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Changes in rpy2

Release 2.4.0-dev

Bugs fixed

  • Missing mapping to ggplot2’s scale_shape_discrete function
  • Constructor for POSIXct improved (and fixed)

Changes

  • Python 3-only. Python 2 is no longer supported.
  • The function set_writeconsole() and func:get_writeconsole are now called set_writeconsoleex() and func:get_writeconsoleex. The callback function must have a signature like (message, messagetype) (see the documentation for details) (#contributed by bbruce)

New features

  • New module rpy2.interactive.ipython (so far plotting automatically a ggplot2 figure in the iPython’s console)
  • It is now possible to set the rclass.

Relase 2.3.4

Bugs fixed

  • Spurious error when running unit tests with Python 3 and numpy installed
  • Missing mapping to ggplot2’s geom_dotplot function
  • Warnings are not longer printed (see Changes below)

Changes

  • Bumped target version of ggplot2 to 0.9.3.1
  • Warnings are not longer printed. The C-level function in R became hidden in R-3.0, and the cost of an R-level check/print is relatively high if the R code called is very short. This might evolve into printing warnings only if interactive mode in Python (if this can be checked reliably).

Release 2.3.3

Bug fixed

  • Some of the data.frames converted from pandas were triggering a TypeError when calling repr()
  • In rpy2.robjects.lib.ggplot2, a mapping to coord_fixed was missing (PR #120)
  • Using the parameter lib_loc in a call to rpy2.robjects.packages.importr() was resulting in an error (PR #119)
  • Creating a layer through the rpy2.robjects.lib.ggplot2 interface did not accept parameters (PR #122)
  • Testing the Python version was crashing of a number of unsupported Python versions (<= 2.6) (PR #117)

New features

  • New module pandas2ri to convert from mod:pandas DataFrame objects
  • New classes rpy2.robjects.lib.grid.Unit and rpy2.robjects.lib.grid.Gpar to model their counterparts in R’s grid package as they were previously missing from rpy2.

Release 2.3.2

Bug fixed

  • Building on Win64 (pull request #6)
  • Fetching data from an R package through importr was masking any R object called data in that package. The data are now under the attribute name __rdata__. This is not completely safe either, although much less likely, a warning will be issued if still masking anything.

Changes

  • More informative error message when failing to build because R CMD config does not return what is expected

Release 2.3.1

Bugs fixed

  • default console print callback with Python (issue #112 linked to it)
  • deprecation warnings with ggplot2 (issue #111 and contributed patch)

Release 2.3.0

New Features

rpy2.rinterface:

  • C-level API, allowing other C-level modules to make use of utilities without going through the Python level. The exact definition of the API is not yet fixed. For now there is PyRinteractive_IsInitialized() to assess whether R was initialized (through rpy2.rinterface or not).
  • C-module _rpy_device, allowing one to implement R graphical devices in Python [(very) experimental]
  • Tracking of R objects kept protected from garbage collection by rpy2 is now possible.
  • New method Sexp.rid() to return the identifier of the R object represented by a Python/rpy2 object

rpy2.rinteractive:

  • Dynamic build of Python docstrings out of the R manual pages

rpy2.robjects.help:

  • Build dynamic help

rpy2.robjects.packages:

  • Build anonymous R packages from strings
  • When using importr(), the datasets are added as an attribute data, itself an instance of a new class PackageData. It no longer possible to access datasets are regular objects from a code package (because of changes in R), and the new system is more robust against quirks.

Changes

rpy2.rinterface:

  • SexpClosure.env to replace the method closureenv.

Release 2.2.6

Bugs fixed

Release 2.2.5

Bugs fixed

  • install process: Library location for some of the R installations

  • should compile on win32 (thanks to a patch from Evgeny Cherkashin),

    a work to a limited extend

Release 2.2.4

Bugs fixed

  • Memory leak when creating R vectors from Python (issue #82)

Release 2.2.3

Bugs fixed

  • Dynamic construction of S4 classes was looking for R help as ‘class.<class>’ rather than ‘<class>-class’
  • The cleanup of temporary directories created by R was not happening if the Python process terminated without calline rpy2.rinterface.endr() (issue #68, and proof-of-principle fix by chrish42)

Release 2.2.2

Bugs fixed

  • With the robjects layer, repr() on a list containing non-vector elements was failing

