Hello community, here is the log from the commit of package python-rpy2 for openSUSE:Leap:15.2 checked in at 2020-03-09 18:11:14 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Leap:15.2/python-rpy2 (Old) and /work/SRC/openSUSE:Leap:15.2/.python-rpy2.new.26092 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-rpy2" Mon Mar 9 18:11:14 2020 rev:3 rq:777103 version:3.2.6 Changes: -------- --- /work/SRC/openSUSE:Leap:15.2/python-rpy2/python-rpy2.changes 2020-01-15 15:52:43.447573169 +0100 +++ /work/SRC/openSUSE:Leap:15.2/.python-rpy2.new.26092/python-rpy2.changes 2020-03-09 18:11:15.153186835 +0100 @@ -1,0 +2,194 @@ +Mon Feb 10 15:10:53 UTC 2020 - Todd R <[email protected]> + +- Update to 3.2.6 + + Bugs fixed + * The conversion of date/time object with specified timezones + was wrong when different than the local time zone + * Iterating over :mod:`rpy2.situation.iter_info()` could result + in a error because of a typo in the code. + + Changes + * :mod:`pandas` 1.0.0 breaks the conversion layer. A warning + is not emitted whenever trying to use `pandas` >= 1.0. + +------------------------------------------------------------------- +Thu Jan 30 15:31:13 UTC 2020 - Todd R <[email protected]> + +- Update to 3.2.5 + * Delimit multi-line expressions with parenthesis rather than backslash. + * Use Rf_initEmbeddedR(), remove setup_Rmainloop() (not necessary, it seems). +- Update to 3.2.4 + * Fix ABI mode +- Update to 3.2.3 + * Backport fix for segfault when parsing. + +------------------------------------------------------------------- +Wed Nov 27 16:05:54 UTC 2019 - Todd R <[email protected]> + +- Update to version 3.2.2 + + Bugs fixed + * Python format error when trying to report that the system is not reported + on Windows. + * The setup script would error on build if R is not installed. It is now + printing an error message. +- Update to version 3.2.1 + + Bugs fixed + * The wrapper for the R package `dbplyr` could not import the underlying + package (refactoring elsewhere was not propagated there). + * Creating R objects called `names` `globalenv` caused the method + :meth:`Sexp.names` to fail. + * Whenever the pandas conversion was activated :class:`FloatSexpVector` instances + with the R class `POSIXct` attached where not corrected mapped back to pandas + datetime arrays.. + * Fix installation when an installation when a prefix without write access is used. +- Update to version 3.2.0 + + New features + * rpy2 can built and used with :mod:`cffi`'s ABI or API modes (releases 3.0.x and + 3.1.x were using the ABI mode exclusively). At the time of writing the default + is still the ABI mode but the choice can be controlled through the environment variable + `RPY2_CFFI_MODE`. If set, possible values are `ABI` (default if the environment + variable is not set), `API`, or `BOTH`. When the latter, both `API` and `ABI` + modes are built, and the choice of which one to use can be made at run time. + + Changes + * The "consoleread" callback (reading input to the R console) is now assuming UTF-8 + (was previously assuming ASCII) and is no longer trying to add a "new line" character + at the end of the input. + * Querying an R environment with an invalid key will generate a :class:`TypeError` + or a :class:`ValueError` depending on the issue (rather than always :class:`ValueError` + before. + + Bugs fixed + * `setup.py` is now again compatible with Python2. + * Unit tests were failing if numpy is not installed. + * :mod:`rpy2.situation` is no longer breaking when R is not the in path and + there is no environment variable `R_HOME`. + * Build script for the cffi interface is now using the environment + variable `R_HOME` whenever defined (rather that always infer it from the + R in the PATH). + * Converting R strings back to Python was incorrectly using `Latin1` while `UTF-8` was + intended. +- Update to version 3.1.0 + + New features + * Python matrix multiplication (`__matmul__` / `@`) added to + R :class:`Matrix` objects. + * An :class:`threading.RLock` is added to :mod:`rpy2.rinterface_lib.openrlib` and is + used by the context manager :func:`rpy2.rinterface_lib.memorymanagement.rmemory` + to ensure that protect/unprotect cycles cannot be broken by thread switching, at least + as long as the context manager is used to handle such cycles (see issue #571). + * The documentation covers the use of notebooks (mainly Jupyter/Jupyterlab). + * The PNG output in Jupyter notebooks R cells can now specify an argument `--type` + (passed as the named argument `type` in the R function `png`). + For example on some Linux systems and R installations, the type `cairo` + can fix issues when alpha transparency is