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