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conda.R
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conda.R
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#' Conda Tools
#'
#' Tools for managing Python `conda` environments.
#'
#' @param envname The name of, or path to, a conda environment.
#'
#' @param conda The path to a `conda` executable. Use `"auto"` to allow
#' `reticulate` to automatically find an appropriate `conda` binary.
#' See **Finding Conda** and [conda_binary()] for more details.
#'
#' @param forge Boolean; include the [conda-forge](https://conda-forge.org/)
#' repository?
#'
#' @param channel An optional character vector of conda channels to include.
#' When specified, the `forge` argument is ignored. If you need to
#' specify multiple channels, including the conda forge, you can use
#' `c("conda-forge", <other channels>)`.
#'
#' @param packages A character vector, indicating package names which should be
#' installed or removed. Use \verb{<package>==<version>} to request the installation
#' of a specific version of a package. A `NULL` value for [conda_remove()]
#' will be interpretted to `"--all"`, removing the entire environment.
#'
#' @param environment The path to an environment definition, generated via
#' (for example) [conda_export()], or via `conda env export`. When provided,
#' the conda environment will be created using this environment definition,
#' and other arguments will be ignored.
#'
#' @param python_version The version of Python to be used in this conda
#' environment. The associated Python package from conda will be requested
#' as `python={python_version}`. When `NULL`, the default `python` package
#' will be used instead. For example, use `python_version = "3.6"` to request
#' that the conda environment be created with a copy of Python 3.6. This
#' argument will be ignored if `python` is specified as part of the `packages`
#' argument, for backwards compatibility.
#'
#' @param file The path where the conda environment definition will be written.
#'
#' @param json Boolean; should the environment definition be written as JSON?
#' By default, conda exports environments as YAML.
#'
#' @param pip Boolean; use `pip` for package installation? By default, packages
#' are installed from the active conda channels.
#'
#' @param pip_ignore_installed Ignore already-installed versions when using pip?
#' (defaults to `FALSE`). Set this to `TRUE` so that specific package versions
#' can be installed even if they are downgrades. The `FALSE` option is useful
#' for situations where you don't want a pip install to attempt an overwrite of
#' a conda binary package (e.g. SciPy on Windows which is very difficult to
#' install via pip due to compilation requirements).
#'
#' @param pip_options An optional character vector of additional command line
#' arguments to be passed to `pip`. Only relevant when `pip = TRUE`.
#'
#' @param python_version The version of Python to be installed. Set this if
#' you'd like to change the version of Python associated with a particular
#' conda environment.
#'
#' @param clone The name of the conda environment to be cloned.
#'
#' @param all Boolean; report all instances of Python found?
#'
#' @param additional_create_args An optional character vector of additional
#' arguments to use in the call to `conda create`.
#'
#' @param additional_install_args An optional character vector of additional
#' arguments to use in the call to `conda install`.
#'
#' @param ... Optional arguments, reserved for future expansion.
#'
#'
#' @section Finding Conda:
#'
#' Most of `reticulate`'s conda APIs accept a `conda` parameter, used to control
#' the `conda` binary used in their operation. When `conda = "auto"`,
#' `reticulate` will attempt to automatically find a conda installation.
#' The following locations are searched, in order:
#'
#' 1. The location specified by the `reticulate.conda_binary` \R option,
#' 2. The location specified by the `RETICULATE_CONDA` environment variable,
#' 3. The [miniconda_path()] location (if it exists),
#' 4. The program `PATH`,
#' 5. A set of pre-defined locations where conda is typically installed.
#'
#' To force `reticulate` to use a particular `conda` binary, we recommend
#' setting:
#'
#' ```r
#' options(reticulate.conda_binary = "/path/to/conda")
#' ```
#'
#' This can be useful if your conda installation lives in a location that
#' `reticulate` is unable to automatically discover.
#'
#' @name conda-tools
#' @seealso [conda_run2()]
NULL
#' @returns
#' `conda_list()` returns an \R `data.frame`, with `name` giving the name of
#' the associated environment, and `python` giving the path to the Python
#' binary associated with that environment.
