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Choose file or directory to open via'Python'

Description

Choose a directory, one or multiple files to open, or choose a file to save.

Usage

choose_fileopen(  initialfile = NULL,  multiple = FALSE,  title = ifelse(multiple, "Choose Files", "Choose a File"),  message = "",  verbose = FALSE,  force = FALSE)choose_filesave()choose_directory(  initialdir = NULL,  title = "Choose a Directory",  message = "",  verbose = FALSE)

Arguments

Details

Base-R hasfile.choose function to choose files. However,users cannot select multiple files nor directories. These functions fillthe gap by using'Python''tkinter' package. Please makesure that one-time setup functionconfigure_conda has executedbefore running these functions.

The functions must run as interactive mode. If you run the functions on aserver, most likely you will get nothing. The functions themselves do notcheck if you are running under interactive sessions. You must check byyourself.

Value

User-selected paths. If the users select nothing, thenNULLwill be returned. For multiple file selection, multiple paths willbe returned.

Examples

if(interactive()) {  choose_fileopen(multiple = TRUE)}

'Miniconda' environment

Description

These functions/variables are used to configure'Miniconda' environment.

Usage

CONDAENV_NAME(env_name)conda_path()conda_bin()env_path(env_name = NA)list_pkgs(..., env_name = NA)configure_matlab(matlab, python_ver = "auto")configure_conda(  python_ver = "auto",  packages = NULL,  matlab = NULL,  update = FALSE,  force = FALSE,  standalone = FALSE,  env_name = CONDAENV_NAME())conda_tos(channel, agree = TRUE, silent_fail = FALSE)remove_conda(ask = TRUE, env_name = NA)add_packages(packages = NULL, python_ver = "auto", ..., env_name = NA)ensure_rpymat(verbose = TRUE, cache = TRUE, env_name = NA)matlab_engine()call_matlab(  fun,  ...,  .options = getOption("rpymat.matlab_opt", "-nodesktop -nojvm"),  .debug = getOption("rpymat.debug", FALSE))

Arguments

Value

None

Background & Objectives

Packagereticulate provides sophisticated tool-sets thatallow us to callpython functions withinR. However, theinstallation of 'Miniconda' andpython can be tricky on manyplatforms, for example, the 'M1' chip, or some other 'ARM' machines.The packagerpymat provides easier approach to configure on thesemachines with totally isolated environments. Any modifications to thisenvironment will not affect your other set ups.

Since 2014, 'Matlab' has introduced its official compiler forpython.The packagerpymat provides a simple approach to link thecompiler, provided that you have proper versions of 'Matlab' installed.Here is a list of'Matlab' versions with official compilers and their correspondingpython versions.

Configuration

If 'Matlab' compiler is not to be installed, In most of the cases,functionconfigure_conda with default arguments automaticallydownloads the latest 'Miniconda' and configures the latestpython.If any other versions of 'Miniconda' is ought to be installed,please set options"reticulate.miniconda.url" to change thesource location.

If 'Matlab' is to be installed, please specify the 'Matlab' path whenrunningconfigure_conda. If the environment has been setup,configure_matlab can link the 'Matlab' compilers withoutremoving the existing environment. For 'ARM' users, unfortunately,there will be no 'Matlab' support as the compilers are written forthe 'Intel' chips.

Initialization

Onceconda andpython environment has been installed, make sureyou runensure_rpymat() before running anypython code. Thisfunction will make sure correct compiler is linked to your currentR session.

