Revision: 521
http://rpy.svn.sourceforge.net/rpy/?rev=521&view=rev
Author: lgautier
Date: 2008-05-14 10:46:33 -0700 (Wed, 14 May 2008)
Log Message:
-----------
First stab at ensuring compatibility with the current RPy (1.x)
Added Paths:
-----------
branches/rpy_nextgen/rpy/rpy_classic.py
Added: branches/rpy_nextgen/rpy/rpy_classic.py
===================================================================
--- branches/rpy_nextgen/rpy/rpy_classic.py (rev 0)
+++ branches/rpy_nextgen/rpy/rpy_classic.py 2008-05-14 17:46:33 UTC (rev
521)
@@ -0,0 +1,282 @@
+"""
+Implementation of RPy 1.x (for compatibility)
+"""
+
+import rpy2.rinterface as ri
+import array
+
+
+
+# --- options in 'rpy_options.py'
+
+rpy_options = {
+ 'RHOME':None, # R Installation Directory
+ 'RVERSION':None, # R Version *string*
+ 'RVER':None, # R Version *number*
+ 'RUSER':None, # R User's Home Directory
+ 'USE_NUMERIC':None, # Is Numeric module available
+ 'VERBOSE':False, # Should status messages be displated.
+ 'SETUP_READ_CONSOLE': True, # False for no standard console read config
+ 'SETUP_WRITE_CONSOLE': True, # False for no standard console write config
+ 'SETUP_SHOWFILES': True # False for no standard console file viewerd
config
+ }
+
+# --- more options
+
+VERBOSE = True
+RVERSION = None
+RHOME = None
+
+TOP_CONVERSION = 4
+PROC_CONVERSION = 4
+CLASS_CONVERSION = 3
+BASIC_CONVERSION = 2
+VECTOR_CONVERSION = 1
+NO_CONVERSION = 0
+NO_DEFAULT = -1
+
+# from RPy.h
+TOP_MODE = 4
+
+
+# --- init R
+
+ri.initEmbeddedR()
+
+class RPyException(Exception):
+ """ Generic exeception for RPy """
+ pass
+class RPyTypeConversionException(RPyException):
+ pass
+class RPyRException(RuntimeError):
+ """ Runtime error while running R code. """
+ pass
+
+# for backwards compatibility
+RException = RPyException
+
+# I/O setters
+# FIXME: sort out the details of what RPy is doing with that
+# and what is the amount that is user-defined (and/or used).
+set_rpy_output = None
+set_rpy_input = None
+get_rpy_output = None
+get_rpy_input = None
+
+
+# --- "CONVERSION" system
+
+
+class ModuleMode(object):
+ # same default as in "rpymodule.c"
+ __mode = -1
+
+ def __init__(self):
+ pass
+
+ @classmethod
+ def __eq__(self, val):
+ return ModuleMode.__mode == val
+ @classmethod
+ def set_mode(val):
+ ModuleMode.__mode == val
+ @classmethod
+ def get_mode():
+ return ModuleMode.__mode
+
+default_mode = ModuleMode()
+
+# Wrap a function in safe modes to avoid infinite recursion when
+# called from within the conversion system
+def with_mode(i, fun):
+ def f(*args, **kwds):
+ try:
+ e = get_default_mode()
+ set_default_mode(i)
+ return fun(*args, **kwds)
+ finally:
+ set_default_mode(e)
+ return f
+
+# Manage the global mode
+def set_default_mode(mode):
+ if not isinstance(mode, int):
+ raise ValueError("mode should be an int.")
+ if (mode < -1) or (mode > TOP_MODE):
+ raise ValueError("wrong mode.")
+ default_mode.set_mode(mode)
+
+def get_default_mode():
+ return default_mode.get_mode()
+
+
+
+# note: inherits from dict: not considering pre-2.2 versions of Python
+class Dict_With_Mode(dict):
+ def __setitem__(self, key, value):
+ v = with_mode(BASIC_CONVERSION, value)
+ if type(key) not in [str, tuple]:
+ k = with_mode(BASIC_CONVERSION, key)
+
+ super(Dict_With_Mode, self).__setitem__(k, v)
+
+proc_table = Dict_With_Mode({})
+class_table = Dict_With_Mode({})
+
+
+
+def py2rpy(obj):
+ if isinstance(obj, int):
+ robj = ri.SexpVector([obj, ], ri.INTSXP)
+ return robj
+ if isinstance(obj, float):
+ robj = ri.SexpVector([obj, ], ri.REALSXP)
+ return robj
+ if isinstance(obj, str):
+ robj = ri.SexpVector([obj, ], ri.STRSXP)
+ return robj
+ if isinstance(obj, complex):
+ robj = ri.SexpVector([obj, ], ri.CPLSXP)
+ return robj
+ if isinstance(obj, list):
+ types = [bool, int, float, str]
+ has_type = [False, False, False, False]
+ for tp_i, tp in enumerate(types):
+ for elt in obj:
+ if isinstance(elt, tp):
+ has_type[tp_i] = True
+ r_type = None
+ if has_type[3]:
+ r_type = ri.STRSXP
+ elif has_type[2]:
+ r_type = ri.REALSXP
+ elif has_type[1]:
+ r_type = ri.INTSXP
+ elif has_type[0]:
+ r_type = ri.LGLSXP
+ if r_type is not None:
+ robj = ri.SexpVector(obj, r_type)
+ return robj
+ raise ValueError("Don't know what to do with 'obj'.")
