Revision: 712
http://rpy.svn.sourceforge.net/rpy/?rev=712&view=rev
Author: lgautier
Date: 2008-12-03 12:09:01 +0000 (Wed, 03 Dec 2008)
Log Message:
-----------
merging recent changes from version 2.0.x
(doc + fix when using env variable R_HOME)
Modified Paths:
--------------
rpy2/trunk/NEWS
rpy2/trunk/demos/example01.py
rpy2/trunk/doc/source/conf.py
rpy2/trunk/doc/source/index.rst
rpy2/trunk/doc/source/overview.rst
rpy2/trunk/doc/source/robjects.rst
rpy2/trunk/rpy/__init__.py
rpy2/trunk/rpy/rinterface/__init__.py
rpy2/trunk/setup.py
Added Paths:
-----------
rpy2/trunk/doc/source/robjects_convert.rst
Property Changed:
----------------
rpy2/trunk/doc/
Modified: rpy2/trunk/NEWS
===================================================================
--- rpy2/trunk/NEWS 2008-12-03 11:40:00 UTC (rev 711)
+++ rpy2/trunk/NEWS 2008-12-03 12:09:01 UTC (rev 712)
@@ -1,7 +1,14 @@
-SVN
-===
+Release 2.0.1
+=============
+Bugs fixed
+----------
+
+- Having the environment variable R_HOME specified resulted in an error
+ when importing :mod:`rpy2.rinterface` # root of the problem spotted by Peter
+
+
Release 2.0.0
=============
Modified: rpy2/trunk/demos/example01.py
===================================================================
--- rpy2/trunk/demos/example01.py 2008-12-03 11:40:00 UTC (rev 711)
+++ rpy2/trunk/demos/example01.py 2008-12-03 12:09:01 UTC (rev 712)
@@ -26,13 +26,10 @@
r.biplot(pca, main="biplot")
-if not r.require("GO")[0]:
+if not r.require("GO.db")[0]:
raise(Exception("Bioconductor Package GO missing"))
goItem = r.GOTERM["GO:0000001"]
-## goItem in an instance of an S4 class
-## slots can be accessed as Python attributes
-goItem.Term
Property changes on: rpy2/trunk/doc
___________________________________________________________________
Added: svn:mergeinfo
+ /rpy2/trunk/doc:691-700,702
Modified: rpy2/trunk/doc/source/conf.py
===================================================================
--- rpy2/trunk/doc/source/conf.py 2008-12-03 11:40:00 UTC (rev 711)
+++ rpy2/trunk/doc/source/conf.py 2008-12-03 12:09:01 UTC (rev 712)
@@ -45,8 +45,8 @@
# The short X.Y version.
version = '2.0'
# The full version, including alpha/beta/rc tags.
-release = '2.0.0dev'
-releaselevel = 'dev'
+release = '2.0.0'
+releaselevel = ''
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
Modified: rpy2/trunk/doc/source/index.rst
===================================================================
--- rpy2/trunk/doc/source/index.rst 2008-12-03 11:40:00 UTC (rev 711)
+++ rpy2/trunk/doc/source/index.rst 2008-12-03 12:09:01 UTC (rev 712)
@@ -9,6 +9,7 @@
introduction
robjects
numpy
+ robjects_convert
rinterface
rpy_classic
rlike
Modified: rpy2/trunk/doc/source/overview.rst
===================================================================
--- rpy2/trunk/doc/source/overview.rst 2008-12-03 11:40:00 UTC (rev 711)
+++ rpy2/trunk/doc/source/overview.rst 2008-12-03 12:09:01 UTC (rev 712)
@@ -208,4 +208,7 @@
of the implementation questions were found there.
Contributors
- Their names are in Section Changes.
+ The help of people, donating time, ideas or software patches
+ is much appreciated.
+ Their names can be found in this documentation (mostly around the
+ section Changes).
Modified: rpy2/trunk/doc/source/robjects.rst
===================================================================
--- rpy2/trunk/doc/source/robjects.rst 2008-12-03 11:40:00 UTC (rev 711)
+++ rpy2/trunk/doc/source/robjects.rst 2008-12-03 12:09:01 UTC (rev 712)
@@ -518,69 +518,3 @@
fit = robjects.r('lm(%s)' %fmla.r_repr())
-
-Mapping rpy2 objects to arbitrary python objects
-=====================================================
-
-The conversion, often present when working with RPy-1.x, is no longer
-necessary as the R objects can be either passed on to R functions
-or used in Python.
-
-However, there is a low-level mapping between `R` and `Python` objects
-performed behind the (Python-level) scene, done by the :mod:`rpy2.rinterface`,
-while an higher-level mapping is done between low-level objects and
-higher-level objects using the functions:
-
-:meth:`conversion.ri2py`
- :mod:`rpy2.rinterface` to Python. By default, this function
- is just an alias for the function :meth:`default_ri2py`.
-
-:meth:`conversion.py2ri`
- Python to :mod:`rpy2.rinterface`. By default, this function
- is just an alias for the function :meth:`default_py2ri`.
-
-:meth:`conversion.py2ro`
- Python to :mod:`rpy2.robjects`. By default, that one function
- is merely a call to :meth:`conversion.py2ri`
- followed by a call to :meth:`conversion.ri2py`.
-
-Those functions can be re-routed to satisfy all requirements, with
-the easiest option being to write a custom function calling itself
-the default functions.
