--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/r2py.py	Thu Dec 19 10:24:45 2019 -0500
@@ -0,0 +1,126 @@
+#!/usr/bin/env python3
+import os
+import atexit
+import socket
+import time
+import config
+import pyRserve
+
+def shutdown(port):
+    try:
+        conn = pyRserve.connect(port=port)
+        print("Shutting down Rserv...", end="")
+        conn.shutdown()
+        print("Done")
+    except pyRserve.rexceptions.RConnectionRefused:
+        print("connection to Rserve refused, server is probably already down")
+
+def get_open_port():
+    s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+    s.bind(("", 0))
+    s.listen(1)
+    port = s.getsockname()[1]
+    s.close()
+    return port
+
+    # find free port
+def create_connection():
+    '''Start R Rserver and test connection, port is
+    stored in config.RSERVE_PORT
+    '''
+    config.RSERVE_PORT = get_open_port()
+    print('Trying to start Rserve...',)
+    os.system(
+        "R CMD Rserve --RS-port {} -q --no-save ".format(config.RSERVE_PORT))
+        # wait for server to start accepting connections
+    time.sleep(1)
+    try:
+        conn = pyRserve.connect(port=config.RSERVE_PORT)
+        print("connection OK")
+        conn.close()
+        atexit.register(shutdown, config.RSERVE_PORT)
+        return config.RSERVE_PORT
+    except:
+        print("Connection with Rserve was not established!")
+        raise
+
+
+class setFunctionName():
+    # decorator
+
+    def __init__(self, f, name):
+        self.f = f
+        self.name = name
+
+    def __call__(self, *args, **kwargs):
+        return self.f(self.name, *args, **kwargs)
+
+
+def convert_types(fn):
+    ''' decorator function to convert type for r2py'''
+    allowed_classes = [str, int, float, list, bool, type(None)]
+    # everything else is converted to str
+
+    def fn_wrapper(*args, **kwargs):
+        new_args = list(args)
+        new_kwargs = kwargs
+        for i, value in enumerate(args):
+            if any(type(value) is i for i in allowed_classes):
+                new_args[i] = value
+            else:
+                new_args[i] = str(value)
+        for i, value in kwargs.items():
+            if any(type(value) is i for i in allowed_classes):
+                new_kwargs[i] = value
+            else:
+                new_kwargs[i] = str(value)
+        return fn(*new_args, **new_kwargs)
+
+    return fn_wrapper
+
+
+class R():
+
+    def __init__(self, source, verbose=False):
+        ''' Code in file should defined R functions which will be linked to python function
+        purpose of this is to make it memory efficient - rserve connection will be closed
+        after every exetion so memory is released.
+        warning  - Source code is executed each time function is used so it should only
+        contain function definition!!
+
+        '''
+        self.source = os.path.realpath(source)
+        conn = pyRserve.connect(port=config.RSERVE_PORT)
+        conn.voidEval("source('{}', chdir=TRUE)".format(self.source))
+        # if single object is define then fn return str! conversion neccessary
+        object_names = list(conn.r.ls())
+        if verbose:
+            print("R function loaded:", end=" ")
+        for i in object_names:
+            ## skip these objects - not compatible with older version of rserve
+            ## and not needed to be accessed from python
+            if i in ['DT_OPTIONS', 'HTMLHEADER', 'WD', 'options',
+                     'htmlheader', 'options', 'xcolor_code', 'TANDEM_RANKS', 'RANKS_TANDEM',]:
+                continue
+            try:
+                obj = getattr(conn.r, i)
+                if isinstance(obj, pyRserve.rconn.RFuncProxy):
+                    if verbose:
+                        print(i, end=" ")
+                    @convert_types
+                    def rwrapper(fname, *args, **kwargs):
+                        c = pyRserve.connect(port=config.RSERVE_PORT)
+                        c.r.setwd(os.getcwd())
+                        c.voidEval("source('{}',chdir=TRUE)".format(self.source))
+                        fn = getattr(c.r, fname)
+                        out = fn(*args, **kwargs)
+                        c.close()
+                        return out
+                    rwrapper = setFunctionName(rwrapper, i)
+                    setattr(self, i, rwrapper)
+                    del(rwrapper)
+            except:
+                print("skipping :", i)
+                pass
+        if verbose:
+            print("\r")