#'
#' @rdname conda-tools
#' @export
conda_list <- function(conda = "auto") {
# resolve conda binary
conda <- conda_binary(conda)
local_conda_paths(conda)
if (startsWith(basename(conda), "micromamba")) {
conda_envs <- system2(conda, c("env", "list", "--json"),
stdout = TRUE, stderr = FALSE)
} else {
# list envs -- discard stderr as Anaconda may emit warnings that can
# otherwise be ignored; see e.g. https://github.com/rstudio/reticulate/issues/474
conda_envs <- suppressWarnings(
system2(conda, args = c("info", "--json"),
stdout = TRUE, stderr = FALSE)
)
}
# check for error
status <- attr(conda_envs, "status") %||% 0L
if (status != 0L) {
# show warning if conda_diagnostics are enabled
if (getOption("reticulate.conda_diagnostics", default = FALSE)) {
errmsg <- attr(status, "errmsg")
warning("Error ", status, " occurred running ", conda, " ", errmsg)
}
# return empty data frame
return(data.frame(
name = character(),
python = character(),
stringsAsFactors = FALSE)
)
}
# strip out anaconda cloud prefix (not valid json)
if (length(conda_envs) > 0 && grepl("Anaconda Cloud", conda_envs[[1]], fixed = TRUE))
conda_envs <- conda_envs[-1]
# parse conda info
info <- fromJSON(conda_envs)
# convert to json
conda_envs <- info$envs
# normalize and remove duplicates (seems necessary on Windows as Anaconda
# may report both short-path and long-path versions of the same environment)
conda_envs <- unique(normalizePath(conda_envs, mustWork = FALSE))
# return an empty data.frame when no envs are found
if (length(conda_envs) == 0L) {
return(data.frame(
name = character(),
python = character(),
stringsAsFactors = FALSE)
)
}
# build data frame
name <- basename(conda_envs)
suffix <- if (is_windows()) "python.exe" else "bin/python"
python <- paste(conda_envs, suffix, sep = "/")
# handle base environment specially
# (compare normalized paths for Windows's sake)
prefix <- info$root_prefix %||% ""
isbase <-
normalizePath(prefix, winslash = "/", mustWork = FALSE) ==
normalizePath(conda_envs, winslash = "/", mustWork = FALSE)
name[isbase] <- "base"
data.frame(
name = name,
python = python,
stringsAsFactors = FALSE
)
}
#' @returns
#' `conda_create()` returns the path to the Python binary associated with the
#' newly-created conda environment.
#'
#' @rdname conda-tools
#' @export
conda_create <- function(envname = NULL,
packages = NULL,
...,
forge = TRUE,
channel = character(),
environment = NULL,
conda = "auto",
python_version = miniconda_python_version(),
additional_create_args = character())
{
check_forbidden_install("Conda Environments")
# resolve conda binary
conda <- conda_binary(conda)
local_conda_paths(conda)
# if environment is provided, use it directly
if (!is.null(environment))
return(conda_create_env(envname, environment, conda, additional_create_args))
# resolve environment name
envname <- condaenv_resolve(envname)
# resolve packages argument
if (!any(grepl("^python", packages))) {
python_package <- if (is.null(python_version))
"python"
else
sprintf("python=%s", python_version)
packages <- c(python_package, packages)
}
# create the environment
args <- conda_args("create", envname, packages)
# be quiet
args <- c(args, "--quiet")
# add user-requested channels
channels <- if (length(channel))
channel
else if (forge)
"conda-forge"
for (ch in channels)
args <- c(args, "-c", ch)
# add additional arguments
args <- c(args, additional_create_args)
# invoke conda
result <- system2t(conda, maybe_shQuote(args))
if (result != 0L) {
fmt <- "Error creating conda environment '%s' [exit code %i]"
stopf(fmt, envname, result, call. = FALSE)
}
# return the path to the python binary
conda_python(envname = envname, conda = conda)
}
conda_create_env <- function(envname, environment, conda, additional_create_args) {
check_forbidden_install("Conda Environments")
if (!is.null(envname))
envname <- condaenv_resolve(envname)
args <- c(
"env", "create", "--quiet",
if (is.null(envname))
c()
else if (grepl("/", envname))
c("--prefix", maybe_shQuote(envname))
else
c("--name", maybe_shQuote(envname)),
"-f", maybe_shQuote(environment),
additional_create_args
)
result <- system2t(conda, args)
if (result != 0L) {
fmt <- "Error creating conda environment [exit code %i]"
stopf(fmt, result)
}
# return the path to the python binary
conda_python(envname = envname, conda = conda)
}
#' @returns
#' `conda_clone()` returns the path to Python within the newly-created
#' conda environment.
