This package was BROKEN from the first import.
I've re-imported it to wip, when it's finished there we can reimport it.
Also remove the two packages trying to use this.
Version 0.55.0
This release includes a significant number important dependency upgrades along with a number of new features and bug fixes.
Version 0.54.1
This is a bugfix release for 0.54.0. It fixes a regression in structured array type handling, a potential leak on initialization failure in the CUDA target, a regression caused by Numba’s vendored cloudpickle module resetting dynamic classes and a few minor testing/infrastructure related problems.
Version 0.53.1
This is a bugfix release for 0.53.0. It contains the following four pull-requests which fix two critical regressions and two build failures reported by the openSuSe team:
* Fix regression on gufunc serialization
* Fix regression in CUDA: Set stream in mapped and managed array device_setup
* Ignore warnings from packaging module when testing import behaviour.
* set non-reported llvm timing values to 0.0
Version 0.53.0
This release continues to add new features, bug fixes and stability improvements to Numba.
Highlights of core changes:
Support for Python 3.9
Function sub-typing
Initial support for dynamic gufuncs
Parallel Accelerator (@njit(parallel=True) now supports Fortran ordered arrays
Version 0.52.0
This release focuses on performance improvements, but also adds some new features and contains numerous bug fixes and stability improvements.
Version 1.1.4 (September, 2020)
- Switched from Nose to Pytest for testing. Patch courtesy @kmosiejczuk,
[PR #32](https://github.com/bmc/munkres/pull/32), with some additional
cleanup by me.
- Fix to [Issue #34](https://github.com/bmc/munkres/issues/34), in which
`print_matrix` wasn't handling non-integral values. Patch courtesy @finn0,
via [PR #35](https://github.com/bmc/munkres/pull/35).
- Various changes from `http:` URLs to `https:` URLs, courtesy @finn0
via [PR #36](https://github.com/bmc/munkres/pull/36/).
Version 1.1.3:
**Nonexistent**. Accidentally published before check-in. Deleted from
PyPI. Use version 1.1.4.
Version 1.1.2 (February, 2019)
- Removed `NoReturn` type annotations, to allow compatibility with Python 3.5
releases prior to 3.5.4. Thanks to @jackwilsdon for catching that issue.
Version 1.1.1 (February, 2019)
- Version bump to get past a PyPI publishing issue. (Can't republish
partially published 1.1.0.)
Version 1.1.0 (February, 2019)
- Only supports Python 3.5 or better, from this version forward (since Python
2 is at end of life in 11 months).
- Added `typing` type hints.
- Updated docs to use `pdoc`, since `epydoc` is pretty much dead.
2021-12-31: 1.0.8 release:
* src/Soros.py: fix FutureWarning: Possible nested set at position, reported by Rene Engelhard
* fr.sor:
- use hyphens instead of spaces, e.g. cent-deux, reported by "4560041" at GitHub
- new prefix "informal" for 1100–1900 (onze-cents - dix-neuf-cents)
- add prefix "feminine" and "masculine" (1 -> une/un), bug reports by arena94 at GitGub
* hu_Hung.sor:
- fix transliteration of old Hungarian family names, bug report by Zoltán Óvári
- fix 100–199, 1000–1999, 1000000–1999999 and 1000000000–1999999999 (bad ordering)
– fix conversion of single letters "í", "Í" and "NY";
- fix unnecessary conversion of words ending with "q", e.g. "IQ";
- fix unnecessary conversion of words not ending with unknown letters
* mr.sor: Marathi spelling corrections by Shantanu Oak
* pl.sor: fix ordinal 20-29, reported by Gabryha at GitHub
* uk.sor, CalcAddIn.xcu, description.xml.in: fix spell by Olexandr Nesterenko
- replace apostrophe symbol to U+02BC, reported by Volodymyr Lisivka
- up number to 10^42
- add cardinal, update help
- add uk locale
* zh.sor: add ordinal numbers, use always 二 for 2, reported by Ming-Hua
This flag should be set for packages that import pkg_resources
and thus need setuptools after the build step.
Set this flag for packages that need it and bump PKGREVISION.
This is a minor version of PyTables. The main feature added is that
compatibility with Python 3.10, numpy 1.21 and HDF5 1.12 has been improved,
while support for Python 3.5 has been dropped.
