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Create Install_python_function #46

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e649b78
Create Install_python_function
PiMarchal Feb 6, 2025
b017faf
Rename Install_python_function to inst/Script/Install_python_function.R
PiMarchal Feb 7, 2025
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24 changes: 24 additions & 0 deletions Install_python_function
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# Install python, and all python associated packages

Install_python_spectriPy = function(PATH_miniconda = "~/miniconda3_reticulate",ENV_name = "r-reticulate"){
print("Install reticulate prior to run this")
library(reticulate)
options(timeout = 600)
install_miniconda(path = PATH_miniconda,force = FALSE)

use_python(paste(PATH_miniconda,"/bin/python3",sep = ""))
conda_create(ENV_name)

py_install("matchms==0.28.2",pip = TRUE)
py_install("spectrum_utils",pip = TRUE)
py_install("numpy==2.0.2",pip = FALSE)

conda_install(envname = ENV_name,"matchms==0.28.2",pip = TRUE,python_version = "3.12.2")
conda_install(envname = ENV_name,"spectrum_utils",pip = TRUE)
conda_install(envname = ENV_name,"numpy==2.0.2",pip = FALSE)

print("R packages that needs to be installed for any analysis: BiocManager , Spectra , msdata , AnnotationHub , CompoundDb , GenomeInfoDbData , mzR , basilisk , SpectriPy")
print("Use the options(timeout = 600)")
print("WARNING: use_condaenv(paste(PATH_miniconda,ENV_name,'/bin/python3',sep ='') needs to be run after importing reticulate to tell it where to find the python environment")
return("Python installation finished")
}
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