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Subject: CVS commit: pkgsrc/math/py-rpy
From: Thomas Klausner
Date: 2015-04-08 00:14:19
Message id: 20150407221419.113B698@cvs.netbsd.org
Log Message:
Update to 2.5.6, in the hope it addresses PR 49817.
Release 2.5.6
=============
Bugs fixed
----------
- Detection of the R version during setup on Win8 (issues #255 and #258)
- Segmentation fault when converting :mod:`pandas` :class:`Series` with
elements of type object (issue #264)
- The default converter from Python (non-rpy2) objects to rinterface-level
objects was producing robjects-level objects whenever the input was of
type :class:`list` (discovered while fixing issue #264)
- Implemented suggested fix for issue with unlinking files on Windows
(issue #191)
- Testing rpy2 in the absence of ipython no longer stops with an error
(issue #266)
Release 2.5.5
=============
Bugs fixed
----------
- Crash (segfault) when querying an R object in an R environment triggers an
error (symbol exists, but associated values resolves to an error - issue #251)
- Change in the signature of `rcall` was not updated in the documentation
(issue #259)
- Minor update to the documentation (issue #257)
Release 2.5.4
=============
Bugs fixed
----------
- Filter PNG files on size, preventing empty files causing trouble to be
ipython notebook rendering of graphics later on (slight modification of
the pull request #39)
- Fix installation left unresolved with rpy2-2.5.3 (issue #248)
- Possible segfault with Python 3.4 (issue #249)
Release 2.5.3
=============
Changes
-------
- `setup.py` has `install_requires` in addition to `requires` in the hope to
fix the missing dependency with Python 2 (:mod:`singledispatch` is required
but not installed).
Bugs fixed
----------
- Extracting configuration information from should now work when R is emitting a \
warning (issue #247)
- On OS X the library discovery step can yield nothing (see issue #246). A \
tentative fix is to issue
a warning and keep moving.
Release 2.5.2
=============
Bugs fixed
----------
- String representation of :class:`robjects.R` (issue #238)
- Check during `build_ext` if unsupported version of R (pull request #32)
- HTMl display of columns of factors in a DataFrame (issue #236)
- HTML display of factors (issue #242)
Release 2.5.1
=============
Bugs fixed
----------
- Require singledispatch if Python 3.3 (issue #232)
- Fixed bug when R spits out a warning when asked configuration information \
(issue #233)
- Restored printing of compilation information when running `setup.py`
- Fixed installation issue on some systems (issue #234)
- Workaround obscure failure message from unittest if Python < 3.4 and
:mod:`singledispatch` cannot be imported (issue #235)
Release 2.5.0
=============
New features
------------
- Experimental alternative way to preserve R objects from garbage collection.
This can be activated with `rinterface.initr(r_preservehash=True)` (default
is `False`.
- :class:`GGPlot` object getting a method :meth:`save`
mirroring R's `ggplot2::ggsave()`.
- The conversion system is now using generics/single dispatch.
- New module :mod:`rpy2.ipython.html` with HTML display for rpy2 objects
- [Experimental] New function :func:`robjects.methods.rs4instance_factory`
to type RS4 objects with more specificity.
Changes
-------
- The script `setup.py` was rewritten for clarity and ease of maintenance.
Now it only uses `setuptools`.
Release 2.4.4
=============
Bugs fixed
----------
- Use `input` rather than `raw_input` in the default console callback
with Python 3 (fixes issue #222)
- Issues with conversions, pandas, and rmagic (fixes issue #218 and more)
Release 2.4.3
=============
Bugs fixed
----------
- `geom_raster` was missing from `rpy2.robjects.lib.ggplot2` (pull request #30)
- Fixed issue with SVG rendering in ipython notebook (issue #217)
- Regression with `rx2()` introduced with new conversion (issue #219)
- Fixed documentation (missing `import`) (issue #213)
Release 2.4.2
=============
Bugs fixed
----------
- Assigning an R `DataFrame` into an environment was failing if
the conversion for Pandas was activated. (Issue #207)
Release 2.4.1
=============
Bugs fixed
----------
- :meth:`rpy2.ipython` fixed spurious output to notebook cells.