The CI infrastructure has been moved to GitHub Actions.
Changes from 2.8.0 to 2.8.1
---------------------------
* Fixed dependency list.
* Added ``pyproject.toml`` and modernize the ``setup.py`` script. Thanks to
Antonio Valentino for the PR.
Changes from 2.7.3 to 2.8.0
---------------------------
* Wheels for Python 3.10 are now provided.
* Support for Python 2.7 and 3.5 has been discontinued.
* All residual support for Python 2.X syntax has been removed, and therefore
the setup build no longer makes calls to the `2to3` script. The `setup.py`
has been refactored to be more modern.
* The examples on how to link into Intel VML/MKL/oneAPI now use the dynamic
library.
-Fix crash whem missing closing ceil, floor, |
-Describe piecewise functions in README
-Fixed tick symbol resulting in panic
-Prevent constants from being overridden
-Output numbers with the precision specified
-Float erros margin for comparison operators
-NaN for comparison with imaginary numbers
-Updated interperter tests to expect 0 after comparisons
1.21.5:
BUG: Fix shadowed reference of `dtype` in type stub
BUG: Fix headers for universal2 builds
BUG: ``VOID_nonzero`` could sometimes mutate alignment flag
BUG: Do not use nonzero fastpath on unaligned arrays
BUG: Distutils patch to allow for 2 as a minor version (!)
BUG, SIMD: Fix 64-bit/8-bit integer division by a scalar
BUG, SIMD: Workaround broadcasting SIMD 64-bit integers on MSVC...
REL: Prepare for the NumPy 1.21.4 release.
TST: Fix a `Arrayterator` typing test failure
Release 3.4.5
=============
Changes
-------
- The deprecation warning when using :func:`rpy2.robjects.lib.grid.activate`
was missing (indirectly revealed through issue #804).
- The named argument `LINPACK` in :meth:`rpy2.robjects.vectors.Matrix.svd`
is no longer present in R.
Bugs fixed
----------
- SIGPIPE sent to a process running Python+rpy2 could result in a segfault.
This was caused by an incorrect setting of R signal handlers (issue #809).
Release 3.4.4
==============
Changes
-------
- `RRuntimeError` exceptions raised while evaluating R code
an R magic (ipython/jupyter) are now propagated (issue #792).
Release 3.4.3
=============
New features
------------
- :mod:`rpy2.robjects.lib.ggplot2` maps more functions in the
R package (issue #767)
- Utility function :func:`rpy2.robjects.lib.ggplot2.dict2rvec`
to convert a Python `Dict[str, str]` into an R named vector
of strings.
Bugs fixed
----------
- Calling mod:`rpy2.situation` to report on the environment no longer
stops with an uncaught exception when no R home can be determined
(issue #774)
- Converting pandas series with the older numpy types could result
in an error (issue #781)
- Numpy converter was not properly turing R integer or float arrays
into their numpy equivalent (issue #785)
- The HTML representation of R list without named element was
incorrect (issue #787)
Release 3.4.2
=============
Bugs fixed
----------
- Multithreading during the initialization of the embedded R no longer
triggers a fatal error (issue #729)
Changes
-------
- :mod:`pytest` is now an optional package. Optional sets of packages are
`numpy`, `pandas`, `test`, and `all` (all optional packages). They
can be specified during the installation. For example
`pip install rpy2[test]`. (issue #670)
Release 3.4.1
=============
Bugs fixed
----------
- The file `requirements.txt` was missing from the source distribution
on pypi (issue #764).
Release 3.4.0
=============
New Features
------------
- The mapping of the R C API now includes `Rf_isSymbol()`.
- Singleton class :class:`rpy2.rinterface_lib.sexp.RVersion` to report
the R version for the embedded R.
- :func:`rpy2.rinterface.local_context` to create a context manager
to evaluate R code within a local environment.
- The `staticmethod` :meth:`rpy2.robjects.vectors.DateVector.isrinstance`
will tell whether an R objects is an R `Date` array.
Changes
-------
- The dynamic generation of docstrings for R man pages
is now using R's `Rd2txt`.
- The :func:`rpy2.rinterface_lib._rinterface_capi._findVarInFrame`
is replaced by the function
:func:`rpy2.rinterface_lib._rinterface_capi._findvar_in_frame`
(see fix to issue #710).