Examples

# The script will interactively install \code{conda} to `R_user_dir`## Not run: # Install conda and python 3.9configure_conda(python_ver = '3.9')# Add packages h5py, pandas, jupyteradd_packages(c('h5py', 'pandas', 'jupyter'))# Add pip packagesadd_packages("itk", pip = TRUE)# Initialize the isolated environmentensure_rpymat()# Remove the environmentremove_conda()## End(Not run)

Whether supports customized'conda' environment

Description

Whether supports customized'conda' environment

Usage

custom_env_support()

Value

true or false on whether multiple customized environment issupported

Install, register, launch 'Jupyter' notebook to the virtual environment

Description

Install, register, launch 'Jupyter' notebook to the virtual environment

Usage

add_jupyter(..., register_R = TRUE)jupyter_bin()jupyter_register_R(  user = NULL,  name = "ir",  displayname = "R",  rprofile = NULL,  prefix = NULL,  sys_prefix = NULL,  verbose = getOption("verbose"))jupyter_options(  root_dir,  host = "127.0.0.1",  port = 8888,  open_browser = FALSE,  token = rand_string(),  base_url = "/jupyter/")jupyter_launch(  host = "127.0.0.1",  port = 8888,  open_browser = TRUE,  workdir = getwd(),  async = FALSE,  ...,  dry_run = FALSE)jupyter_check_launch(  port = 8888,  host = "127.0.0.1",  open_browser = TRUE,  workdir = getwd(),  async = "auto",  ...)jupyter_server_list()jupyter_server_stop(port, ...)jupyter_server_stop_all(...)

Arguments

Value

jupyter_bin returns the 'Jupyter' notebook binary path;jupyter_options returns the 'Jupyter' configuration in strings;jupyter_server_list returns a table of existing local 'Jupyter'server hosts, ports, and tokens;jupyter_check_launch returns trueif a new server has been created, or false if there has been an existingserver at the port;other functions return nothing.

Examples

## Not run: # Requires installation of condalibrary(rpymat)# Install conda, if you have done so, skipconfigure_conda()# Install Jupyter notebookadd_jupyter(register_R = TRUE)# Utility functionsjupyter_bin()# Please install `dipsaus` package to enable `async=TRUE` with# better experiencejupyter_launch(async = FALSE, open_browser = TRUE)## End(Not run)

Get 'Python' built-in object

Description

Get 'Python' built-in object

Usage

py_builtin(name, convert = FALSE)

Arguments

Value

A python built-in object specified byname

Examples

if(interactive() && dir.exists(env_path())) {# ------ Basic case: use python `int` as an R function ---------py_int <- py_builtin("int", convert = TRUE)# a is an R object nowa <- py_int(9)print(a)class(a)# ------ Use python `int` as a Python function -----------------py_int2 <- py_builtin("int", convert = FALSE)# b in a python objectb <- py_int2(9)# There is no '[1] ' when printingprint(b)class(b)# convert to R objectpy_to_r(b)}

List in 'Python'

Description

List in 'Python'

Usage

py_list(..., convert = FALSE)

Arguments

Value

List instance, or an R vector if converted

Examples

if(interactive() && dir.exists(env_path())) {  py_list(list(1,2,3))  py_list(c(1,2,3))  py_list(array(1:9, c(3,3)))  py_list(list(list(1:3), letters[1:3]))}

Slice index in 'Python' arrays

Description

Slice index in 'Python' arrays

Usage

py_slice(...)

Arguments

Value

Index slice instance

Examples

if(interactive() && dir.exists(env_path())) {  x <- np_array(array(seq(20), c(4, 5)))  # equivalent to x[::2]  x[py_slice(NULL, NULL, 2L)]}

Read data frame from a'xlsx' file

Description

Tries to use'readxl' package or'pandas' to read data frame.

Usage

read_xlsx(  path,  sheet = NULL,  method = c("auto", "pandas", "readxl"),  n_max = Inf,  ...)

Arguments

Value

Adata.frame table

Examples

## Not run: rpymat::read_xlsx("Book1.xlsx", sheet = 1)rpymat::read_xlsx("Book1.xlsx", sheet = "sheet1")## End(Not run)

Objects exported from other packages

Description

These objects are imported from other packages. Follow the linksbelow to see their documentation.

glue

glue

Enable interactive 'python' from R

Description

Allows users to type 'python' command from Rconsole for quick code evaluation or debugging.

