ormr: 'ormr': work with Python packages and scripts from R.

In richelbilderbeek/ormr: Work With Python Installed At A Custom Location

ormr: work with Python packages and scripts from R.

Description

ormr allows a user to install Python packages, create a Conda environment and run Python scripts with only one point of contact.

Details

ormr was written to write simpler Singularity (https://singularity.hpcng.org/) (a type of containerization software, similar to Docker) scripts.

reticulate is great when using its default folders on a local computer. However, for a Singularity container, it is recommended to install libraries in a systems folder. In that setting, reticulate is harder to work with.

ormr allows to install install Python packages, create a Conda environment and run Python scripts in any folder easily, for example, in a system folder (/opt/ormr) of a Singularity container.

Author(s)

Richèl J.C. Bilderbeek

Examples

# Install a package
if (plinkr::is_on_ci()) {
  install_python_package(
    package_name = "scipy"
  )
}

# Run a Python scripts
if (plinkr::is_on_ci()) {
  python_script_path <- system.file(
  "extdata", "hello_world.py", package = "ormr"
  )
  run_python_script(
    python_script_path = python_script_path
  )
}

# Run a Python script with arguments
if (plinkr::is_on_ci()) {
  python_script_path <- system.file(
    "extdata", "show_args.py", package = "ormr"
  )
  run_python_script_with_args(
    python_script_path = python_script_path,
    args = c("Hello", "world")
  )
}

richelbilderbeek/ormr documentation built on May 23, 2022, 1:15 p.m.