- The functions :func:`rpy2.robjects.numpy.activate()` and
:func:`rpy2.robjects.pandas.activate()` are deprecated and will
be removed in rpy2-3.5.0.
- :func:`rpy2.rinterface_lib.embedded.setinitialized` was renamed to
:func:`rpy2.rinterface_lib.embedded._setinitialized` to indicate that
one should not use it.
- :meth:`rpy2.robjects.lib.ggplot2.vars` to map the R function
`ggplot2::vars` (issue #742).
- Report correctly the class of R matrix objects with R>=4.0: it is
now `('matrix', 'array')`. With R<4.0 `('matrix')` is still reported.
- The conversion of R/rpy2 objects to python objects using R class name mapping
is extended to more classes. The documentation about conversion covers the topic.
- If `R_NilValue` is not null when the initialization of the embedded R is attempted,
it is now assumed that R was initialized through other means (e.g., an other C library in the
same process) and the C-level initialization is be skipped.
- The conversion `rpy2py` is now working with any Python object inheriting
from `_rinterface_capi.SupportsSEXP`.
Bugs fixed
----------
- The C function `Rf_findVarInFrame()` in the R API can trigger
in an R-level error, and while this is rare, when it does
when embedded in Python it creates a segfault. Calls are
now wrapped in `R_ToplevelExec()` to limit the propagation
of R exceptions. This solved issue #710.
- More complete and correct mapping of R class names in
:func:`rpy2.rinterface_lib.sexp.rclass_get`.
- Initializing the embedded R caused the loss of ability to use Ctrl-C
to send SIGINT to a Python process (issue #723)
- :mod:`rpy2.sitation` is now working when the environment variable
`R_HOME` is set even though R is not in the `PATH` or in the Windows
registry (issue #744).
- Handling an R language objects could result in a segfault when its
R class was queried (issue #749).
- The conversion of R string arrays to `numpy` arrays was leaving
R's `NA` value as R NA objects. NAs in this type of arrays are now
turned to `None` in the resulting `numpy` array (issue #751).
- `rpy2.situation.get_rlib_path()` was returning an environment variable
with an invalid separator on Windows (mentioned in issue #754).
- R strings encoded with something else than 'utf-8' could result in
errors when trying to convert to Python strings (issue #754).
- Extracting documentation pages for R objects in packages could
generate spurious warnings when several "section" tags are present.
- R `Date` arrays/vectors were not wrapped into
:class:`rpy2.robjects.vectors.DateVector` objects but left as
R arrays of floats (which they are at the C level).
- The HTML representation of short R lists without names could
fail with an error.
- The :meth:`__repr__` of `robjects`-level objects was not displaying
the rpy2 class the R object is mapped to.
Release 3.3.6
=============
Bugs fixed
----------
- The unit tests for importing R packages with `lib_loc` were
broken (issue #720).
- Trying to create a memoryview for an R array with complex values
was failing with an attribute error.
- Fix the constructor of metaclass
:class:`rpy2.robjects.methods.RS4Auto_Type`.
- Fix call to end the embedded R in :class:`rpy2.robjects.R.__cleanup__`
(issue #734).
Release 3.3.5
=============
Bugs fixed
----------
- The callback handler to read input to R returned an
invalid result, leading to R asking for input
without ever acknowledging it received it.
Release 3.3.4
=============
Bugs fixed
----------
- Creating an R vector object from a Python object implementing
the buffer protocol could give incorrect results as C-level
incompatibilities could be missed (issue #702).
- :func:`rpy2.robjects.packages.importr` could fail when `lib_loc`
was specified (issue #705).
Release 3.3.3
=============
Bugs fixed
----------
- Fallback for when `str2lang` is missing (R < 3.6)
- Fix segfault with :meth:`PairListSexpVector.__getitem__` when
elements of the R pairlist have a `NILSXP` name (issue #700)
Release 3.3.2
=============
Bugs fixed
----------
- Initial fixes to have rpy2 running in ABI mode on Windows.
Few tests are not passing (many in callbacks for R's C API).
- System detection is now checking for FreeBSD.
Release 3.3.1
=============
Bugs fixed
-----------
- :meth:`rpy2.robjects.conversion.NameClassMap.update` can update
the mapping (:class:`dict`) or the default class.
