Install & Configure 'python' environment for 'RAVE'

Installs 'python' environment for 'RAVE'

Usage

validate_python(verbose = TRUE)

configure_python(python_ver = "3.9", 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

if (FALSE) {

# -------- 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()



}