-
-Switching to `numpy`-to-`rpy2` is using this mechanism.
-
-As an example, let's assume that one want to return atomic values
-whenever an R numerical vector is of length one. This is only a matter
-of writing a new function `ri2py` that handles this, as shown below:
-
-.. code-block:: python
-
- import rpy2.robjects as robjects
-
- def my_ri2py(obj):
- res = robjects.default_ri2py(obj)
- if isinstance(res, robjects.RVector) and (len(res) == 1):
- res = res[0]
- return res
-
- robjects.conversion.ri2py = my_ri2py
-
-Once this is done, we can verify immediately that this is working with:
-
->>> pi = robjects.r.pi
->>> type(pi)
-<type 'float'>
->>>
-
-The default behavior can be restored with:
-
->>> robjects.conversion.ri2py = default_ri2py
-
-The docstrings for :meth:`default_ri2py`, :meth:`default_py2ri`, and
:meth:`py2ro` are:
-
-.. autofunction:: rpy2.robjects.default_ri2py
-.. autofunction:: rpy2.robjects.default_py2ri
-.. autofunction:: rpy2.robjects.default_py2ro
-
-
Copied: rpy2/trunk/doc/source/robjects_convert.rst (from rev 711,
rpy2/branches/version_2.0.x/doc/source/robjects_convert.rst)
===================================================================
--- rpy2/trunk/doc/source/robjects_convert.rst (rev 0)
+++ rpy2/trunk/doc/source/robjects_convert.rst 2008-12-03 12:09:01 UTC (rev
712)
@@ -0,0 +1,71 @@
+
+Mapping rpy2 objects to arbitrary python objects
+=====================================================
+
+Switching between a conversion and a no conversion mode,
+an operation often present when working with RPy-1.x, is no longer
+necessary as the R objects can be either passed on to R functions
+or used in Python.
+
+However, there is a low-level mapping between `R` and `Python` objects
+performed behind the (Python-level) scene, done by the :mod:`rpy2.rinterface`,
+while an higher-level mapping is done between low-level objects and
+higher-level objects using the functions:
+
+:meth:`conversion.ri2py`
+ :mod:`rpy2.rinterface` to Python. By default, this function
+ is just an alias for the function :meth:`default_ri2py`.
+
+:meth:`conversion.py2ri`
+ Python to :mod:`rpy2.rinterface`. By default, this function
+ is just an alias for the function :meth:`default_py2ri`.
+
+:meth:`conversion.py2ro`
+ Python to :mod:`rpy2.robjects`. By default, that one function
+ is merely a call to :meth:`conversion.py2ri`
+ followed by a call to :meth:`conversion.ri2py`.
+
+Those functions can be re-routed to satisfy all requirements, with
+the easiest option being to write a custom function calling itself
+the default function when the custom conversion should not apply.
+
+A simple example
+----------------
+
+As an example, let's assume that one want to return atomic values
+whenever an R numerical vector is of length one. This is only a matter
+of writing a new function `ri2py` that handles this, as shown below:
+
+.. code-block:: python
+
+ import rpy2.robjects as robjects
+
+ def my_ri2py(obj):
+ res = robjects.default_ri2py(obj)
+ if isinstance(res, robjects.RVector) and (len(res) == 1):
+ res = res[0]
+ return res
+
+ robjects.conversion.ri2py = my_ri2py
+
+Once this is done, we can verify immediately that this is working with:
+
+>>> pi = robjects.r.pi
+>>> type(pi)
+<type 'float'>
+>>>
+
+The default behavior can be restored with:
+
+>>> robjects.conversion.ri2py = default_ri2py
+
+Default functions
+-----------------
+
+The docstrings for :meth:`default_ri2py`, :meth:`default_py2ri`, and
:meth:`py2ro` are:
+
+.. autofunction:: rpy2.robjects.default_ri2py
+.. autofunction:: rpy2.robjects.default_py2ri
+.. autofunction:: rpy2.robjects.default_py2ro
+
+
Modified: rpy2/trunk/rpy/__init__.py
===================================================================
--- rpy2/trunk/rpy/__init__.py 2008-12-03 11:40:00 UTC (rev 711)
+++ rpy2/trunk/rpy/__init__.py 2008-12-03 12:09:01 UTC (rev 712)
@@ -1,2 +1 @@
__version__ = '2.1.0dev'
-
Modified: rpy2/trunk/rpy/rinterface/__init__.py
===================================================================
--- rpy2/trunk/rpy/rinterface/__init__.py 2008-12-03 11:40:00 UTC (rev
711)
+++ rpy2/trunk/rpy/rinterface/__init__.py 2008-12-03 12:09:01 UTC (rev
712)
@@ -1,7 +1,7 @@
import os, sys
try:
- R_HOME = os.environ["R_HOME"]
+ R_HOME = (os.environ["R_HOME"], )
except KeyError:
R_HOME = os.popen("R RHOME").readlines()
Modified: rpy2/trunk/setup.py
===================================================================
--- rpy2/trunk/setup.py 2008-12-03 11:40:00 UTC (rev 711)
+++ rpy2/trunk/setup.py 2008-12-03 12:09:01 UTC (rev 712)
@@ -4,6 +4,7 @@
pack_name = 'rpy2'
+
pack_version = '2.1.0dev'
RHOMES = os.getenv('RHOMES')
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