Changes
-------
- Adding local converters was overwriting the base `NameClassMap`.
Release 3.3.0
=============
New features
------------
- Trying to import an R package that is not installed will now raise an
exception :class:`rpy2.robjects.packages.PackageNotInstalledError`.
- The R C API functions `void SET_FRAME(SEXP x, SEXP v)`,
`void SET_ENCLOS(SEXP x, SEXP v)` and `void SET_HASHTAB(SEXP x, SEXP v)`
are now accessible through rpy2.
- The module :mod:`rpy2.situation` can now return `LD_LIBRARY_PATH`
information about R. For example with
`python -m rpy2.situation LD_LIBRARY_PATH`
- :meth:`rpy2.robjects.methods.RS4.extends` lists the class names in the
inheritance line.
- The conversion of R objects to Python allows much more flexibility
and better allow the use of independent code converting different classes.
This is currently limited to R objects that are lists, environments, or
S4 objects. The Sphinx documentation contains an example. While this is
still work in progress this should already address concerns
at the origin of issue #539 about S4 classes.
- :class:`rpy2.robjects.language.LangVector` to map R language objects at
the `robjects` level.
- :class:`rpy2.robjects.vectors.PairlistVector` to map R pairlist objects at
the `robjects` level.
- An alternative function to display the output of R cells can be
specified using `-d` or `--display` in the magic arguments
(in :mod:`rpy2.ipython.rmagic`).
- Python classes representing underlying R objects no longer have to
exclusively rely on inheritance from :mod:`rpy2.rinterface` objects`.
An abstract class :class:`rpy2.rinterface_lib.sexp.SupportsSEXP` is added
to identify objects supporting a `__sexp__` protocol, and that abstract
class can also be used with type hints.
- :func:`rpy2.robjects.functions.wrap_r_functions` can create Python functions
with matching signature from R functions
- :func:`rpy2.robjects.functions.wrap_r_functions` can create Python functions
with matching signature from R functions.
- New class :class:`rpy2.rinterface_lib._rinterface_capi.UninitializedRCapsule`
to allow the instanciation of "placeholder" rpy2 objects before the
embedded R is initialized. This facilitate the use of static typing checks
such as mypy, mocking for tests that do not involve the execution of R
code, and allow cleaner implementations of module-level globals
that are R objects.
- New class :class:`rpy2.robjects.vectors.DateVector` to represent R dates.
- :class:`pandas.Series` containing date objects can now be converted to R
`Date` vectors.
Changes
-------
- When calling R C-API's `R_ParseVector` and a error occurs, the
exception message now contains the parsing status.
- :mod:`rpy2.rinterface_lib.embedded` has a module-level "constant"
`DEFAULT_C_STACK_LIMIT` used when initializing the embedded R.
- When creating a :mod:`rpy2.robjects.vectors.DataFrame` from (name, vector)
pairs, the names are no longer transformed to syntactically valid R
symbols (issue #660).
- The value `nan` in :mod:`pandas` Series with strings is now converted
to R NA (issue #668).
- Initial support for :const:`pandas.NA` (still experimental in pandas
at the time of writing, and rpy2 support is limited to arrays of strings).
- :mod:`pandas` series of dtype :class:`pandas.StringDType`, experimental in pandas 1.0,
are now supported by the converted (in the pandas-to-R direction) (issue #669)
- Version checking for the mapping of R packages in :mod:`rpy2.robjects.lib` is
now more permissive (check that version prefixes are matching).
Bugs fixed
-----------
- Building ABI only mode could require an API build environment (and fail
with an error when not present).
- SVG output for the R magic were incorrectly bytes objects.
- :meth:`rpy2.rinterface_lib.sexp.StrSexpVector.__getitem__` was returning the string
`'NA'` when an R NA value. Not it returns `rpy2.rinterface_lib.na_values.NA_Character`.
Release 3.2.7
=============
Bugs fixed
----------
- An f-string in `_rinterface_cffi_build.py` prevented installation
on Python 3.5 (issue #654).
Release 3.2.6
=============
Bugs fixed
----------
- The conversion of date/time object with specified timezones
was wrong when different than the local time zone (issue #634)
- 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 now emitted whenever trying to use `pandas` >= 1.0.