#'
#' @rdname conda-tools
#' @export
conda_clone <- function(envname, ..., clone = "base", conda = "auto") {
# resolve conda binary
conda <- conda_binary(conda)
local_conda_paths(conda)
# resolve environment name
envname <- condaenv_resolve(envname)
# create the environment
args <- conda_args("create", envname)
# be quiet
args <- c(args, "--quiet")
# add cloned environment
args <- c(args, "--clone", clone)
# invoke conda
result <- system2t(conda, maybe_shQuote(args))
if (result != 0L) {
fmt <- "Error creating conda environment '%s' [exit code %i]"
stopf(fmt, envname, result, call. = FALSE)
}
# return the path to the python binary
conda_python(envname = envname, conda = conda)
}
#' @returns
#' `conda_export()` returns the path to the exported environment definition,
#' invisibly.
#'
#' @rdname conda-tools
#' @export
conda_export <- function(envname,
file = if (json) "environment.json" else "environment.yml",
json = FALSE,
...,
conda = "auto")
{
# resolve parameters
conda <- conda_binary(conda)
local_conda_paths(conda)
envname <- condaenv_resolve(envname)
# build conda argument list,
args <- c(
"env", "export",
if (json)
"--json",
if (grepl("/", envname))
c("--prefix", shQuote(envname))
else
c("--name", shQuote(envname)),
">", shQuote(file)
)
# execute conda
status <- system2(conda, args)
if (status != 0L) {
fmt <- "Error exporting conda environment [error code %i]"
stopf(fmt, status, call. = FALSE)
}
# notify user
fmt <- "* Environment '%s' exported to '%s'."
writeLines(sprintf(fmt, envname, file))
# return path to generated environment
invisible(file)
}
#' @rdname conda-tools
#' @export
conda_remove <- function(envname,
packages = NULL,
conda = "auto")
{
# resolve conda binary
conda <- conda_binary(conda)
local_conda_paths(conda)
# resolve environment name
envname <- condaenv_resolve(envname)
# no packages means everything
if (is.null(packages))
packages <- "--all"
# remove packages (or the entire environment)
args <- conda_args("remove", envname, packages)
result <- system2t(conda, maybe_shQuote(args))
if (result != 0L) {
stop("Error ", result, " occurred removing conda environment ", envname,
call. = FALSE)
}
}
#' @rdname conda-tools
#' @export
conda_install <- function(envname = NULL,
packages,
forge = TRUE,
channel = character(),
pip = FALSE,
pip_options = character(),
pip_ignore_installed = FALSE,
conda = "auto",
python_version = NULL,
additional_create_args = character(),
additional_install_args = character(),
...)