used. + + Changes + * Added callbacks for `ptr_R_Busy()` and `ptr_R_ProcessEvents()`. + * `rstart` now an objects in :mod:`rpy2.rinterface_lib.embedded` + (set to `None` until R is initialized). + * Unit tests are included in a subpackage :mod:`rpy2.tests` as was the + case before release 3.0.0. + * Experimental initialization for Microsoft Windows. + * :mod:`rpy2.situation` is now also reporting the rpy2 version. + * :func:`rpy2.robjecs.package_utils.default_symbol_check_after` was + renamed :func:`rpy2.robjecs.package_utils.default_symbol_resolve`. + The named parameters `default_symbol_check_after` present in few methods + in :mod:`rpy2.robjects.packages` and :mod:`rpy2.robjects.functions` were + modified to keep a consistent naming. + * Trying to instantiate an :class:`rpy2.rlike.container.OrdDict` with a + a :class:`dict` will result in a :class:`TypeError` rather than a + :class:`ValueError`. + * Methods of :class:`rpy2.rlike.container.OrdDict` now raises a + :class:`NotImplementedError` when not implemented. + * The creation of R vectors from Python sequences is now relying on a method + :meth:`_populate_r_vector` that allows vectorized implementation to + to improve speed. + * Continuous integration tests run against Python 3.6, 3.7, and 3.8. It is + no longer checked against Python 3.5. + + Bugs fixed + * `aes` in :mod:`rpy2.robjects.lib.ggplot2` had stopped working with the + R package ggplot2 reaching version 3.2.0.. + * Better handling of recent :mod:`pandas` arrays with missing values. + * The mapping of the R operator `%in%` reachable through the attribute `ro` + of R vectors was always returning `True`. It is now working properly. + * R POSIXct vectors with `NA` dates were triggering an error when converted + in a data frame converted to :mod:`pandas`. + +------------------------------------------------------------------- +Thu Jul 25 17:54:48 UTC 2019 - Todd R <[email protected]> + +- Update to Release 3.0.5 + + Bugs fixed + * No longer allow installation if Python 3 but < 3.5. + * Fixed error `undefined symbol: DATAPTR` if R < 3.5. +- Update to Release 3.0.4 + + Bugs fixed + * Fixed conversion of `pandas` :class:`Series` of dtype `pandas.Int32Dtype`, + or `pandas.Int64Dtype`. +- Update to Release 3.0.3 + + Bugs fixed + * Fixed the evaluation of R code using the "R magic" was delaying all + output to the end of the execution of that code, independently of + whether the attribute `cache_display_data` was `True` or `False`. + * Fixed conversion of :class:`pandas.Series` of `dtype` "object" when + all items are either all of the same type or are :obj:`None`. +- Update to Release 3.0.2 + + Bugs fixed + * Failing to import `pandas` or `numpy` when loading the "R magic" extension + for jupyter/ipython was hiding the cause of the error in the `ImportError` + exception. + * Fallback when an R `POSIXct` vector does not had an attribute `"tzone"`. + * Callback for console reset was not set during R initialization. + * Fixed rternalized function returning rpy2 objects. + * `--vanilla` is no longer among the default options used to initialize R. +- Update to Release 3.0.1 + + Bugs fixed + * Script to install R packages for docker image never made it to version + control. + * Conversion of R arrays/matrices into numpy object trigged a segfault + during garbage collection. +- Update to Release 3.0.0 + + New features + * rpy2 can be installed without a development environment. + * Unit tests are now relying on the Python module `pytest`. + * :attr:`rpy2.rinterface.NA_Integer` is now only defined when the embedded R + is initialized. + + Changes + * complete rewrite of :mod:`rpy2.rinterface`. + :mod:`cffi` is now used to interface with the R compiled shared library. + This allows ABI calls and removes the need to compile binaries. However, if + compilation is available (when installing or preparing pre-compiled binaries) + faster implementations of performance bottlenecks will be available. + * calling :func:`rpy2.rinterface.endr` multiple times is now only ending R + the first time it is called (note: an ended R cannot successfully be + re-initialized). + * The conversion system in the mod:`rpy2.robjects.conversion` now has only + two conversions `py2rpy` and rpy2py`. `py2rpy` tries to convert any + Python object into an object rpy2 can use with R and `rpy2py` tries + to convert any rpy2 object into a either a non-rpy2 Python object or + a mod:`rpy2.robjects` level object. + * The method `get` for R environments is now called `find()` to avoid + confusion with the method of the same name in Python (:meth:`dict.get`). + * :class:`rpy2.robjects.vectors.Vector`, :class:`rpy2.robjects.vectors.Matrix`, + and :class:`rpy2.robjects.vectors.Array` can no longer be used to create + R arrays of unspecified type. New type-specific classes (for example for + vectors :class:`rpy2.robjects.vectors.IntVector`, + :class:`rpy2.robjects.vectors.BoolVector`, + :class:`rpy2.robjects.vectors.FloatVector`, + :class:`rpy2.robjects.vectors.ComplexVector`, or + :class:`rpy2.robjects.vectors.StrVector`) should be used instead. + * mod:`rpy2.rpy_classic`, an implementation of the `rpy` interface using + :mod:`rpy2.rinterface` is no longer available. + * :class:`rpy2.robjects.ParsedCode` and + :class:`rpy2.robjects.SourceCode` are moved to + :class:`rpy2.robjects.packages.ParsedCode` and + :class:`rpy2.robjects.packages.SourceCode`. + + Bugs fixed + * Row names in R data frames were lost when converting to pandas data frames. + + Known issues + * Mismatch between R's POSIXlt `wday` and Python time struct_time's `tm_wday`. +- Update to Release 2.9.6 + + Bugs fixed + * Latest release of :mod:`pandas` deprecated :meth:`DataFrame.from_items`. + * Latest release of :mod:`pandas` requires categories to be a list + (not an other sequence). + + Known issues + * The numpy buffer implemented by R arrays is broken for complex numbers + +------------------------------------------------------------------- Old: ---- rpy2-2.9.5.tar.gz New: ---- rpy2-3.2.6.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ python-rpy2.spec ++++++ --- /var/tmp/diff_new_pack.63aYEi/_old 2020-03-09 18:11:15.797187759 +0100 +++ /var/tmp/diff_new_pack.63aYEi/_new 2020-03-09 18:11:15.797187759 +0100 @@ -1,7 +1,7 @@ # # spec file for package python-rpy2 # -# Copyright (c) 2018 SUSE LINUX GmbH, Nuernberg, Germany. +# Copyright (c) 2020 SUSE LLC # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -12,40 +12,32 @@ # license that conforms to the Open Source Definition (Version 1.9) # published by the Open Source Initiative. -# Please submit bugfixes or comments via http://bugs.opensuse.org/ +# Please submit bugfixes or comments via https://bugs.opensuse.org/ # %{?!python_module:%define python_module() python-%{**} python3-%{**}} %define skip_python2 1 -%bcond_with test Name: python-rpy2 -Version: 2.9.5 +Version: 3.2.6 Release: 0 Summary: A Python interface to the R Programming Language License: GPL-2.0-or-later -Group: Development/Libraries/Python -Url: https://bitbucket.org/rpy2/rpy2 +URL: https://bitbucket.org/rpy2/rpy2 Source: https://files.pythonhosted.org/packages/source/r/rpy2/rpy2-%{version}.tar.gz -BuildRequires: %{python_module devel} -BuildRequires: %{python_module numpy-devel} +BuildRequires: %{python_module cffi >= 1.13.1} +BuildRequires: %{python_module numpy} BuildRequires: %{python_module setuptools} BuildRequires: R-base >= 3.2 -BuildRequires: R-base-devel >= 3.2 BuildRequires: fdupes -BuildRequires: libbz2-devel -BuildRequires: libicu-devel -BuildRequires: pcre-devel BuildRequires: python-rpm-macros -BuildRequires: readline-devel BuildRequires: texinfo BuildRequires: texlive-latex -BuildRequires: xz-devel -BuildRequires: zlib-devel Requires: R-base >= 2.12 +Requires: python-cffi >= 1.13.1 Requires: python-numpy Requires: readline - +BuildArch: noarch %python_subpackages %description @@ -58,7 +50,7 @@ This code is inspired by RSPython from the Omegahat project. %prep -%setup -qn rpy2-%{version} +%setup -q -n rpy2-%{version} sed -i 's/\r$//' README.rst %build @@ -67,28 +59,23 @@ %install %python_install -%{python_expand chmod a+x %{buildroot}%{$python_sitearch}/rpy2/tests.py -sed -i "s|^#!/usr/bin/env python$|#!%__$python|" %{buildroot}%{$python_sitearch}/rpy2/tests.py -$python -m compileall -d %{$python_sitearch} %{buildroot}%{$python_sitearch}/rpy2/ -$python -O -m compileall -d %{$python_sitearch} %{buildroot}%{$python_sitearch}/rpy2/ -%fdupes %{buildroot}%{$python_sitearch} -} - -%if %{with test} -%check -mkdir -p tester -pushd tester -%{python_expand export PYTHONPATH=%{buildroot}%{$python_sitearch} -$python -B -m rpy2.tests -} -popd -%endif +%python_expand %fdupes %{buildroot}%{$python_sitelib} + +# Test files have been removed +# %%check +# mkdir -p tester +# pushd tester +# %%{python_expand export PYTHONPATH=%%{buildroot}%%{$python_sitearch} +# $python -B -m rpy2.tests +# } +# popd %files %{python_files} -%defattr(-,root,root) %doc AUTHORS NEWS README.rst %license gpl-2.0.txt -%{python_sitearch}/rpy2/ -%{python_sitearch}/rpy2-%{version}-py*.egg-info +%{python_sitelib}/rpy2/ +%{python_sitelib}/rpy2-%{version}-py*.egg-info +%pycache_only %{python_sitelib}/__pycache__/_rinterface*.py* +%{python_sitelib}/_rinterface*.py* %changelog ++++++ rpy2-2.9.5.tar.gz -> rpy2-3.2.6.tar.gz ++++++ ++++ 45534 lines of diff (skipped)
