）
+  suppressWarnings({
+    Sys.setenv(RETICULATE_PYTHON = python_path)
+    reticulate::use_python(python_path, required = TRUE)
+  })
+
+
   check_flair_version <- function() {
     # flair_version_command <- paste(python_path, "-c 'import flair; print(flair.__version__)'")
     flair_version_command <- paste(python_path, "-c \"import flair; print(flair.__version__)\"")
@@ -66,113 +129,35 @@
     return(list(paste("flair", paste0("\033[32m", "\u2713", "\033[39m"),result[1], sep = " "), TRUE, result[1]))
   }
 
-  flair_version <- check_flair_version()
-  torch_version <- check_torch_version()
+  flair_version <- suppressMessages(check_flair_version())
 
   if (isFALSE(flair_version[[2]])) {
     packageStartupMessage(sprintf(" Flair %-50s", paste0("is installing from Python")))
-
     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")
     )
-    command_statuses <- vapply(commands, system, FUN.VALUE = integer(1))
 
-    flair_check_again <- check_flair_version()
+    tryCatch({
+      for (cmd in commands) {
+        system(cmd, intern = TRUE)
+      }
+    }, error = function(e) {
+      packageStartupMessage(paste("Failed to install packages:", e$message))
+    })
+
+    flair_check_again <- suppressMessages(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.")
     }
   } 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 = "")))
+    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 = "")))
   }
 }
 
 
-# .onAttach <- function(...) {
-#   # Docker 環境檢查及 Python 設置
-#   Sys.unsetenv("RETICULATE_PYTHON")
-#   in_docker <- file.exists("/.dockerenv")
-#
-#   if (in_docker) {
-#     # 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)
-#   }
-#
-#   # 檢查 Python 路徑
-#   if (python_path == "") {
-#     packageStartupMessage("Cannot locate Python executable. Ensure Python is installed and in PATH.")
-#     return(invisible(NULL))
-#   }
-#
-#   # 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.")
-#       return(invisible(NULL))
-#     }
-#   }, error = function(e) {
-#     packageStartupMessage(paste("Failed to check Python version:", e$message))
-#     return(invisible(NULL))
-#   })
-#
-#   # Version check functions
-#   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]))
-#   }
-#
-#   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]))
-#   }
-#
-#   flair_version <- check_flair_version()
-#   torch_version <- check_torch_version()
-#
-#   if (isFALSE(flair_version[[2]])) {
-#     packageStartupMessage(sprintf(" Flair %-50s", paste0("is installing from Python")))
-#
-#     # 安裝命令
-#     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")
-#       )
-#     } 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")
-#       )
-#     }
-#
-#     command_statuses <- vapply(commands, system, FUN.VALUE = integer(1))
-#
-#     flair_check_again <- check_flair_version()
-#     if (isFALSE(flair_check_again[[2]])) {
-#       packageStartupMessage("Failed to install Flair. Please install manually.")
-#     }
-#   } 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 = "")))
-#   }
-# }
+
+
diff --git a/README.Rmd b/README.Rmd
@@ -106,26 +106,24 @@ __Intel/AMD Processors:__
 ```r
 # Pull image
 docker pull ghcr.io/davidycliao/flair-rstudio:latest
-```
 
-```r
 # Run container
-docker run -p 8787:8787 ghcr.io/davidycliao/flair-rstudio:latest
+docker run -d -p 8787:8787 --user root --name flair-rstudio ghcr.io/davidycliao/flair-rstudio:latest
 ```
 
 
 __Apple Silicon (M1/M2 Mac):__
 
 ```r
-# Pull and run with platform specification
+# Pull image
 docker pull --platform linux/amd64 ghcr.io/davidycliao/flair-rstudio:latest
-```
 
-```r
-docker run --platform linux/amd64 -p 8787:8787 ghcr.io/davidycliao/flair-rstudio:latest
+# Run container
+docker run -d -p 8787:8787 --platform linux/amd64 --user root --name flair-rstudio ghcr.io/davidycliao/flair-rstudio:latest
 ```
 
-After running these commands in terminal (or powershell), open your browser and navigate to [`http://localhost:8787`]() to access RStudio.
+
+After running these commands in terminal (or powershell), open your browser and navigate to [`http://localhost:8787`](http://localhost:8787) to access RStudio.
 For detailed installation instructions, please visit [Quick Start Guide](https://davidycliao.github.io/flaiR/articles/quickstart.html#flair-installation).
 
 </div>

diff --git a/README.md b/README.md
@@ -92,27 +92,25 @@ library(flaiR)
 ``` r
 # Pull image
 docker pull ghcr.io/davidycliao/flair-rstudio:latest
-```
 
-``` r
 # Run container
-docker run -p 8787:8787 ghcr.io/davidycliao/flair-rstudio:latest
+docker run -d -p 8787:8787 --user root --name flair-rstudio ghcr.io/davidycliao/flair-rstudio:latest
 ```
 
 **Apple Silicon (M1/M2 Mac):**
 
 ``` r
-# Pull and run with platform specification
+# Pull image
 docker pull --platform linux/amd64 ghcr.io/davidycliao/flair-rstudio:latest
-```
 
-``` r
-docker run --platform linux/amd64 -p 8787:8787 ghcr.io/davidycliao/flair-rstudio:latest
+# Run container
+docker run -d -p 8787:8787 --platform linux/amd64 --user root --name flair-rstudio ghcr.io/davidycliao/flair-rstudio:latest
 ```
 
 After running these commands in terminal (or powershell), open your
-browser and navigate to [`http://localhost:8787`]() to access RStudio.
-For detailed installation instructions, please visit [Quick Start
+browser and navigate to [`http://localhost:8787`](http://localhost:8787)
+to access RStudio. For detailed installation instructions, please visit
+[Quick Start
 Guide](https://davidycliao.github.io/flaiR/articles/quickstart.html#flair-installation).
 
 </div>