Interface to use R from Python
GPL-2.0 License
Published by lgautier 10 months ago
Published by lgautier over 1 year ago
Release 3.5.13
==============
New features
------------
- R is setting a number of environment variables in a wrapper script. Those
variables were not set by default by rpy2 and this could lead to issues (see issue #1033).
The variables are now added to `os.environ`.
Bugs fixed
----------
- `python -m rpy2.situation LD_LIBRARY_PATH` could incorrectly truncate the value
for `LD_LIBRARY_PATH` when the variable `LD_LIBRARY_PATH` is already defined.
Changes
-------
- The dependency on :mod:`pytz`, a deprecated package, was
removed and replaced by a dependency to :mod:`zoneinfo`.
If Python < 3.9 the package :mod:`backports.zoneinfo`
is an added dependency.
- The depency on :mod:`tzlocal` does no longer limit it
to `<5.0` (issue #1035).
- Remove dependency on :mod:`distutils` in Python's standard library. That package is
deprecated and removed in Python 3.12 (see https://peps.python.org/pep-0632/ and
issue #1040).
:func:rpy2.rinterface.evalr_expr_with_visible
to evaluate
an expression and return the visibility status of the
value returned.
More events in the intialization and termination of an
embedded R logged by :mod:rpy2.rinterface_lib.embedded.logger
at INFO
and DEBUG
levels.
:meth:rpy2.robjects.R.__call__
has 2 named arguments "visible" and
"print_r_warnings" to handle R "invisible" results and print R warnings
at the end of the evaluation. Invisible results happen when doing
rpy2.robjects.r("x <- 1")
. R will return the value of x "invisibly".
The default are invisible is True
and print_r_warnings is True
.
Evaluating a string as R code using :meth:rpy2.robjects.R.__call__
(e.g., rpy2.robjects.r("1+2")
) now shows R warnings at the end
of the evaluation by default.
:meth:rpy2.robjects.R.__call__
returns the results invisibly by default
(see section "New features" for this release).
Published by lgautier over 1 year ago
pandas.Categorical
objects are now converted to Rfactor
objects.:mod:pandas
2.0 makes API-breaking changes that made
conversion fail (issue #1013).
The default converter for R magic was dropping R factors
to :mod:numpy
arrays of integers rather than convert them
to pandas :class:Category
(issue #1010).
The fix for issue #1010 (see above) changes the numpy conversion
for R factors. It returns an arrays with the level factors rather
than the integer codes for the levels.
:func:rpy2.rojects.pandas2ri.py2rpy_categoryseries
raises a
:class:DeprecationWarning
.
:mod:rpy2.situation
reports cffi interface type information.
The ipython/jupyter R magic can now have jpeg
as a default graphics format
for static figures in addition to png
and svg
.
Building the path to the R shared library was incorrectly
using the output of R CMD config LIBnn
(issue #982).
R started raising warnings when calling formals
on BUILTINSXP
R objects.
Internal functions in :mod:rpy.robjects.functions
calling formals
no
longer propagate the warnings.
Published by lgautier over 1 year ago
rpy2
are now checked with mypy
.Building the path to the R shared library was incorrectly
using the output of R CMD config LIBnn
(issue #982).
R started raising warnings when calling formals
on SPECIALSXP
R objects.
Internal functions rpy.robjects.functions
calling formals
no longer
propagate the warnings.
The numpy
converter was not turning NA_character_
into
None
(issue #979).
rpy2.situation
included an eager import rpy2
that could cause a version
mismatch error with some build/install toolchain (issue #984). The import is now
lazy/delayed.
Installation targets pandas
, all
, and test
now specify pandas>=1.2.0
(which should limit frequencies of issues like #998).
rpy2.robjects.conversion.Converter
objects are no longer functioning contextrpy2.robjects.conversion.Converter.context
should be used instead.Published by lgautier over 1 year ago
_DEFAULT_R_INTERACTIVE
in :mod:rpy2.rinterface_lib.embedded
.:func:rpy2.rinterface.initr_checkenv
(aliased to
:func:rpy2.rinterface.initr
) did not include
initialization parameters for interactive
, _want_setcallbacks
,
and _c_stack_limit
(issue #976).
The numpy converter was not listing R objects of type CHARSXP
as
vectors. This make R NA_character_
values wrapped in rpy2
Python
objects to be passed as-is (issue #983).
Published by lgautier almost 2 years ago
Changelog here:
https://github.com/rpy2/rpy2/blob/RELEASE_3_5_7/NEWS
Published by lgautier almost 2 years ago
Published by lgautier about 2 years ago
Published by lgautier over 2 years ago
Published by lgautier over 2 years ago