CVS commit: pkgsrc/math/py-rpy

["Thomas Klausner" <wiz%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   wiz
Date:           Tue Apr  7 22:14:19 UTC 2015

Modified Files:
        pkgsrc/math/py-rpy: Makefile PLIST distinfo

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)


To generate a diff of this commit:
cvs rdiff -u -r1.33 -r1.34 pkgsrc/math/py-rpy/Makefile
cvs rdiff -u -r1.13 -r1.14 pkgsrc/math/py-rpy/PLIST
cvs rdiff -u -r1.11 -r1.12 pkgsrc/math/py-rpy/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.