{
check_forbidden_install("Python packages")
# check that 'packages' argument was supplied
if (missing(packages)) {
if (!is.null(envname)) {
fmt <- paste(
"argument \"packages\" is missing, with no default",
"- did you mean 'conda_install(<envname>, %1$s)'?",
"- use 'py_install(%1$s)' to install into the active Python environment",
sep = "\n"
)
stopf(fmt, deparse1(substitute(envname)), call. = FALSE)
} else {
packages
}
}
# resolve conda binary
conda <- conda_binary(conda)
local_conda_paths(conda)
# resolve environment name
envname <- condaenv_resolve(envname)
# honor request for specific version of Python package
python_package <- if (is.null(python_version))
NULL
else if (grepl("[><=]", python_version))
paste0("python", python_version)
else
sprintf("python=%s", python_version)
# check to see if we already have a valid Python installation for
# this conda environment
python <- tryCatch(
conda_python(envname = envname, conda = conda),
error = identity
)
# if this conda environment doesn't seem to exist, auto-create it
if (inherits(python, "error") || !file.exists(python)) {
conda_create(
envname = envname,
packages = python_package %||% "python",
forge = forge,
channel = channel,
conda = conda,
additional_create_args = additional_create_args
)
python <- conda_python(envname = envname, conda = conda)
}
# prepare user-requested channels
channels <- if (length(channel))
channel
else if (forge)
"conda-forge"
channel_args <- character()
for (ch in channels)
channel_args <- c(channel_args, "-c", ch)
# if the user has requested a specific version of Python, ensure that
# version of Python is installed into the requested environment
# (should be no-op if that copy of Python already installed)
if (!is.null(python_version)) {
args <- conda_args("install", envname, python_package)
args <- c(args, channel_args, additional_install_args)
status <- system2t(conda, maybe_shQuote(args))
if (status != 0L) {
fmt <- "installation of '%s' into environment '%s' failed [error code %i]"
msg <- sprintf(fmt, python_package, envname, status)
stop(msg, call. = FALSE)
}
}
# delegate to pip if requested
if (pip) {
result <- pip_install(
python = python,
packages = packages,
pip_options = pip_options,
ignore_installed = pip_ignore_installed,
conda = conda,
envname = envname
)
return(result)
}
# otherwise, use conda
args <- conda_args("install", envname)
# add user-requested channels
args <- c(args, channel_args)
args <- c(args, python_package, packages, additional_install_args)
result <- system2t(conda, maybe_shQuote(args))
# check for errors
if (result != 0L) {
fmt <- "one or more Python packages failed to install [error code %i]"
stopf(fmt, result)
}
invisible(packages)
}
#' @rdname conda-tools
#' @export
conda_binary <- function(conda = "auto") {
# automatic lookup if requested
if (identical(conda, "auto") || isTRUE(is.na(conda))) {
conda <- find_conda()
if (is.null(conda))
stop("Unable to find conda binary. Is Anaconda installed?", call. = FALSE)
conda <- conda[[1]]
}
conda <- normalizePath(conda, winslash = "/", mustWork = FALSE)
if (!grepl("^(conda|mamba|micromamba)", basename(conda)))
warning("Supplied path is not a conda binary: ", sQuote(conda))
# if the user has requested a conda binary in the 'condabin' folder,
# try to find and use its sibling in the 'bin' folder instead as
# we rely on other tools typically bundled in the 'bin' folder
# https://github.com/rstudio/keras/issues/691
if (!is_windows()) {
altpath <- file.path(dirname(conda), "../bin", basename(conda))
if (file.exists(altpath))
return(normalizePath(altpath, winslash = "/", mustWork = TRUE))
} else {
# on Windows it's preferable to conda.bat located in the 'condabin'
# folder. if the user passed the path to a 'Scripts/conda.exe' we will
# try to find the 'conda.bat'.
altpath <- file.path(dirname(conda), "../condabin/conda.bat")
if (file.exists(altpath))
return(normalizePath(altpath, winslash = "/", mustWork = TRUE))
}
# validate existence
if (!file.exists(conda))
stop("Specified conda binary '", conda, "' does not exist.", call. = FALSE)
# return conda
conda
}
#' @rdname conda-tools
#' @export
conda_exe <- conda_binary
#' @rdname conda-tools
#' @export
conda_version <- function(conda = "auto") {
conda_bin <- conda_binary(conda)
local_conda_paths(conda_bin)
out <- system2(conda_bin, "--version", stdout = TRUE)
