From 2bc07f3a170c1040741258fc9a30585feb48ab37 Mon Sep 17 00:00:00 2001 From: davidycliao Date: Mon, 6 Jan 2025 17:50:15 +0000 Subject: [PATCH 1/2] refactor: optimize Python environment setup for flaiR package --- R/zzz.R | 90 ++++++++++++++++++++--------------------------------- flaiR.Rproj | 1 + 2 files changed, 34 insertions(+), 57 deletions(-) diff --git a/R/zzz.R b/R/zzz.R index 725ff14c..4609d111 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -89,75 +89,51 @@ # } # } - - .onAttach <- function(...) { - # 总是先清除环境变量，避免冲突 + # Check and set Python environment Sys.unsetenv("RETICULATE_PYTHON") - - # 使用 reticulate 的 py_discover_config 来检测 Python - tryCatch({ - python_config <- reticulate::py_discover_config() - python_path <- python_config$python + venv <- "flair_env" + + # Get Python path based on OS + python_path <- tryCatch({ + if (Sys.info()["sysname"] == "Windows") { + normalizePath(Sys.which("python"), winslash = "/", mustWork = TRUE) + } else { + Sys.which("python3") + } }, error = function(e) { - # 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) - }) - - # 检查 Python 路径 - if (!file.exists(python_path)) { - packageStartupMessage("Cannot locate Python. Please ensure Python 3 is installed.") + packageStartupMessage("Cannot locate Python. Please install Python 3.") return(invisible(NULL)) - } - - # 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__)\"") - 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])) + # Create/use virtual environment + if (!reticulate::virtualenv_exists(venv)) { + reticulate::virtualenv_create(venv) } + reticulate::use_virtualenv(venv, required = TRUE) - 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") - ) - + # Check flair and install if needed + if (!reticulate::py_module_available("flair")) { + packageStartupMessage("Installing flair NLP in virtual environment: ", venv) tryCatch({ - for (cmd in commands) { - system(cmd, intern = TRUE) - } + reticulate::py_install(c("torch", "flair", "scipy==1.12.0"), envname = venv) }, error = function(e) { - packageStartupMessage(paste("Failed to install packages:", e$message)) + packageStartupMessage("Failed to install flair: ", e$message) + return(invisible(NULL)) }) + } - 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 { + # Get flair version + version <- tryCatch({ + reticulate::py_eval("import flair; flair.__version__") + }, error = function(e) { + return(NULL) + }) + + if (!is.null(version)) { 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 = ""))) + paste("\033[1m\033[33m", version, "\033[39m\033[22m", sep = ""))) + } else { + packageStartupMessage("Failed to load flair. Please install manually.") } } - - - - diff --git a/flaiR.Rproj b/flaiR.Rproj index 7da37875..80fbf0a8 100644 --- a/flaiR.Rproj +++ b/flaiR.Rproj @@ -1,4 +1,5 @@ Version: 1.0 +ProjectId: 3aead98c-0fea-4674-b3c2-5c86bd2ee926 RestoreWorkspace: Default SaveWorkspace: Default From f32a2046179ca12d95fc614929adb96147469581 Mon Sep 17 00:00:00 2001 From: davidycliao Date: Mon, 6 Jan 2025 18:01:14 +0000 Subject: [PATCH 2/2] refactor: optimize Python environment setup for flaiR package Changed Python path detection and virtual environment configuration to improve stability on different OS platforms. --- NAMESPACE | 4 +- R/zzz.R | 161 +++++++++++++++++++++++++++----------------- man/dot-onAttach.Rd | 32 +++++---- 3 files changed, 122 insertions(+), 75 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 47a73ecd..0ed7f964 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -43,5 +43,7 @@ importFrom(htmltools,HTML) importFrom(reticulate,import) importFrom(reticulate,py_get_attr) importFrom(reticulate,py_install) -importFrom(reticulate,py_module_available) +importFrom(reticulate,use_virtualenv) +importFrom(reticulate,virtualenv_create) +importFrom(reticulate,virtualenv_exists) importFrom(stringr,str_replace_all) diff --git a/R/zzz.R b/R/zzz.R index 4609d111..0ca7a581 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -1,24 +1,109 @@ -#' @title Install Python Dependencies and Load the flaiRnlp -#' @description .onAttach sets up a virtual environment, checks for Python availability, -#' and ensures the 'flair' module is installed in flair_env in Python. +#' @title Initialize Python Environment and Load flaiR NLP +#' @description Sets up Python environment, manages virtual environment, and installs required flair NLP packages. #' -#' @param ... A character string specifying the name of the virtual environment. +#' @param ... Additional arguments passed to startup functions #' #' @details #' The function performs the following steps: #' \itemize{ -#' \item Checks if the virtual environment specified by `venv` exists. -#' If not, it creates the environment. -#' \item Activates the virtual environment. -#' \item Checks for the availability of Python. If Python is not available, -#' it displays an error message. -#' \item Checks if the 'flair' Python module is available in the virtual -#' environment. If not, it attempts to install 'flair'. If the -#' installation fails, it prompts the user to install 'flair' manually. +#' \item Clears any existing Python environment variables +#' \item Detects Python installation based on operating system (Windows/Unix) +#' \item Manages 'flair_env' virtual environment: +#' - Uses existing environment if available +#' - Creates new environment if needed +#' \item Verifies and installs required packages: +#' - torch +#' - flair +#' - scipy (version 1.12.0) +#' \item Validates flair installation and displays version information #' } -#' @importFrom reticulate py_module_available -#' @importFrom reticulate py_install +#' +#' The function includes comprehensive error handling and provides status messages +#' throughout the initialization process. +#' +#' @note +#' Requires Python 3.x installed on the system. Will create a virtual environment +#' named 'flair_env' if it doesn't exist. +#' +#' @importFrom reticulate virtualenv_exists virtualenv_create use_virtualenv py_install #' @keywords internal + +.onAttach <- function(...) { + # Check and set Python environment + Sys.unsetenv("RETICULATE_PYTHON") + venv <- "flair_env" + + # Get Python path based on OS + python_path <- tryCatch({ + if (Sys.info()["sysname"] == "Windows") { + normalizePath(Sys.which("python"), winslash = "/", mustWork = TRUE) + } else { + Sys.which("python3") + } + }, error = function(e) { + packageStartupMessage("Cannot locate Python. Please install Python 3.") + return(invisible(NULL)) + }) + + # Define version check function + 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])) + } + + # Check if flair_env exists + if (reticulate::virtualenv_exists(venv)) { + packageStartupMessage("Using existing virtual environment: ", venv) + reticulate::use_virtualenv(venv, required = TRUE) + + # Check flair in existing environment + flair_status <- suppressMessages(check_flair_version()) + if (!flair_status[[2]]) { + packageStartupMessage("Installing missing flair in existing environment...") + tryCatch({ + reticulate::py_install(c("torch", "flair", "scipy==1.12.0"), envname = venv) + }, error = function(e) { + packageStartupMessage("Failed to install flair: ", e$message) + return(invisible(NULL)) + }) + flair_status <- suppressMessages(check_flair_version()) + } + } else { + # Create new virtual environment + packageStartupMessage("Creating new virtual environment: ", venv) + reticulate::virtualenv_create(venv) + reticulate::use_virtualenv(venv, required = TRUE) + + # Install in new environment + packageStartupMessage("Installing flair NLP in new environment...") + tryCatch({ + reticulate::py_install(c("torch", "flair", "scipy==1.12.0"), envname = venv) + }, error = function(e) { + packageStartupMessage("Failed to install flair: ", e$message) + return(invisible(NULL)) + }) + flair_status <- suppressMessages(check_flair_version()) + } + + # Display final status + if (flair_status[[2]]) { + packageStartupMessage(sprintf("\033[1m\033[34mflaiR\033[39m\033[22m: \033[1m\033[33mAn R Wrapper for Accessing Flair NLP\033[39m\033[22m %-5s", + paste("\033[1m\033[33m", flair_status[[3]], "\033[39m\033[22m", sep = ""))) + } else { + packageStartupMessage("Failed to load flair. Please install manually.") + } +} + + + + + + +#' # .onAttach <- function(...) { # # Determine Python command # python_cmd <- if (Sys.info()["sysname"] == "Windows") "python" else "python3" @@ -89,51 +174,3 @@ # } # } -.onAttach <- function(...) { - # Check and set Python environment - Sys.unsetenv("RETICULATE_PYTHON") - venv <- "flair_env" - - # Get Python path based on OS - python_path <- tryCatch({ - if (Sys.info()["sysname"] == "Windows") { - normalizePath(Sys.which("python"), winslash = "/", mustWork = TRUE) - } else { - Sys.which("python3") - } - }, error = function(e) { - packageStartupMessage("Cannot locate Python. Please install Python 3.") - return(invisible(NULL)) - }) - - # Create/use virtual environment - if (!reticulate::virtualenv_exists(venv)) { - reticulate::virtualenv_create(venv) - } - reticulate::use_virtualenv(venv, required = TRUE) - - # Check flair and install if needed - if (!reticulate::py_module_available("flair")) { - packageStartupMessage("Installing flair NLP in virtual environment: ", venv) - tryCatch({ - reticulate::py_install(c("torch", "flair", "scipy==1.12.0"), envname = venv) - }, error = function(e) { - packageStartupMessage("Failed to install flair: ", e$message) - return(invisible(NULL)) - }) - } - - # Get flair version - version <- tryCatch({ - reticulate::py_eval("import flair; flair.__version__") - }, error = function(e) { - return(NULL) - }) - - if (!is.null(version)) { - 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", version, "\033[39m\033[22m", sep = ""))) - } else { - packageStartupMessage("Failed to load flair. Please install manually.") - } -} diff --git a/man/dot-onAttach.Rd b/man/dot-onAttach.Rd index 03096c75..b4b9bd3b 100644 --- a/man/dot-onAttach.Rd +++ b/man/dot-onAttach.Rd @@ -2,28 +2,36 @@ % Please edit documentation in R/zzz.R \name{.onAttach} \alias{.onAttach} -\title{Install Python Dependencies and Load the flaiRnlp} +\title{Initialize Python Environment and Load flaiR NLP} \usage{ .onAttach(...) } \arguments{ -\item{...}{A character string specifying the name of the virtual environment.} +\item{...}{Additional arguments passed to startup functions} } \description{ -.onAttach sets up a virtual environment, checks for Python availability, -and ensures the 'flair' module is installed in flair_env in Python. +Sets up Python environment, manages virtual environment, and installs required flair NLP packages. } \details{ The function performs the following steps: \itemize{ -\item Checks if the virtual environment specified by \code{venv} exists. -If not, it creates the environment. -\item Activates the virtual environment. -\item Checks for the availability of Python. If Python is not available, -it displays an error message. -\item Checks if the 'flair' Python module is available in the virtual -environment. If not, it attempts to install 'flair'. If the -installation fails, it prompts the user to install 'flair' manually. +\item Clears any existing Python environment variables +\item Detects Python installation based on operating system (Windows/Unix) +\item Manages 'flair_env' virtual environment: +- Uses existing environment if available +- Creates new environment if needed +\item Verifies and installs required packages: +- torch +- flair +- scipy (version 1.12.0) +\item Validates flair installation and displays version information } + +The function includes comprehensive error handling and provides status messages +throughout the initialization process. +} +\note{ +Requires Python 3.x installed on the system. Will create a virtual environment +named 'flair_env' if it doesn't exist. } \keyword{internal}