Release 2.2.1

Bugs fixed

  • MANIFEST.in was missing from MANIFEST.in, required with Python 3

Release 2.2.0

New Features

  • Support for Python 3, and for some of its features ported to Python 2.7

rpy2.robjects:

rpy2.rinterface:

  • NA_Complex and NAComplexType for missing complex values.
  • SexpExtPtr to represent R objects of type EXTPTR (external pointers).
  • rpy2.rinterface.parse() to parse a string a R code
  • rpy2.rinterface.rternalise() to wrap Python function as SexpClosure that can be called by R just as it was a function of its own.
  • rpy2.rinterface.RNULLType for R’s C-level NULL value and rpy2.rinterface.UnboundValueType for R’s C-level R_UnboundValue (both singletons).
  • rinterface.SexpVector.index(), of similar behaviour to list.index().
  • rpy2.rinterface.Sexp.list_attrs() to list the names of all R attributes for a given object.
  • rpy2.rinterface.ByteSexpVector to represent R ‘raw’ vectors.
  • constant R_LEN_T_MAX to store what is the maximum length for a vector in R.
  • tuple R_VERSION_BUILD to store the version of R rpy2 was built against
  • getter Sexp.rclass to return the R class associated with an object

rpy2.rlike:

  • container.OrdDict get proper methods keys() and get

rpy2.interactive:

  • A new sub-package to provide utilities for interactive work, either for handling R interactive events or use Python for interactive programming (as often done with the R console)

Changes

rpy2.robjects:

  • NA_bool, NA_real, NA_integer, NA_character and NA_complex are now deprecated (and removed). NA_Logical, NA_Real, NA_Integer, NA_Character, NA_Complex should be used.
  • rpy2.robjects.packages.Package now inherits from types.ModuleType
  • classes representing R vector also inherit their type-specific rinterface-level counterpart.
  • Importing the rpy2.robjects.numpy2ri is no longer sufficient to active the conversion. Explicit activation is now needed; the function activate can do that.

rpy2.rinterface:

  • IntSexpVector, FloatSexpVector, StrSexpVector, BoolSexpVector, ComplexSexpVector are now defined at the C level, improving performances and memory footprint whenever a lot of instances are created.

Bugs fixed

  • Better and more explicit detection system for needed libraries when compiling rpy2 (ported to release 2.1.6)
  • Long-standing issue with readline fixed (issue #10)

Release 2.1.9

Bugs fixed

  • The R class in rpy2.robjects is now truly a singleton
  • When using numpy 1.5 and Python >= 2.7, the exposed buffer for R numerical (double) vectors or arrays was wrong.

Release 2.1.8

Bugs fixed

  • Fixed issue with R arrays with more than 2 dimensions and numpy arrays (issue #47 - backported from the branch 2.2.x).

Release 2.1.7

Bugs fixed

  • More fixes for the automated detection of include and libraries at build time.

Release 2.1.6

Bugs fixed

  • Further fixes in the automatic detection of includes and libraries needed to compile rpy2 against R. The detection code has been refactored (backport from the 2.2.x branch)

Release 2.1.5

Bugs fixed

  • fixes the automatic detection of R_HOME/lib during building/compiling when R_HOME/lib is not in lib/ (issue #54)

Release 2.1.4

New features

Bugs fixed

  • Install script when the BLAS library used by R is specified as a library file (patch by Michael Kuhn)

Release 2.1.3

Bugs fixed

  • Spurious error message when using DataFrame.from_csvfile() without specifying col_names or row_names
  • Patch to finally compile with Python < 2.6 (contribDuted by Denis Barbier)

Release 2.1.2

New Features

rpy2.robjects:

  • NA_Logical, NA_Real, NA_Integer, NA_Character from rpy2.rinterface are imported by robjects.

Changes

rpy2.robjects:

  • NA_bool, NA_real, NA_integer, NA_character and NA_complex are now robjects-level vectors (they were rinterface-level vectors). Consider using the rinterface-defined NAs instead of them.

