Code cleanup

README.md

@@ -50,11 +50,11 @@ Once you have renv installed, you can create an R environment by a simple comman
 renv -n myenv
 ```
 
-An environment folder `myenv` will be created under `$HOME/beRi_envs`. 
+An environment folder `myenv` will be created under `$HOME/.renv`.
 
 To activate the environment 
 ```
-cd $HOME\beRi_envs\myenv\bin
+cd $HOME\.renv\myenv\bin
 . ./activate 
 ```
 

renv/core.py

@@ -1,7 +1,6 @@
 from venv import EnvBuilder
 import logging
 import os
-import shutil
 import subprocess
 import sys
 import types
@@ -80,7 +79,7 @@ def create(self, env_dir, env_name=None):
         if env_dir:
             env_dir = os.path.abspath(env_dir)
         else:
-            env_dir = utils.get_beri_path()
+            env_dir = utils.get_renv_path()
             if env_name:
                 env_dir = os.path.join(env_dir, env_name)
             else:
@@ -132,16 +131,33 @@ def ensure_directories(self, env_dir):
         r_script = "Rscript"
         context.R_exe = r_exe
         context.R_script = r_script
-        context.R_version = os.path.split(self.r_path)[1]
         if self.r_bin_path:
             context.abs_R_exe = os.path.join(self.r_bin_path, r_exe)
             context.abs_R_script = os.path.join(self.r_bin_path, r_script)
         else:
             context.abs_R_exe = os.path.join(self.r_path, "bin", r_exe)
             context.abs_R_script = os.path.join(self.r_path, "bin", r_script)
         context.abs_R_path = self.r_path
-        logging.info(f"System R(version):  {self.r_path}({context.R_version})")
 
+        # Get the version of R
+        # Major Version
+        Rcmd = f"{context.abs_R_script} " \
+               f"-e \'R.version$major\'"
+        recommended_pkgs = subprocess.Popen([Rcmd], stderr=subprocess.PIPE, stdout=subprocess.PIPE,
+                                            shell=True, encoding='utf-8')
+        error = recommended_pkgs.stderr.readlines()
+        major = recommended_pkgs.stdout.readlines()
+        recommended_pkgs.wait()
+        # Minor Version
+        Rcmd = f"{context.abs_R_script} " \
+               f"-e \'R.version$minor\'"
+        recommended_pkgs = subprocess.Popen([Rcmd], stderr=subprocess.PIPE, stdout=subprocess.PIPE,
+                                            shell=True, encoding='utf-8')
+        error = recommended_pkgs.stderr.readlines()
+        minor = recommended_pkgs.stdout.readlines()
+        recommended_pkgs.wait()
+        context.R_version = f"{major}.{minor}"
+        logging.info(f"System R(version):  {self.r_path}({context.R_version})")
         # Begin with R-Environment R files/paths
         # Continue with system R files/paths
         if sys.platform == 'win32':  # Windows
@@ -393,15 +409,3 @@ def format_pkg_list(self, config_dict):
             fmtd_list[list_name] = pkg_list_string
 
         return fmtd_list
-
-    # def install_r(self):
-    #     # New: install specified version of R in the R environment.
-    #     pass
-    #
-    # def setup_r_profile(self, context):
-    #     # New
-    #     pass
-    #
-    # def setup_r_environ(self):
-    #     # New
-    #     pass

renv/utils.py

@@ -2,6 +2,7 @@
 import subprocess as sp
 from shutil import rmtree
 
+
 def get_r_path():
     """
     Get current R installed path in Linux
@@ -33,17 +34,18 @@ def get_user_home_dir():
     sp_out = sp.run(["echo $HOME"], shell=True, stdout=sp.PIPE, encoding="utf8")
     return sp_out.stdout.strip()
 
-def get_beri_path(has_root_access=False):
+
+def get_renv_path(has_root_access=False):
     """
     Get the default R environment path
     # TODO make this function cross-platform
     :param has_root_access: whether user has root access in Linux.
-    :return: path to beRi_envs, inclusive.
+    :return: path to .renv, inclusive.
     """
     if has_root_access:
-        return os.path.join(get_r_installed_root(), "beRi_envs")
+        return os.path.join(get_r_installed_root(), ".renv")
     else:
-        return os.path.join(get_user_home_dir(), "beRi_envs")
+        return os.path.join(get_user_home_dir(), ".renv")
 
 
 def create_directory(directory, clear=False):
@@ -65,6 +67,7 @@ def create_directory(directory, clear=False):
     else:
         os.makedirs(directory)
 
+
 def create_symlink(src, dst, subfolders=[]):
     """
     Create symlink in the dst folder from the src folder.