# mamba --version gives multi-line output, with the conda version on the last line.
tail(out, 1)
}
#' @rdname conda-tools
#' @export
conda_update <- function(conda = "auto") {
# resolve conda
conda <- conda_binary(conda)
local_conda_paths(conda)
# compute base path
prefix <- system2(conda, c("info", "--base"), stdout = TRUE)
# figure out if this is anaconda or 'plain' conda
json <- system2(conda, c("list", "--prefix", shQuote(prefix), "--json"), stdout = TRUE)
envlist <- jsonlite::fromJSON(json)
name <- if ("anaconda" %in% envlist$name) "anaconda" else "conda"
# attempt update
system2t(conda, c("update", "--prefix", maybe_shQuote(prefix), "--yes", name))
}
numeric_conda_version <- function(conda = "auto", version_string = conda_version(conda)) {
# some plausible version strings:
# "conda 4.6.0"
# "conda 4.6.0b0"
# "conda 4.6.0rc1"
# "conda 4.6.0rc1.post3+64bde06"
v <- version_string
v <- sub("^conda ", "", v) # drop hardcoded prefix
# https://github.com/conda/conda/blob/c1579681d1468af3d1b4af3083bed33f8391e861/conda/_vendor/auxlib/packaging.py#L142
# if dev version string: "{0}.post{1}+{2}".format(version, post_commit, hash)
v <- sub("\\.post(\\d)\\+.+$", ".\\1", v)
# substitute rc|beta|alpha|whatever suffix with .
v <- sub("[A-Za-z]+", ".", v)
if (grepl("\\.$", v))
v <- paste0(v, "9000")
numeric_version(v)
}
#' @rdname conda-tools
#' @export
conda_python <- function(envname = NULL,
conda = "auto",
all = FALSE)
{
# resolve envname
envname <- condaenv_resolve(envname)
# for fully-qualified paths, construct path explicitly
if (grepl("[/\\\\]", envname)) {
suffix <- if (is_windows()) "python.exe" else "bin/python"
path <- file.path(envname, suffix)
if (file.exists(path))
return(path)
fmt <- "no conda environment exists at path '%s'"
stop(sprintf(fmt, envname))
}
# otherwise, list conda environments and try to find it
conda_envs <- conda_list(conda = conda)
env <- subset(conda_envs, conda_envs$name == envname)
if (nrow(env) == 0)
stop("conda environment '", envname, "' not found")
# NOTE: it's possible to have multiple environments with the same name;
# e.g. because the user might've installed multiple copies of Anaconda
# (e.g. both miniconda and miniforge). we should think about having a way
# of disambiguating this, but for now just pick the first one
python <- if (all) env$python else env$python[[1L]]
path.expand(python)
}
#' @returns
#' `conda_search()` returns an \R `data.frame` describing packages that
#' matched against `matchspec`. The data frame will usually include
#' fields `name` giving the package name, `version` giving the package
#' version, `build` giving the package build, and `channel` giving the
#' channel the package is hosted on.
#'
#' @param matchspec A conda MatchSpec query string.
#'
#' @rdname conda-tools
#' @export
conda_search <-
function(matchspec,
forge = TRUE,
channel = character(),
conda = "auto",
...) {
conda <- conda_binary(conda)
local_conda_paths(conda)
args <- c("search", matchspec)
# add user-requested channels
channels <- if (length(channel))
channel
else if (forge)
"conda-forge"
for (ch in channels)
args <- c(args, "-c", ch)
args = c(args, "--json")
output <- system2(conda, shQuote(args), stdout = TRUE)
status <- attr(output, "status") %||% 0L
# check for errors
if (status != 0L) {
fmt <- "error searching for packages [error code %i]"
stopf(fmt, status)
}
parsed <- jsonlite::fromJSON(output)
all_colnames <- unique(unlist(lapply(parsed, names)))
df <- do.call(rbind, lapply(parsed, function(x) {
if(any(missing_cols <- setdiff(all_colnames, names(x))))
x[missing_cols] <- NA
x
}))
