Package 'ravemanager'

Install & Configure 'python' environment for 'RAVE'

Description

Installs 'python' environment for 'RAVE'

Usage

validate_python(verbose = TRUE)

configure_python(python_ver = "3.11", verbose = TRUE)

remove_conda(ask = TRUE)

ensure_rpymat()

Arguments

verbose	whether to verbose messages
python_ver	python version; default is automatically determined. If a specific python version is needed, please specify explicitly, for example, python_ver='3.8'
ask	whether to ask before resetting the 'python' environment

Details

Use ravemanager::configure_python() to install and configure python environment using miniconda. The conda binary and environment will be completely isolated. This means the installation will be safe and it will not affect any existing configurations on the computer.

In this isolated environment, the following packages will be installed: numpy, scipy, pandas, h5py, jupyterlab, pynwb, mat73, mne. You can always add more conda packages via rpymat::add_packages(...) or pip packages via rpymat::add_packages(..., pip = TRUE).

To use the 'python' environment, please run rpymat::ensure_rpymat() to activate in your current session. If you are running via 'RStudio', open any 'python' script and use 'ctrl/cmd+enter' to run line-by-line. To switch from R to python mode, using command rpymat::repl_python()

A jupyterlab will be automatically installed during the configuration. To launch the jupyterlab, use rpymat::jupyter_launch()

If you want to remove this conda environment, use R command rpymat::remove_conda(). This procedure is absolutely safe and will not affect your other installations.

Examples

## Not run: 

# -------- Install & Configure python environment for RAVE --------
ravemanager::configure_python()

# Add conda packages
rpymat::add_packages("numpy")

# Add pip packages
rpymat::add_packages("nipy", pip = TRUE)

# -------- Activate RAVE-python environment --------
rpymat::ensure_rpymat()

# run script from a temporary file
f <- tempfile(fileext = ".py")
writeLines(c(
  "import numpy",
  "print(f'numpy installed: {numpy.__version__}')"
), f)
rpymat::run_script(f)

# run terminal command within the environment
rpymat::run_command("pip list")

# run python interactively, remember to use `exit` to exit
# python mode
rpymat::repl_python()




## End(Not run)

---

Print 'RAVE' debugging information

Description

This function will generate a report. Please include the report when you file an issue. Useful for reporting issues to 'RAVE' developers.

Usage

debug_info(max_lines)

Arguments

max_lines

maximum number of log entries to print

---

Print out 'RAVE' session log

Description

Print out 'RAVE' session log

Usage

export_logs(
  session = NULL,
  modules = NULL,
  max_lines = Sys.getenv("RAVEMANAGER_BUGREPORT_MAX", "200"),
  verbose = TRUE
)

Arguments

session	'RAVE' session string; default is the most recent (active) session
modules	which module to read; default is all
max_lines	maximum number of lines to read; default is 200
verbose	whether to print out the log; default is true

Value

characters of log

---

Find packages with empty files

Description

Check whether packages are installed correctly. In rare cases (possibly network issues), packages downloaded contain empty files. This function provides a method to check empty files in packages.

Usage

find_packages_with_empty_files(lib = get_libpaths(check = TRUE))

Arguments

lib	library path where packages are installed; default is set to user library path.

Value

A list of packages (and files) containing empty files.

Examples

find_packages_with_empty_files()

---

Install/Update R or Python packages to RAVE environment

Description

Install/Update R or Python packages to RAVE environment

Usage

add_r_package(
  pkg,
  lib = get_libpaths(check = TRUE),
  repos = get_mirror(),
  type = getOption("pkgType"),
  ...,
  INSTALL_opts = "--no-lock"
)

add_py_package(pkg, method = c("pip", "conda"))

Arguments

pkg	name of the package
repos, lib, type, INSTALL_opts, ...	internally used
method	whether to use 'pip' or 'conda'; default is 'pip'

Value

Nothing

Examples

## Not run: 


# ---- R --------------------------------------------------------
# Install R packages (CRAN, BioC, or RAVE's repository)
add_r_package("ravebuiltins")
add_r_package("rhdf5")

# Install from Github (github.com/dipterix/threeBrain)
add_r_package("dipterix/threeBrain")

# Install Github branch
add_r_package("dipterix/threeBrain@custom-electrode-geom")

# ---- Python ----------------------------------------------------

# Normal pypi packages
add_py_package("threebrainpy")

# Add through conda
add_py_package("fftw", method = "conda")



## End(Not run)

---

Install or upgrade 'RAVE'

Description

Installs the newest version of 'RAVE' and its dependence packages; executes the scripts to finalize installation to update configuration files.