Bugs fixed

  • Missing conditional C definition to compile with Python 2.4 # issue 38
  • Fixed error when calling robjects.vectors.Vector.iteritems() on an R vector without names
  • Fixed automatic conversion issues (issue #41)

Release 2.1.1

Bugs fixed

Release 2.1.0

New Features

rpy2.robjects:

  • Method formals() for Function (formerly RFunction)
  • Methods slotnames(), isclass(), and validobject() for RS4
  • Vector-like objects now in a module rpy2.robjects.vectors
  • set_accessors() for adding simply accessors to a class inheriting from RS4
  • RS4_Type for metaclass-declared accessors
  • Delegating classes ExtractDelegator and DoubleExtractDelegator for extracting the R-way
  • DataFrame (formerly RDataFrame) can now be created from :rlike.container.OrdDict instances, or any other object inheriting from dict.
  • FactorVector to represent R factors
  • the conversion is now returning subclasses of robjects.vectors.Vector -formerly RVector- (such as IntVector, FloatVector, etc...) rather than only return Vector
  • StrVector has a method factor() to turn a vector of strings into an R factor
  • Matrix was added the methods: dot(), svd(), crossprod(), tcrossprod(), transpose().
  • IntVector.tabulate() to count the number of times a value is found in the vector
  • Vector.sample() to draw a (random) sample of arbitrary size from a vector
  • NA_Bool, NA_Real, NA_Integer, NA_Character, NA_Complex as aliases for R’s missing values.
  • ComplexVector for vectors of complex (real + imaginary) elements
  • packages to provide utility functions to handle R packages (import of R packages)
  • functions to provide classes related to R functions, with the new class SignatureTranslatedFunction
  • DataFrame.iter_row() and DataFrame.iter_column(), iterating through rows and columns respectively.
  • DataFrame.cbind() and DataFrame.rbind() for binding columns or rows to a DataFrame.
  • Vector.iteritems() to iterate on pairs of names and values.
  • Robject.__rname__ to store the “R name”

rpy2.rinterface:

  • New functions for specifying callback functions for R’s front-ends: set_showmessage(), set_flushconsole(), set_choosefile(), set_showfiles()
  • New object MissingArg, exposing R’s special object for representing a “missing” parameter in a function call. (#this was first a patch by Nathaniel Smith with a function getMissingArgSexp)
  • Initial commit of a callback-based implementation of an R graphical device (this is for the moment very experimental - and not fully working)
  • SexpClosure.rcall() is now taking 2 parameters, a tuple with the parameters and an SexpEnvironment in which the call is to be evaluated.
  • Sexp.__sexp__ now has a setter method. This permits the rebinding of the underlying R SEXP, and allows to expose foo<- type of R methods as Python function/methods with side effects.
  • Objects of R type RAWSXP are now exposed as instances of class SexpVector.
  • Factory function unserialize() to build Sexp* instances from byte string serialized with R’s own ‘serialize’.
  • Method Sexp.__reduce__() for pickling/unpickling
  • Ability to specify a callback function for R_CleanUp (called upon exiting R) through get_cleanup() and set_cleanup() [very experimental]
  • Class ListSexpVector for creating R lists easily (complementing IntSexpVector, StrSexpVector, and friends)
  • colnames(), rownames() for Array (formerly RArray) are now property-style getters
  • Pairlists (LISTSXP) now handled
  • Experimental function set_interactive() to set whether R is in interactive mode or not (#following an issue reported by Yaroslav Halchenko)
  • New object R_NilValue, exposing R’s special object for representing a “NULL”.
  • ComplexSexpVector for vectors of complex (real + imaginary) elements
  • Scalar Python parameters of type int, long, double, bool, and None in a call (using SexpClosure) are now automatically converted to length-one R vectors (at the exception of None, converted to R_NilValue).
  • Python slices can now be used on R vector-like objects
  • Better handling of R’s missing values NA, NA_integer_, NA_real_, and NA_character_.

rpy2.rlike:

  • iteritems() for OrdDict (formerly:class:ArgDict) and TaggedList
  • static method from_iteritems() for TaggedList, for creating a TaggedList from any object having a method iteritems()

Changes

  • The setup.py script is now taking command-line arguments when specifying R library-related paths are wished. python setup.py –help build_ext will list them

rpy2.robjects:

