From e649b782d090324e7f8cccde4bfb79c02aa1d71e Mon Sep 17 00:00:00 2001
From: PiMarchal <166733270+PiMarchal@users.noreply.github.com>
Date: Thu, 6 Feb 2025 15:32:56 +0100
Subject: [PATCH 1/2] Create Install_python_function

Function to install python and python packages with R (similar to what is done in the other quarto document)
---
 Install_python_function | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 Install_python_function

diff --git a/Install_python_function b/Install_python_function
new file mode 100644
index 0000000..0a6b7ae
--- /dev/null
+++ b/Install_python_function
@@ -0,0 +1,24 @@
+# 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")
+}

From b017fafc9fa071c0f6a012f4a20de4cd3b97e744 Mon Sep 17 00:00:00 2001
From: PiMarchal <166733270+PiMarchal@users.noreply.github.com>
Date: Fri, 7 Feb 2025 09:21:43 +0100
Subject: [PATCH 2/2] Rename Install_python_function to
 inst/Script/Install_python_function.R

Added to a new folder, as a .R file
---
 Install_python_function => inst/Script/Install_python_function.R | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename Install_python_function => inst/Script/Install_python_function.R (100%)

diff --git a/Install_python_function b/inst/Script/Install_python_function.R
similarity index 100%
rename from Install_python_function
rename to inst/Script/Install_python_function.R