Usage

add_shortcuts()

finalize_installation(
  packages = NULL,
  upgrade = c("config-only", "ask", "always", "never", "data-only"),
  async = FALSE,
  ...
)

clear_cache()

install(
  allow_cache = FALSE,
  upgrade_manager = FALSE,
  finalize = TRUE,
  force = FALSE,
  python = FALSE,
  migrate_packages = FALSE,
  lib_path = NA,
  ...
)

update_rave(
  allow_cache = FALSE,
  upgrade_manager = FALSE,
  finalize = TRUE,
  force = FALSE,
  python = FALSE,
  migrate_packages = FALSE,
  lib_path = NA,
  ...
)

upgrade_installer(reload = TRUE)

Arguments

packages	packages to run finalizing installation scripts
upgrade	upgrade type
async	whether to execute finalizing installation scripts in other processes
...	passed to internal functions
allow_cache	whether to allow cache; default is true
upgrade_manager	whether to upgrade the installer (ravemanager) before updating other packages
finalize	whether to run finalizing installation scripts
force	whether to force updating packages even the installed have the latest versions
python	whether to install python; default is false
migrate_packages	whether to migrate (copy) packages installed in the system path to the user library; used as alternative option when there are existing packages installed in the system library path that could be hard to resolve or out-dated; default is FALSE
lib_path	library path where 'RAVE' should be installed; default is automatically determined.
reload	whether to reload ravemanager after installation; default is true. This tries to load the upgraded ravemanager without restarting the R session; however, this solution not always works. In such case, restarting R session is always the solution.

Value

Nothing

---

Get current 'RAVE' installer's version

Description

Get current 'RAVE' installer's version

Usage

ravemanager_version()

Value

Returns the ravemanager version

---

Run tutorials

Description

Run tutorials

Usage

run_tutorials(topic = NULL, ...)

Arguments

topic	integers of which topic to launch, leave it blank, then 'RAVE' will ask you to select a topic
...	other parameters to pass to shiny::runApp()

Examples

## Not run: 

ravemanager::run_tutorials()


## End(Not run)

---

Get system requirements for 'RAVE'

Description

Get system requirements for 'RAVE'

Usage

system_requirements(
  os = NULL,
  os_release = NULL,
  curl = Sys.which("curl"),
  sudo = FALSE,
  ...
)

Arguments

os, os_release	operating system and release version, currently only supports 'ubuntu', 'centos', 'redhat', 'opensuse', and 'sle'; see https://github.com/rstudio/r-system-requirements#operating-systems
curl	the location of the curl binary on your system
sudo	whether to pre-pend 'sudo' to the commands
...	reserved for future use

Examples

if("remotes" %in% loadedNamespaces()) {
# Please check your operating system & version!!!

# =============== On Ubuntu Linux ===============

# Ubuntu 20
ravemanager::system_requirements("ubuntu", "20")

# Ubuntu 18
ravemanager::system_requirements("ubuntu", "18")

# Ubuntu 16
ravemanager::system_requirements("ubuntu", "16")

# =============== On Red Hat Enterprise Linux ===============

# Red Hat Enterprise Linux 8
ravemanager::system_requirements("redhat", "8")

# Red Hat Enterprise Linux 7
ravemanager::system_requirements("redhat", "7")

# =============== On CentOS ===============

# Red Hat Enterprise Linux 8
ravemanager::system_requirements("centos", "8")

# Red Hat Enterprise Linux 7
ravemanager::system_requirements("centos", "7")

# =============== On OpenSUSE ===============

# openSUSE 42.3
ravemanager::system_requirements("opensuse", "42")

# =============== On SUSE Linux Enterprise ===============

# SUSE Linux Enterprise 12.3
ravemanager::system_requirements("sle", "12")

}

---

Uninstall RAVE components

Description

Remove cache, python, and/or all settings. Please be aware that R, 'RStudio', and already installed R packages will not be uninstalled. Please carefully read printed messages.

Usage

uninstall(components = c("cache", "python", "all"))

Arguments

components

which component to remove, see example for choices.

Examples

if( FALSE ) {

  # remove cache only
  ravemanager::uninstall("cache")

  # remove python environment
  ravemanager::uninstall("python")

  # remove all sample data, settings files
  ravemanager::uninstall("all")

}

---

Print out 'RAVE' version information

Description

Print out 'RAVE' version information

Usage

version_info(vanilla = FALSE)

Arguments

vanilla

whether to use vanilla packages in this function

---