Release 3.2.5
=============
Bugs fixed
----------
- Latest release for R package `rlang` broke import through `importr()`.
A workaround for :mod:`rpy2.robjects.lib.ggplot2` is to rename the
offending R object (issue #631).
Changes
-------
- f-string requiring Python >= 3.6 removed.
Release 3.2.4
=============
Bugs fixed
----------
- An incomplete backport of the bug fixed in 3.2.3 broke the ABI mode.
Release 3.2.3
=============
Bugs fixed
-----------
- Error when parsing strings as R codes could result in a segfault.
Release 3.2.2
=============
Bugs fixed
----------
- Python format error when trying to report that the system is not reported
on Windows (issue #597).
- The setup script would error on build if R is not installed. It is now
printing an error message.
Release 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 (issue #587).
- Whenever the pandas conversion was activated :class:`FloatSexpVector` instances
with the R class `POSIXct` attached where not corrected mapped back to pandas
datetime arrays. (issue #594).
- Fix installation when an installation when a prefix without write access is used
(issue #588).
Release 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 (issue #580).
- 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 (issue #537).
Release 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 (issue #528).
- 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. (issue #562).
- Better handling of recent :mod:`pandas` arrays with missing values
(related to issue #544).
- 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` (issue #561).
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 (issue #565).
Release 3.0.4
=============
Bugs fixed
----------
- Fixed conversion of `pandas` :class:`Series` of dtype `pandas.Int32Dtype`,
or `pandas.Int64Dtype` (issue #544).
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`
(issue #543).
- Fixed conversion of :class:`pandas.Series` of `dtype` "object" when
all items are either all of the same type or are :obj:`None` (issue #540).
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"`
(issue #533).
- Callback for console reset was not set during R initialization.
- Fixed rternalized function returning rpy2 objects (issue #538).
- `--vanilla` is no longer among the default options used to initialize R
(issue #534).
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 (issue #524).
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
(issue #484).
Known issues
------------
- Mismatch between R's POSIXlt `wday` and Python time struct_time's `tm_wday`
(issue #523).
Release 2.9.6
=============
Bugs fixed
----------
- Latest release of :mod:`pandas` deprecated :meth:`DataFrame.from_items`.
(issue #514).
- 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
Release 2.9.5
=============
Bugs fixed
----------
- Missing values in pandas :class:`Category` series were creating
invalid R factors when converted (issue #493).
Release 2.9.4
=============
Bugs fixed
----------
- Fallback for failure to import numpy or pandas is now dissociated from
failure to import :mod:`numpy2ri` or :mod:`pandas2ri` (issue #463).
- :func:`repr` for R POSIX date/time vectors is now showing a string
representation of the date/time rather than the timestamp as a float
(issue #467).
- The HTML representation of R data frame (the default representation in the
Jupyter notebook) was displaying an inconsistent number of rows
(found while workin on issue #466).
- Handle time zones in timezones in Pandas when converting to R data frames
(issue #454).
- When exiting the Python process, the R cleanup is now explicitly request
to happen before Python's exit. This is preventing possible segfaults
the process is terminating (issue #471).
- dplyr method `ungroup()` was missing from
:class:`rpy2.robjects.lib.dplyr.DataFrame` (issue #473).
Release 2.9.3
=============
Bugs fixed
----------
- Delegate finding where is local time zone file to either a user-specified
module-level variable `default_timezone` or to the third-party
module :mod:`tzlocal` (issue #448).
Release 2.9.2
=============
Changes
-------
- The pandas converter is converting :class:`pandas.Series` of `dtype` `"O"`
to :class:`rpy2.robjects.vectors.StrVector` objects, issueing a warning
about it (See issue #421).
- The conversion of pandas data frame is now working with columns rather
than rows (introduce in bug fix for issue #442 below) and this is expected
to result in more efficient conversions.
Bugs fixed
----------
- Allow floats in figure sizes for R magic (Pull request #63)
- Fixed pickling unpickling of robjects-level instances,
regression introduced in fix for issue #432 with release 2.9.1 (issue #443).
- Fixed broken unit test for columns of `dtype` `"O"` in `pandas` data frames.
- Fixed incorrect conversion of R factors in data frames to columns of
integers in pandas data frame (issue #442).
version 1.5.8
* Fix Enum bug (issue 1128): the enum_dict member of an EnumType read from a file
contains invalid values when the enum is large enough (more than 127 or 255
members).