rownames(df) <- NULL
# reverse row order, so most recent versions are (likely) first. In an ideal
# world we'd use `order(numeric_version(df$version))`, but we can't depend on
# the version string being parseable.
if(nrow(df))
df <- df[rev(seq_len(nrow(df))), ]
# reorder columns
to_front <- intersect(c("name", "version", "build", "channel"), names(df))
df <- df[c(unique(to_front, names(df)))]
df
}
find_conda <- function() {
# allow specification of conda executable
conda <- getOption("reticulate.conda_binary")
if (!is.null(conda))
return(conda)
conda <- Sys.getenv("RETICULATE_CONDA", unset = NA)
if (!is.na(conda))
return(conda)
# if miniconda is installed, use it
if (miniconda_exists())
return(miniconda_conda())
# if there is a conda executable on the PATH, use it
conda <- Sys.which("conda")
if (nzchar(conda))
return(conda)
# otherwise, search common locations for conda
prefixes <- c("~/opt/", "~/", "/opt/", "/")
names <- c("anaconda", "miniconda", "miniforge")
versions <- c("", "2", "3", "4")
combos <- expand.grid(versions, names, prefixes, KEEP.OUT.ATTRS = FALSE, stringsAsFactors = FALSE)
combos <- combos[rev(seq_along(combos))]
conda_locations <- unlist(.mapply(paste0, combos, NULL))
# find the potential conda binary path in each case
conda_locations <- if (is_windows()) {
paste0(conda_locations, "/condabin/conda.bat")
} else {
paste0(conda_locations, "/bin/conda")
}
# look for caskroom version (why does it live in a 'base' subdir?)
caskroom_conda <- "/opt/homebrew/Caskroom/miniforge/base/bin/conda"
if (file.exists(caskroom_conda))
conda_locations <- c(conda_locations, caskroom_conda)
# ensure we expand tilde prefixes
conda_locations <- path.expand(conda_locations)
# on Windows, check the registry for a compatible version of Anaconda
if (is_windows()) {
anaconda_versions <- windows_registry_anaconda_versions()
anaconda_versions <- subset(anaconda_versions, anaconda_versions$arch == .Platform$r_arch)
if (nrow(anaconda_versions) > 0) {
conda_scripts <- utils::shortPathName(
file.path(anaconda_versions$install_path, "Scripts", "conda.exe")
)
conda_bats <- utils::shortPathName(
file.path(anaconda_versions$install_path, "condabin", "conda.bat")
)
# prefer versions found in the registry to those found in default locations
conda_locations <- c(conda_bats, conda_scripts, conda_locations)
}
}
# keep only conda locations that exist
conda_locations <- conda_locations[file.exists(conda_locations)]
if (length(conda_locations))
return(conda_locations)
# explicitly return NULL when no conda found
NULL
}
condaenv_resolve <- function(envname = NULL) {
python_environment_resolve(
envname = envname,
resolve = identity
)
}
condaenv_path <- function(envname = NULL) {
python_environment_resolve(
envname = envname,
resolve = function(name) {
python <- conda_python(name)
info <- python_info(python)
info$root
}
)
}
#' @export
#' @rdname conda-tools
condaenv_exists <- function(envname = NULL, conda = "auto") {
# check that conda is installed
condabin <- tryCatch(conda_binary(conda = conda), error = identity)
if (inherits(condabin, "error"))
return(FALSE)
# check that the environment exists
python <- tryCatch(conda_python(envname, conda = conda), error = identity)
if (inherits(python, "error"))
return(FALSE)
# validate the Python binary exists
file.exists(python)
}
conda_args <- function(action, envname = NULL, ...) {
envname <- condaenv_resolve(envname)
# use '--prefix' as opposed to '--name' if envname looks like a path
args <- c(action, "--yes")
if (grepl("[/\\]", envname))
args <- c(args, "--prefix", envname, ...)
else
args <- c(args, "--name", envname, ...)