  • RS4 no longer makes R’s slots as Python attributes through __attr__()
  • The package is split into modules
  • The broken variables NA_STRING, NA_INTEGER, NA_LOGICAL, and NA_REAL are removed. The documentation on missing values was revised.
  • globalEnv and baseNameSpaceEnv were renamed to globalenv and baseenv respectively
  • The parameter wantFun in Environment.get() (formerly REnvironment.get()) is now wantfun
  • Vector.r does not have a __getitem__ method any longer (see in .rx and .rx2 in the new features)
  • colnames(), rownames(), nrow(), ncol() for DataFrame are now property-style getters
  • nrow(), ncol() for Array are now property-style getters
  • static method from_csvfile() and instance method to_csvfile() for DataFrame
  • module lib to store modules representing R packages
  • module lib.ggplot2 for the CRAN package ggplot2.
  • renaming of few classes, the R prefix: Formula (from RFormula), DataFrame (from RDataFrame), Array (from RArray), Matrix (from RMatrix), Environment (from REnvironment), Function (from RFunction), Vector (from RVector).
  • robjects.vectors.Vector lost the (now redundant) methods subset and assign. Those operations were just aliases to the ExtractDelegator

rpy2.rinterface:

  • globalEnv, baseNameSpaceEnv, and emptyEnv were renamed to globalenv, baseenv and emptyenv respectively
  • The parameter wantFun in SexpEnvironment.get() is now wantfun
  • The call-back getters and setters are now get_readconsole(), set_readconsole(), get_writeconsole(), set_writeconsole(), get_flushconsole(), and set_flushconsole().
  • Functions also accept named parameters equal to Py_None, and transform them to R NULL (previously only accepted parameters inheriting from Sexp).

rpy2.rlike:

  • ArgDict becomes OrdDict.
  • tags() of TaggedList is now a property (with a getter and a setter)

rpy2.rpy_classic:

  • R named lists are returned as Python dict, like rpy-1.x does it, with the notable difference that duplicate names are not silently overwritten: an exception of class ValueError is thrown whenever happening

Bugs fixed

  • REnvironment.get() now accepts a named parameter wantFun (like rinterface.SexpEnvironment() does)
  • rinterface.SexpVector will now properly raise an exception when trying to create vector-like object of impossible type
  • Crash when trying to create a SexpVector of a non-vector type
  • R objects of class matrix are now properly converted into RMatrix (instead of Array)
  • Robj.as_py() was not working at all (and now it does to some extent)

Release 2.0.7

Bugs fixed

  • On win32, printing an object was leaving an open file handle behind each time, leading to an error and the impossibility to print (# bug report and fix by Christopher Gutierrez)

Release 2.0.6

No user-visible change. Win32-specific additions to the C module were made to compile it.

Release 2.0.5

Bugs fixed

  • Crash when calling SexpEnvironment.get() with an empty string #bug report by Walter Moreira
  • SexpEnvironment.__getitem__() called with an empty string caused unpredictable (and bad) things

Release 2.0.4

Bugs fixed

  • Added missing named parameter wantfun to method REnvironment.get() (making it similar to SexpEnvironment.get())
  • Leak in reference counting when creating SexpVector objects fixed (the symptom was a process growing in size when creating R vector from Python list or numpy arrays)
  • R CMD config LAPACK_LIBS could return an empty string when R was compiled with the veclib framework, causing the setup.py script to raise an exception. setup.py now only print a message about an empty string returned from R CMD config
  • Numpy arrays with complex elements are no longer causing segfaults
  • Calls to SexpClosure.rcall() with something else that the expected kind of tuple could cause a segfault

Release 2.0.3

New Features

rpy2.rinterface:

  • process_revents(), a Wrapper for R_ProcessEvents (# suggested by June Kim to help with issues related to interactive display on win32), and for R_RunHandlers on UNIX-like systems (# patch by Nathaniel Smith).

  • All callbacks are getting a get<callback> to complement the set<callback>. (# Patch by Nathaniel Smith)

  • Sexp.__deepcopy__() to copy an object (calling Rf_Duplicate)

    (# from a patch by Nathaniel Smith)

Changes

  • the default for reading and writing the console are now using sys.stdin and sys.stdout (# patch submitted by Nathaniel Smith)
  • console IO callbacks (reading and writing) are complemented by one to flush the console
  • Sexp.do_slot_assign() now creates the slot if missing (design-fix - # patch by Nathaniel Smith)

Bugs fixed

  • fixed problem of numpy interface with R boolean vectors. They are now presented as ‘i’ rather than ‘b’ to numpy (# patch submitted by Nathaniel Smith)
  • The mechanism for setting arbitrary callaback functions for console I/O now ensures that a traceback is printed to stderr whenever an error occurs during the evalutation of the callback (the raised exception used to be silently propagated to the next python call, leading to problems).