* Binary wheels for aarch64 and python 3.10.
version 1.5.7
* don't try to mask vlens with default _FillValue, since vlens don't have a default _FillValue.
This gets rid of numpy DeprecationWarning (issue 1099).
* update docs to reflect the fact that a variable must be in collective mode before writing
compressed data to it in parallel. Added a test for this (examples/mpi_example_compressed.py).
* Fix OverflowError when dimension sizes become greater than 2**32-1 elements on Windows (Issue 1112).
* Don't return masked arrays for vlens (only for primitive and enum types
Summary of bugs fixed for version 6.4.0 (2021-10-30)
----------------------------------------------------
Improvements and fixes
- Reduce memory usage in BISTs for `copyobj`, `hgsave`.
- `hgsave.m`, `copyobj.m`: Use `'qt'` graphics toolkit in BISTs.
- `main.cc`: Use `getopt` to parse command line arguments.
- `main.cc`: Remove invalid case.
- Disable `getopt` error reporting in wrapper program.
- `interp1.m`: Don't interpret later numeric input as `xi`.
- `pkg`: Improve similar package name suggestion.
- Store parent name in function object when caching parents in scope.
- Avoid internal error and segfault with `eval` and scripts.
- `rmpath`: Prevent removing the current directory from the load path.
GUI
- Fix missing interpreter event in `octave-scintilla`.
- Fix opening a file in a custom editor.
Documentation
- Improve docstring for `disable_diagonal_matrix`, `disable_diagonal_matrix`,
and `disable_range`.
- `cbrt`: Clarify that function errors for non-real input.
- `dsearchn.m`: Added optional distance output description.
- Add Hungarian translation for project description files.
- Document fsolve output "info" -2.
Build system
- Correct error message for incompatible CXSparse.
Summary of bugs fixed for version 6.3.0 (2021-07-11)
----------------------------------------------------
Important notice
- This bug fix release breaks ABI compatiblity with Octave 6.2.0. Re-build
binaries (like .oct or .mex files) when updating to this version.
Improvements and fixes
- `ls-hdf5.cc`: Avoid throwing inside HDF5 function.
- `ls-hdf5.cc`: Handle non-zero terminated type strings.
- Fix occasional segfault in `symbfact`.
- `fsolve.m`: Fix undefined output error when using `Output` function.
- Fix compilation error with `iconv_t` on Solaris.
- build: Check for `stropts.h`.
- Avoid ambiguous call to `pow`.
- Fix context link when creating handle to nested function.
- `print.m`: Warn when figure is too large to be printed to output page.
- Defer clearing function vars until stack frame is deleted.
- Avoid memory leaks when returning handles to nested functions.
- Hold references to closure frames in anon functions if needed.
- `eigs`: Prevent possible segmentation fault at exit.
- Issue warning when gnuplot graphics toolkit is initialized.
- mpoles.m: Fix detection of pole multiplicity.
- Perform shutdown actions in interpreter destructor.
- build: Make relocation of dependencies with Octave optional.
- `qz.cc`: Return correct number of eigenvalues.
- `qz.cc`: Let test pass with LAPACK 3.9.1 and earlier versions.
- `pkg.m`: Use default prefixes unless otherwise set previously.
- `betaincinv.m`: Correctly handle small inputs.
- `betaincinv.m`: Correctly handle inputs very close to 1.0.
- `unistd-wrappers.c`: Allocate sufficient memory for `new_argv`.
- Mark system functions correctly if `OCTAVE_HOME` is non-canonical.
- Mark compiled system functions correctly if `OCTAVE_HOME` is non-canonical.
- Fix error if test suite is run before Octave is installed.
- `lo-array-errwarn.cc`: Include `<limits>`.
- Use `std::size_t` and `std::ptrdiff_t` in C++ code.
- Use `std::size_t` in more instances.
- Return proper number of stack frames for `dbstack (N)` call.
- Avoid ambiguous match of overloaded function.
- `lscov.m`: Relax BIST tolerance to pass with OpenBLAS.
- `print`: Fix error when `"px"` word is present in a figure.
- `logm.m`: Fix check for real negative values in complex vector.