Release 2.4.0
=============
Changes
-------
- Conversion system slightly changed, with the optional
conversions for :mod:`numpy` and :mod:`pandas` modified
accordingly. The changes should only matter if using
third-party conversion functions.
- The Python 3 version is now a first class citizen. `2to3`
is no longer used, and the code base is made directly
compatible with Python. This lowers significantly the
installation time with Python 3
(which matters when developping rpy2).
- The default options to initialize R (`rpy2.rinterface.initoptions') are no longer
`('rpy2', '--quiet', '--vanilla', '--no-save')` but now
`('rpy2', '--quiet', '--no-save')`.
- :class:`robjects.vectors.ListVector` can be instanciated from
any objects with a method `items()` with the expectation that the method
returns an iterable of (name, value) tuples, or even be an iterable
of (name, value) tuples.
New features
------------
- For instances of :class:`rpy2.robjects.Function`,
the `__doc__` is now a property fetching information
about the parameters in the R signature.
- Convenience function :func:`rpy2.robjects.packages.data`
to extract the datasets in an R pacakges
- :mod:`ipython`'s `rmagic` is now part of :mod:`rpy`. To use, `%load_ext
rpy2.ipython` from within IPython.
- new method :meth:`rpy2.rinterface.SexpEnvironment.keys`, returnings
the names in the environment as a tuple of Python strings.
- convenience class :class:`robjects.packages.InstalledPackages`, with a \
companion function
:func:`robjects.packages.isinstalled`.
- new class :class:`rinterface.SexpSymbol` to represent R symbols
Bugs fixed
----------
- :meth:`rpy2.rinterface.Sexp.do_slot` was crashing when
the parameter was an empty string (PR #155)
Release 2.3.10
==============
Bugs fixed
----------
- `setup.py build` was broken when new R compiled with OpenMP (Issue #183)
Release 2.3.9
=============
- Changes in pandas 0.13.0 broke the rpy2 conversion layer (Issue #173)
Release 2.3.8
=============
Bugs fixed
----------
- Crash with R-3.0.2. Changes in R-3.0.2's C API coupled to a strange behaviour
with R promises caused the problem. (PR #150)
Release 2.3.7
=============
Bugs fixed
----------
- ggplot2's "guides" were missing
- ggplot2's "theme_classic" was missing (PR #143)
- ggplot2's "element_rect" was missing (PR #144)
- :func:`rpy2.interactive.packages` was broken (PR #142)
Release 2.3.6
=============
Bugs fixed
----------
- Several reports of segfault on OS X (since rpy2-2.3.1 - PR #109)
- More fixes in converting `DataFrames` with dates from `pandas`
Relase 2.3.5
============
Bugs fixed
----------
- Missing mapping to ggplot2's `scale_shape_discrete` function
- Better handling of dates in Pandas
- Constructor for POSIXct improved (and fixed)
Changes
-------
- The attribute :attr:`rclass` is no longer read-only and can be set
(since R allows it)
- Importing the module :mod:`rpy2.interactive` no longer activates
event processing by default (triggering concurrency errors
when used with ipython).
New features
------------
- New module :mod:`rpy2.interactive.ipython` (so far plotting
automatically a ggplot2 figure in the iPython's console)
- It is now possible to set the :attr:`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
=============
Bugs fixed
----------
- Some of the data.frames converted from :mod:`pandas` were triggering
a :class:`TypeError` when calling :func:`repr`
- In :mod:`rpy2.robjects.lib.ggplot2`, a mapping to `coord_fixed` was
missing (PR #120)
- Using the parameter `lib_loc` in a call to
:func:`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 :class:`rpy2.robjects.lib.grid.Unit` and
:class:`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)
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