Release 2.0.2

Bugs fixed

  • Fix installation bug when the include directories contain either ‘-‘ or ‘I’ #spotted by James Yoo
  • Failing to initialize R now throws a RuntimeError
  • Copying an R “NA” into Python returns a None (and no longer a True) (#fixes a bug reported by Jeff Gentry)

Release 2.0.1

New features

rpy2.robjects:

  • Property names for the RVector methods getnames() and setnames() (this was likely forgotten for Release 2.0.0).
  • Property rclass for RObjectMixin

Changes

rpy2.robjects:

  • rclass() becomes getrclass()

Bugs fixed

  • Having the environment variable R_HOME specified resulted in an error when importing rpy2.rinterface # root of the problem spotted by Peter
  • Setup.py has no longer a (possibly outdated) static hardcoded version number for rpy2
  • Testing no longer stops with an error in the absence of the third-party module numpy
  • rpy2.rlike.container.TaggedList.pop() is now returning the element matching the given index

Release 2.0.0

New features

  • New module rpy2.robjects.conversion.
  • New module rpy2.robjects.numpy2ri to convert numpy objects into rpy2 objects. # adapted from a patch contributed by Nathaniel Smith

Changes

  • RObject.__repr__() moved to RObject.r_repr()

Bugs fixed

  • Informative message returned as RuntimeError when failing to find R’s HOME
  • Use the registry to find the R’s HOME on win32 # snatched from Peter’s earlier contribution to rpy-1.x

Release 2.0.0rc1

rpy2.rpy_classic:

  • rpy_classic.RObj.getSexp() moved to a property rpy_classic.Robj.sexp.

rpy2.robjects:

  • RObject.__repr__() moved to RObject.r_repr()
  • ri2py(), ro2py(), and py2ri() moved to the new module conversion. Adding the prefix conversion. to calls to those functions will be enough to update existing code

Bugs fixed

  • Informative message returned as RuntimeError when failing to find R’s HOME
  • Use the registry to find the R’s HOME on win32 # snatched from Peter’s earlier contribution to rpy-1.x

Release 2.0.0rc1

New features

  • added __version__ to rpy2/__init__.py

rpy2.robjects:

  • added classes StrVector, IntVector, FloatVector, BoolVector

rpy2.rinterface:

  • added missing class BoolSexpVector.

Changes

rpy2.robjects:

  • does not alias rinterface.StrSexpVector, rinterface.IntSexpVector, rinterface.FloatSexpVector anymore
  • Constructor for rpy2.robjects.RDataFrame checks that R lists are data.frames (not all lists are data.frame)
  • Formerly new attribute _dotter for R is now gone. The documentaion now points to rpy2.rpy_classic for this sort of things.

Bugs fixed

  • conditional typedef in rinterface.c to compile under win32 # reported and initial proposed fix from Paul Harrington
  • __pow__ was missing from the delegator object for robjects.RVector (while the documentation was claiming it was there) # bug report by Robert Nuske
  • Earlier change from Sexp.typeof() to getter Sexp.typeof was not reflected in rpy2.rpy_classic # bug report by Robert Denham

Release 2.0.0b1

New features

rpy2.robjects:

  • added setenvironment() for RFormula, and defined environment as a property
  • defined names as a property for RVector

rpy2.rinterface:

  • added functions get_initoptions() and set_initoptions().
  • new attribute _dotter for R singleton. Setting it to True will translate ‘_’ into ‘.’ if the attribute is not found

Changes

rpy2.robjects:

  • constructor for RDataFrame now now accepts either rlike.container.TaggedList or rinterface.SexpVector

rpy2.rinterface:

  • sexpTypeEmbeddedR() is now called str_typeint().
  • initOptions is now called initoptions. Changes of options can only be done through set_initoptions().