args
}
is_condaenv <- function(dir) {
file.exists(file.path(dir, "conda-meta"))
}
conda_list_packages <- function(envname = NULL, conda = "auto", no_pip = TRUE) {
conda <- conda_binary(conda)
local_conda_paths(conda)
envname <- condaenv_resolve(envname)
# create the environment
args <- c("list")
if (grepl("[/\\]", envname)) {
args <- c(args, "--prefix", envname)
} else {
args <- c(args, "--name", envname)
}
if (no_pip)
args <- c(args, "--no-pip")
args <- c(args, "--json")
output <- system2(conda, shQuote(args), stdout = TRUE)
status <- attr(output, "status") %||% 0L
if (status != 0L) {
fmt <- "error listing conda environment [status code %i]"
stopf(fmt, status)
}
parsed <- jsonlite::fromJSON(output)
data.frame(
package = parsed$name,
version = parsed$version,
requirement = paste(parsed$name, parsed$version, sep = "="),
channel = parsed$channel,
stringsAsFactors = FALSE
)
}
conda_installed <- function() {
condabin <- tryCatch(conda_binary(), error = identity)
if (inherits(condabin, "error"))
return(FALSE)
else
return(TRUE)
}
conda_run <- function(cmd, args = c(), conda = "auto", envname = NULL,
run_args = c("--no-capture-output"), ...) {
# `conda run` is very unreliable, best avoided. known issues:
# - fails if user doesn't have write permissions to conda installation
# - fails if arguments need to be quoted
conda <- conda_binary(conda)
local_conda_paths(conda)
envname <- condaenv_resolve(envname)
if (numeric_conda_version(conda) < "4.9")
stopf(
"`conda_run()` requires conda version >= 4.9.
Run `miniconda_update('%s')` to update conda.", conda)
if (grepl("[/\\]", envname))
in_env <- c("--prefix", shQuote(normalizePath(envname)))
else
in_env <- c("--name", envname)
system2t(conda, c("run", in_env, run_args,
shQuote(cmd), args), ...)
}
#' Run a command in a conda environment
#'
#' This function runs a command in a chosen conda environment.
#'
#' Note that, whilst the syntax is similar to [`system2()`], the function
#' dynamically generates a shell script with commands to activate the chosen
#' conda environent. This avoids issues with quoting, as discussed in this
#' [GitHub issue](https://github.com/conda/conda/issues/10972).
#'
#' @param cmd The system command to be invoked, as a character string.
#' @param args A character vector of arguments to the command. The arguments should
#' be quoted e.g. by `shQuote()` in case they contain space or other special
#' characters (a double quote or backslash on Windows, shell-specific special
#' characters on Unix).
#' @param cmd_line The command line to be executed, as a character string. This
#' is automatically generated from `cmd` and `args`, but can be provided
#' directly if needed (if provided, it overrides `cmd` and `args`).
#' @param conda The path to a `conda` executable. Use `"auto"` to allow
#' `reticulate` to automatically find an appropriate `conda` binary.
#' See **Finding Conda** and [conda_binary()] for more details.
#' @param envname The name of, or path to, a conda environment.
#' @param intern A logical (not `NA`) which indicates whether to capture the
#' output of the command as an R character vector. If `FALSE` (the default), the
#' return value is the error code (`0` for success).
#' @param echo A logical (not `NA`) which indicates whether to echo the command to
#' the console before running it.
#'
#'
#' @returns
#' `conda_run2()` runs a command in the desired conda environment. If
#' `intern = TRUE` the output is returned as a character vector; if `intern = FALSE` (the
#' deafult), then the return value is the error code (0 for success). See
#' [shell()] (on windows) or [`system2()`] on macOS or Linux for more details.
#'
#' @export
#' @seealso [`conda-tools`]
# executes a cmd with a conda env active, implemented directly to avoid using `conda run`
# https://github.com/conda/conda/issues/10972
conda_run2 <- function(cmd, args = c(), conda = "auto", envname = NULL,
cmd_line = paste(shQuote(cmd), paste(args, collapse = " ")),
intern = FALSE, echo = !intern) {
run <- if (is_windows()) conda_run2_windows else conda_run2_nix
run(
conda = conda,
envname = envname,
cmd_line = cmd_line,
intern = intern,
echo = echo
)
}
conda_run2_windows <-
function(cmd, args = c(), conda = "auto", envname = NULL,
cmd_line = paste(shQuote(cmd), paste(args, collapse = " ")),
intern = FALSE, echo = !intern) {
conda <- normalizePath(conda_binary(conda))
local_conda_paths(conda)
if (identical(envname, "base"))
envname <- file.path(dirname(conda), "../..")
else
envname <- condaenv_resolve(envname)
if (grepl("[/\\]", envname))
envname <- normalizePath(envname)
activate.bat <- normalizePath(file.path(dirname(conda), "activate.bat"),