Isolated `Miniconda`, `Python`, and `Matlab` (experimental) Environment

R-CMD-check

The goal of rpymat is to create a single isolated Miniconda and Python environment for reproducible pipeline scripts. The package is a shell of reticulate package, but provides more stable behaviors, especially on ‘ARM’ machines.

Installation

You can install the released version of rpymat from CRAN with:

 install.packages("rpymat")

Configure environment

Configure python after installation

 # change `python_ver` accordingly
rpymat::configure_conda(python_ver = 'auto')

Add Python or conda packages

 # Add conda packages
rpymat::add_packages(c('pandas', 'numpy'))
 
 # Add conda packages from channels
rpymat::add_packages(c('h5py'), channel = "conda-forge")
 
 # Add pip packages
rpymat::add_packages(c('sklearn'), pip = TRUE)

Use `Jupyterlab`

 # Install Jupyterlab, will install
 # numpy, h5py, matplotlib, pandas, 
 # jupyter, jupyterlab, jupyterlab-git, ipywidgets, jupyter-server-proxy
 # jupyterlab_latex, jupyterlab_github, matlab_kernel
rpymat::add_jupyter()
 
 # Launch Jupyterlab
rpymat::jupyter_launch(async = FALSE)

Advanced configurations:

rpymat::jupyter_launch(
 async = TRUE, workdir = "~",
 port = 18888, open_browser = TRUE,
 token = "IwontTellYouMyToken"
)

To query existing servers

rpymat::jupyter_server_list()
 #> host port token
 #> 1 127.0.0.1 8888 3hzWfGPa0EOmonaNS48jrTvpw07KiX7VKerA9ZTFJMkCOJMgfB
 #> 2 127.0.0.1 18888 IwontTellYouMyToken

To stop a server

rpymat::jupyter_server_stop(port = 18888)

Use `rpymat` with `reticulate`

 # Initialize the isolated environment
 
rpymat::ensure_rpymat()
 
rpymat::repl_python()

Then run python code interactively.

Alternatively, you can use rpymat::run_script(path) to execute Python scripts, and use reticulate::py to obtain the results.

Uninstall

The following command will erase the environment completely.

rpymat::remove_conda()

Isolated Miniconda, Python, and Matlab (experimental) Environment