Bugs fixed

  • crash of Sexp.enclos() when R not yet initialized (bug report #2078176)
  • potential crash of Sexp.frame() when R not yet initialized
  • proper reference counting when handling, and deleting, Sexp.__sexp__ generated CObjects
  • setup.py: get properly the include directories (no matter where they are) #bug report and fix adapted from Robert Nuske
  • setup.py: link to external lapack or blas library when relevant
  • added a MANIFEST.in ensuring that headers get included in the source distribution #missing headers reported by Nicholas Lewin-Koh
  • rinterface.str_typeint() was causing segfault when called with 99
  • fixed subsetting for LANGSXP objects

Release 2.0.0a3

New features

rpy2.rinterface:

  • setReadConsole(): specify Python callback for console input
  • R string vectors can now be built from Python unicode objects
  • getter __sexp__ to return an opaque C pointer to the underlying R object
  • method rsame() to test if the underlying R objects for two Sexp are the same.
  • added emptyEnv (R’s C-level R_EmptyEnv)
  • added method Sexp.do_slot_assign()

rpy2.robjects:

  • R string vectors can now be built from Python unicode objects

rpy2.rlike:

  • module functional with the functions tapply(), listify(), iterify().
  • module indexing with the function order()
  • method TaggedList.sort() now implemented

Changes

rpy2.rinterface:

  • initEmbeddedR() is only initializing if R is not started (no effect otherwise, and no exception thrown anymore)
  • the method Sexp.typeof() was replaced by a Python getter typeof.
  • the method Sexp.named() was replaced by a Python getter named.
  • R objects of type LANGSXP are now one kind of vector (... but this may change again)
  • R objects of type EXPRSXP are now handled as vectors (... but this may change again)
  • initEmbeddedR() renamed to initr()
  • endEmbeddedR() renamed to endr()

rpy2.robjects:

  • R remains a singleton, but does not throw an exception when multiple instances are requested

Bugs fixed

  • unable to compile on Python2.4 (definition of aliases to Python2.5-specific were not where they should be).
  • overflow issues on Python 2.4/64 bits when indexing R vector with very large integers.
  • handling of negative indexes for SexpVector‘s __getitem__() and __setitem__() was missing
  • trying to create an instance of SexpVector before initializing R raises a RuntimeException (used to segfault)
  • experimental method enclos() was not properly exported
  • setup.py was exiting prematurely when R was compiled against an existing BLAS library
  • complex vectors should now be handled properly by rpy2.rinterface.robjects.
  • methods rownames() and colnames() for RDataFrame were incorrect.

Release 2.0.0a2

New features

rpy2.rlike:

rpy2.rinterface:

  • method named(), corresponding to R’s C-level NAMED
  • experimental methods frame() and enclos() for SexpEnvironment corresponding to R’s C-level FRAME and ENCLOS
  • method rcall() for ClosureSexp
  • new experimental class SexpLang for R language objects.

Bugs fixed

  • R stack checking is disabled (no longer crashes when multithreading)
  • fixed missing R_PreserveObject for vectors (causing R part of the object to sometimes vanish during garbage collection)
  • prevents calling an R function when R has been ended (raise RuntimeException).

Release 2.0.0a1

New features

rpy2.robjects:

  • method getnames() for RVector
  • experimental methods __setitem__() and setnames() for RVector
  • method ‘getnames’ for RArray
  • new class RFormula
  • new helper class RVectorDelegator (see below)
  • indexing RVector the “R way” with subset is now possible through a delegating attribute (e.g., myvec.r[True] rather than myvec.subset(True)). #suggested by Michael Sorich
  • new class RDataFrame. The constructor __init__() is still experimental (need for an ordered dictionnary, that will be in before the beta
  • filled documentation about mapping between objects

Changes

  • many fixes and additions to the documentation
  • improved GTK console in the demos
  • changed the major version number to 2 in order to avoid confusion with rpy 1.x # Suggested by Peter and Gregory Warnes
  • moved test.py to demos/example01.py

rpy2.robjects:

  • changed method name getNames to getnames where available (all lower-case names for methods seems to be the accepted norm in Python).

Bugs fixed

rpy2.robjects:

  • fixed string representation of R object on Microsoft Windows (using fifo, not available on win32)
  • __getattr__() for RS4 is now using ri2py()

rpy2.rinterface:

  • fixed context of evaluation for R functions (now R_GlobalEnv)

Release 1.0a0

  • first public release

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