installGiottoONTraCEnvironment

Installs a conda environment contains ONTraC. This includes a miniconda installation and also a set of python packages that Giotto may often use. See details for further information

installGiottoONTraCEnvironment(
  python_version = "3.11.9",
  ontrac_version = "latest",
  mini_install_path = NULL,
  confirm = TRUE,
  envname = "giotto_ontrac_env",
  conda = "auto",
  force_miniconda = FALSE,
  force_environment = FALSE,
  verbose = NULL
)

Arguments

python_version

python version to use within the giotto conda environment. Default is v3.11.9

ontrac_version

ONTraC version to install. Default is "latest"

mini_install_path

(optional) desired miniconda installation location. Default is chosen by `reticulate::install_miniconda()`

confirm

whether to pause for confirmation of conda environment install location (default = TRUE)

envname

name to assign environment. Default = "giotto_ontrac_env"

conda

either "auto" (default) to allow reticulate to handle it, or the full filepath to the conda executable. You can also set the option "reticulate.conda_binary" or `Sys.setenv()` "RETICULATE_CONDA" to tell reticulate where to look.

force_miniconda

force reinstallation of miniconda

force_environment

force reinstallation of the giotto environment

verbose

be verbose

packages_to_install

python modules (packages) to install for Giotto.

Value

installs a giotto environment using the reticulate miniconda system

Details

This function will install a local conda environment using the miniconda system as implemented by reticulate. Which contains ONTraC and a set of python packages that Giotto may often use.

Examples

installGiottoONTraCEnvironment()
#> 
#> |---- install giotto environment ----|
#> + /usr/share/miniconda/bin/conda create --yes --name giotto_ontrac_env 'python=3.11.9' --quiet -c conda-forge
#> + /usr/share/miniconda/bin/conda install --yes --name giotto_ontrac_env 'python=3.11.9' -c conda-forge -c vtraag
#> + /usr/share/miniconda/bin/conda install --yes --name giotto_ontrac_env -c conda-forge -c vtraag 'python=3.11.9' 'pandas==2.2.1' 'networkx==2.8.8' 'python-igraph==0.10.2' 'leidenalg==0.9.0' 'scikit-learn==1.1.3'
#> + /usr/share/miniconda/bin/conda install --yes --name giotto_ontrac_env 'python=3.11.9' -c conda-forge