Usage

repl_python(..., env_name = NA)

Arguments

Value

Seerepl_python

Wrappers around'reticulate' package

Description

Almost the same with'reticulate' functions, withrpymat enabled by default and some minor changes(see parameterconvert andlocal)

Usage

import_main(convert = FALSE)tuple(..., convert = FALSE)py_tuple(..., convert = FALSE)py_help(object)np_array(data, ...)import(module, as = NULL, convert = FALSE, delay_load = FALSE)r_to_py(x, convert = FALSE)py_to_r(x)py_to_r_wrapper(x)py_str(object, ...)py_run_string(code, local = TRUE, convert = FALSE)py_bool(x)py_dict(keys, values, convert = FALSE)py_call(x, ...)py_del_attr(x, name)py_del_item(x, name)py_eval(code, convert = FALSE)py_get_attr(x, name, silent = FALSE)py_set_attr(x, name, value)py_get_item(x, key, silent = FALSE)py_set_item(x, name, value)py_len(x, default = NULL)py_none()

Arguments

Value

'Python' built-in objects

Examples

library(rpymat)if(interactive() && dir.exists(env_path())) {  # tuple  x <- tuple(1, 2, "a")  print(x)  # convert to R object  py_to_r(x)  # convert R object to python  y <- r_to_py(list(a = 1, b = "s"))  # get element  py_get_item(y, "a")  # get missing element  py_get_item(y, "c", silent = TRUE)}

Get 'Python' main process environment

Description

py automatically converts 'Python' objects to R objects.import_main does not convert by default; see 'Examples' for details.

Usage

py

Format

An object of classNULL of length 0.

Value

The 'Python' main process as a module

Examples

if(interactive() && dir.exists(env_path())) {py_no_convert <- rpymat::import_main(convert = FALSE)py$a <- matrix(seq_len(16), 4)py_no_convert$apy$a}

Execute command with additional environments

Description

Enables 'conda' environment

Usage

cmd_create(command, shell, use_glue = TRUE)cmd_set_env(command, key, value, quote = TRUE, quote_type = "cmd")cmd_set_workdir(command, workdir)cmd_set_conda(command, conda_path, env_path)cmd_build(command, .env = parent.frame(), ...)detect_shell(suggest = NULL)run_command(  command,  shell = detect_shell(),  use_glue = FALSE,  enable_conda = TRUE,  stdout = "",  stderr = "",  stdin = "",  input = NULL,  env_list = list(),  wait = TRUE,  timeout = 0,  ...,  workdir = getwd(),  dry_run = FALSE,  print_cmd = dry_run,  glue_env = parent.frame(),  env_name = NA)

Arguments

Value

All the functions return a list with classrpymat_system_command except forrun_command, which returns the exit code bysystem2.

Examples

run_command("conda install -y numpy", dry_run = TRUE)a <- "This is a message"run_command('echo "{a}"', dry_run = TRUE,            enable_conda = FALSE, use_glue = TRUE)## Not run: # Use `jupyter_launch()` instead. This is just a demonstrationrun_command('"{jupyter_bin()}" server list', use_glue = TRUE)## End(Not run)

Run 'Python' script

Description

A wrapper ofpy_run_file,but withrpymat enabled

Usage

run_script(  x,  work_dir = NULL,  local = FALSE,  convert = FALSE,  globals = list())run_pyscript(  x,  work_dir = NULL,  local = FALSE,  convert = FALSE,  globals = list(),  env_name = NA,  force_child_process = FALSE,  ...)run_pystring(  code,  work_dir = NULL,  local = FALSE,  convert = FALSE,  globals = list())

Arguments

Value

The values returned bypy_run_file

Examples

## Not run: # Please configure conda environment firstx <- tempfile()writeLines(c(  "import re",  "zipcode = re.findall(r'[0-9]{5,6}', r.address)"), con = x)address <- '2341 Main St., 72381'rpymat::run_script(x)py$zipcode## End(Not run)