Revision: 657
http://rpy.svn.sourceforge.net/rpy/?rev=657&view=rev
Author: lgautier
Date: 2008-10-12 11:49:08 +0000 (Sun, 12 Oct 2008)
Log Message:
-----------
- Mode editing in the doc.
- Attempt at fixing history in the console in examples
- Pydoc statements
Modified Paths:
--------------
branches/rpy_nextgen/demos/radmin.py
branches/rpy_nextgen/doc/source/overview.rst
branches/rpy_nextgen/doc/source/rlike.rst
branches/rpy_nextgen/doc/source/robjects.rst
branches/rpy_nextgen/rpy/rlike/container.py
branches/rpy_nextgen/rpy/robjects/__init__.py
Modified: branches/rpy_nextgen/demos/radmin.py
===================================================================
--- branches/rpy_nextgen/demos/radmin.py 2008-10-12 11:28:18 UTC (rev
656)
+++ branches/rpy_nextgen/demos/radmin.py 2008-10-12 11:49:08 UTC (rev
657)
@@ -434,9 +434,15 @@
_view = None
_evalButton = None
_start_mark = None
+ _history = None #[]
+ _history_i = None #0
def __init__(self):
super(ConsolePanel, self).__init__()
+
+ self._history = [None, ] * 20
+ self._history_i = 0
+
s_window = gtk.ScrolledWindow()
s_window.set_policy(gtk.POLICY_AUTOMATIC,
gtk.POLICY_AUTOMATIC)
@@ -476,15 +482,23 @@
self._firstEnter = False
+
def actionKeyPress(self, view, event):
if (event.keyval == gtk.gdk.keyval_from_name("Return")):
self.append("\n", "input")
self.evaluateAction(self._evalButton)
+ self._history_i = len(self._history) - 1
return True
if (event.keyval == gtk.gdk.keyval_from_name("Up")):
- print('up')
+ self._history_i -= 1
+ if self._history_i == -1:
+ self._history_i = len(self._history)
+ return True
if (event.keyval == gtk.gdk.keyval_from_name("Down")):
- print('down')
+ self._history_i += 1
+ if self._history_i == len(self._history):
+ self._history_i = 0
+ return True
def append(self, text, tag="input"):
tag = self.tag_table.lookup(tag)
@@ -496,6 +510,10 @@
buffer.get_end_iter())
buffer.delete_mark(mark)
+ if tag == "input":
+ self._history[self._history_i] = text
+ self._history_i += 1
+
def evaluateAction(self, widget, data=None):
buffer = self._buffer
start_iter = buffer.get_iter_at_mark(self._start_mark)
Modified: branches/rpy_nextgen/doc/source/overview.rst
===================================================================
--- branches/rpy_nextgen/doc/source/overview.rst 2008-10-12 11:28:18 UTC
(rev 656)
+++ branches/rpy_nextgen/doc/source/overview.rst 2008-10-12 11:49:08 UTC
(rev 657)
@@ -31,7 +31,7 @@
Naturally RPy2 is inspired by RPy, but also by A. Belopolskys's contributions
that were waiting to be included into RPy.
-This effort can be seen as a rewrite of the RPy package.
+This effort can be seen as a redesign and rewrite of the RPy package.
Installation
------------
@@ -150,12 +150,11 @@
The choice of inheritance was made to facilitate the implementation
of mostly inter-exchangeable classes between :mod:`rpy2.rinterface`
-and :mod:`rpy2.robjects`: an :class:`rpy2.rinterface.SexpClosure`
+and :mod:`rpy2.robjects`. For example, an :class:`rpy2.rinterface.SexpClosure`
can be given any :class:`rpy2.robjects.RObject` as a parameter while
any :class:`rpy2.robjects.RFunction` can be given any
-:class:`rpy2.rinterface.Sexp`. Choosing inheritance does not only
-come with advantages: `setters` on `R` objects would be more intuitive
-with a container/delegation approach.
+:class:`rpy2.rinterface.Sexp`. Because of R's functional basis,
+a container-like extension is also present.
The module :mod:`rpy2.rpy_classic` is using delegation, letting us
demonstrate how to extend :mod:`rpy2.rinterface` with an alternative
Modified: branches/rpy_nextgen/doc/source/rlike.rst
===================================================================
--- branches/rpy_nextgen/doc/source/rlike.rst 2008-10-12 11:28:18 UTC (rev
656)
+++ branches/rpy_nextgen/doc/source/rlike.rst 2008-10-12 11:49:08 UTC (rev
657)
@@ -83,14 +83,17 @@
[1, 2, 3]
>>> tl.tags()
('a', 'b', 'c')
->>> tl.settag(0, 'c')
+>>> tl.settag(2, 'a')
>>> tl.tags()
-('c', 'b', 'c')
->>> it = tl.iterontag('c')
+('a', 'b', 'a')
+>>> it = tl.iterontag('a')
>>> [x for x in it]
[1, 3]
+>>> [(t, sum([i for i in tl.iterontag(t)])) for t in set(tl.itertags())]
+[('a', 4), ('b', 2)]
+
The Python docstring for the class is:
.. autoclass:: rpy2.rlike.container.TaggedList
@@ -102,13 +105,27 @@
Tools for working with sequences
================================
+Tools for working with objects implementing the
+the sequence protocol can be found here.