+
+def rpy2py_basic(obj):
+ if hasattr(obj, '__len__'):
+ if obj.typeof() in [ri.INTSXP, ri.REALSXP, ri.CPLSXP,
+ ri.STRSXP]:
+ res = [x for x in obj]
+ elif obj.typeof() in [ri.VECSXP]:
+ res = [rpy2py for x in obj]
+ else:
+ raise ValueError("Invalid type for 'obj'.")
+ return res
+ raise ValueError("Invalid type for 'obj'.")
+
+def rpy2py(obj, mode=default_mode):
+ if mode == NO_CONVERSION:
+ res = obj
+ return res
+ if mode == BASIC_CONVERSION:
+ res = rpy2py_basic(obj)
+ return res
+ raise ValueError("Invalid default mode.")
+
+class Robj(object):
+ """ Class to model any R object.
+ As in the 'classic' RPy (that is versions 1.x),
+ Whether an object is callable or a vector, or else, is
+ resolved at runtime in R and it only exposed as an "R something"
+ to Python.
+ """
+
+ __local_mode = NO_DEFAULT
+
+ def __init__(self, sexp):
+ if not isinstance(sexp, ri.Sexp):
+ raise ValueError('"sexp" must inherit from ri.Sexp')
+ self.__sexp = sexp
+
+ def __call__(self, *args, **kwargs):
+ args_r = []
+ for a in args:
+ if isinstance(a, ri.Sexp):
+ a = a
+ elif isinstance(a, Robj):
+ a = a.getSexp()
+ else:
+ a = py2rpy(a)
+ args_r.append(a)
+ kwargs_r = {}
+ for a_n in kwargs:
+ a = kwargs[a_n]
+ if isinstance(a, ri.Sexp):
+ a = a
+ elif isinstance(a, Robj):
+ a = a.getSexp()
+ else:
+ a = py2rpy(a)
+ kwargs_r[a_n] = a
+ #import pdb; pdb.set_trace()
+ res = self.__sexp(*args_r, **kwargs_r)
+ return res
+
+ def __getitem__(self, item):
+ res = self.__sexp[item]
+ res = rpy2py(res)
+ return res
+
+ ##FIXME: not part of RPy-1.x.
+ def getSexp(self):
+ return self.__sexp
+
+ def __repr__(self):
+ res = rpy2r(self)
+ return res
+
+ def as_py(mode = default_mode):
+ res = rpy2py(self, mode)
+ return res
+
+ def local_mode(mode = default_mode):
+ self.__local_mode = mode
+
+class R(object):
+ def __init__(self):
+ self.get = ri.globalEnv.get
+ self.TRUE = ri.TRUE
+ self.FALSE = ri.FALSE
+
+
+ def __getattr__(self, name):
+ if name.startswith('__') and name.endswith('__'):
+ return super(R, self).__getattr__(name)
+ if len(name) > 1 and name[-1] == '_' and name[-2] != '_':
+ name = name[:-1]
+ name = name.replace('__', '<-')
+ name = name.replace('_', '.')
+ res = self.__getitem__(name)
+ return res
+
+ def __getitem__(self, name):
+ #FIXME: "get function only" vs "get anything"
+ res = ri.globalEnv.get(name)
+ res = rpy2py(res)
+ return res
+
+ def __call__(self, s):
+ return self.eval(self.parse(text=s))
+
+ def __help__(self, *args, **kwargs):
+ helpobj.helpfun(*arg, **kw)
+
+ def __repr__(self):
+ rversion = self.__getitem__('R.version.sting')
+ res = 'RPy version %s [%s]' %(rpy_version, r_version)
+
+ def __str__(self):
+ return repr(self)
+
+ def __cleanup__(self):
+ ri.endEmbeddedR()
+ del(self)
+
+r = R()
Property changes on: branches/rpy_nextgen/rpy/rpy_classic.py
___________________________________________________________________
Name: svn:eol-style
+ native
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