+
+
.. autofunction:: tapply
>>> import rpy2.rlike.functional as rlf
>>> rlf.tapply((1,2,3), ('a', 'b', 'a'), sum)
[('a', 4), ('b', 2)]
+:class:`TaggedList` objects can be used with their tags
+(although more flexibility can be achieved using their
+method :meth:`iterontags`):
+
+>>> import rpy2.rlike.container as rlc
+>>> tl = rlc.TaggedList([1, 2, 3], tags = ('a', 'b', 'a'))
+>>> rlf.tapply(tl, tl.tags(), sum)
+[('a', 4), ('b', 2)]
+
+
.. module:: rpy2.rlike.indexing
Indexing
Modified: branches/rpy_nextgen/doc/source/robjects.rst
===================================================================
--- branches/rpy_nextgen/doc/source/robjects.rst 2008-10-12 11:28:18 UTC
(rev 656)
+++ branches/rpy_nextgen/doc/source/robjects.rst 2008-10-12 11:49:08 UTC
(rev 657)
@@ -67,7 +67,7 @@
* The actual Python attributes for the object masks the R elements
- * '.' (dot) is syntactically valid name for R objects, but not for
+ * '.' (dot) is syntactically valid in names for R objects, but not for
python objects.
That last limitation can partly be removed by setting the attribute
@@ -79,7 +79,27 @@
>>> robjects.r.as_null
# R function as.null() returned
+.. warning::
+ In the case there are R objects which name only differ by '.' and '_'
+ (e.g., 'my_variable' and 'my.variable'), setting :attr:`_dotter` to True
+ can result in confusing results at runtime.
+Behind the scene, the steps for getting an attribute of `r` are
+rather straightforward:
+
+ 1. Check if the attribute is defined as such in the python definition for
+ `r`
+
+ 2. Check if the attribute is can be accessed in R, starting from `globalEnv`
+
+ 3. If :attr:`_dotter` is True, turn all `_` into `.` and repeat the step
above
+
+When safety matters most, we recommed using :meth:`__getitem__` to get
+and R object (and store it in a python variable if wanted):
+
+>>> as_null = robjects.r['as.null']
+
+
Strings as R code
-----------------
@@ -215,11 +235,14 @@
>>> x.r + 1
2:11
-
.. note::
In Python, the operator ``+`` concatenate sequence object, and this behavior
has been conserved.
+.. note::
+ The boolean operator ``not`` cannot be redefined in Python (at least up to
+ version 2.5), and its behavior could be made to mimic R's behavior
+
.. index::
single: names; robjects
@@ -273,6 +296,8 @@
(with :attr:`typeof` equal to *VECSXP*)
or an instance of class :class:`rpy2.rlike.container.TaggedList`.
+>>> robjects.RDataFrame()
+
.. autoclass:: rpy2.robjects.RDataFrame
:show-inheritance:
:members:
@@ -397,7 +422,7 @@
fit = robjects.r('lm(%s)' %repr(fmla))
-Mapping between rpy2 objects and other python objects
+Mapping rpy2 objects to arbitrary python objects
=====================================================
The conversion, often present when working with RPy-1.x, is no longer
@@ -447,7 +472,10 @@
<type 'float'>
>>>
+The default behavoir can be restored with:
+>>> robjects.ri2py = default_ri2py
+
The docstrings for :meth:`default_ri2py`, :meth:`default_py2ri`, and
:meth:`py2ro` are:
.. autofunction:: rpy2.robjects.default_ri2py
Modified: branches/rpy_nextgen/rpy/rlike/container.py
===================================================================
--- branches/rpy_nextgen/rpy/rlike/container.py 2008-10-12 11:28:18 UTC (rev
656)
+++ branches/rpy_nextgen/rpy/rlike/container.py 2008-10-12 11:49:08 UTC (rev
657)
@@ -273,7 +273,6 @@
super(TaggedList, self).sort(reverse = reverse)
self.__tags = [self.__tags[i] for i in o]
-
def tags(self):
"""
Return a tuple of all tags
@@ -295,3 +294,15 @@
self.__tags[i] = t
+# class DataFrame(ArgsDict):
+
+# def __init__(self, s):
+# super(ArgsDict, self).__init__(s)
+
+# if len(self) > 0:
+# nrows = len(self[0])
+# for i, v in enumerate(self):
+# if len(v) != nrows:
+# raise ValueError("Expected length %i for element %i"
+# %(nrows, i))
+
Modified: branches/rpy_nextgen/rpy/robjects/__init__.py
===================================================================
--- branches/rpy_nextgen/rpy/robjects/__init__.py 2008-10-12 11:28:18 UTC
(rev 656)
+++ branches/rpy_nextgen/rpy/robjects/__init__.py 2008-10-12 11:49:08 UTC
(rev 657)
@@ -320,7 +320,14 @@
return self.dim[1]
class RDataFrame(RVector):
+ """ R 'data.frame'.
+ """
+
def __init__(self, tlist):
+ """ Create a new data frame.
+
+ :param tlist: TaggedList
+ """
if isinstance(tlist, rlc.TaggedList):
df = baseNameSpaceEnv["data.frame"].rcall(tlist.items())
super(RDataFrame, self).__init__(df)
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