- build: Set necessary flags to allow execution on Windows Vista.
- Declare base_parser destructor virtual.
- `hist.m`: Improve handling and docstring for third parameter "norm".
- `logm.m`: Allow tolerance in check for real negative values in complex vector.
- `expm.m`, `logm.m`: Use function `isdiag` to detect if input is a diagonal matrix.
- tests: Relax tolerance for some tests on macOS.
- `logspace.m`: Mark tests as known to fail on macOS.
- `hist.m`: Use deterministic test.
- `rgb2ind.m`: Reduce memory usage and eliminate randomness in test.
- `logm.m`: Allow larger tolerance for test on macOS.
- build: Use correct path to `octave` binary in build tree on macOS.
- build: Fix typo in folder to libraries when building `.oct` or `.mex` files.
- build: Set DL_LDFLAGS in the build rules for .oct or .mex files.
- `rgb2ind.m`: Suppress output in test.
- Improve documentation for `log2` function.
- `ind2sub`: Fix typo in "see also" section of docstring.
- `mrdivide`, `mldivide`: Document that functions might return minimum norm solutions.
- Fix scoping issue for handles to sibling nested functions.
- `ls-mat5.cc`: Avoid integer overflow in calculation of buffer size for zlib.
- Move top-level REPL from interpreter to evaluator.
- Avoid crash with `dbquit` when executing command in terminal from GUI.
GUI
- Fix calling external editor.
- Fix missing file suffix .m when saving a new script.
- Do not run files that are not saved as Octave files.
- Fix confirm overwrite for native editor file "save as" dialogs.
- Fix crash when GUI tries to restore missing previous Octave dir.
- Fix restoring the horizontal position of docked GUI widgets.
- Prevent floating widgets from re-opening after restart.
- Avoid crash in GUI for `rmdir("")`.
- Fix EOL mode when saving files under new names.
- Fix auto indentation of switch-structure in GUI editor.
- Avoid crash when closing GUI with open editor tabs.
- `octave-qscintilla.cc` (`contextmenu_run`): Fix keyboard command handling.
Documentation
- Improve Differential Equations chapter and example for lsode.
- Clarify usage of "Depends" keyword in package `DESCRIPTION` file.
- Add note that wildcard patterns for `save` are glob patterns.
- Change example for Delaunay triangulation to match the generating code.
- Document single precision issues with OpenGL graphics toolkits.
- Minor changes to documentation of single precision issues with OpenGL.
- Expand on documentation for command syntax.
- `isprop.m`: Document that function only works on graphics objects in Octave 6.X.
- Explain how to write dual-purpose executable scripts and Octave functions.
- Update keyword docstrings.
- Use Texinfo commands to improve `transpose()` docstring rendering.
- `betainc.m`, `betaincinv.m`: Correct non-TeX definition of beta incomplete integral.
- Grammarcheck documentation ahead of 6.3 release.
- Spellcheck documentation ahead of 6.3 release.
2.8.3 (2021-12-13)
------------------
- Fix more use of 'python' where 'python3' is intended.
2.8.2 (2021-12-06)
------------------
- Update documentation to reflect new 2.8 features.
- Fix array compression for non-native byte order
- Fix use of 'python' where 'python3' is intended.
- Fix schema URI resolving when the URI prefix is also
claimed by a legacy extension.
- Remove 'name' and 'version' attributes from NDArrayType
instances.
2.8.1 (2021-06-09)
------------------
- Fix bug in block manager when a new block is added to an existing
file without a block index.
2.8.0 (2021-05-12)
------------------
- Add ``yaml_tag_handles`` property to allow definition of custom yaml
``%TAG`` handles in the asdf file header.
- Add new resource mapping API for extending asdf with additional
schemas.
- Add global configuration mechanism.
- Drop support for automatic serialization of subclass
attributes.
- Support asdf:// as a URI scheme.
- Include only extensions used during serialization in
a file's metadata.
- Drop support for Python 3.5.
- Add new extension API to support versioned extensions.
- Permit wildcard in tag validator URIs.
- Implement support for ASDF Standard 1.6.0. This version of
the standard limits mapping keys to string, integer, or
boolean.
- Stop removing schema defaults for all ASDF Standard versions,
and automatically fill defaults only for versions <= 1.5.0.
- Stop removing keys with ``None`` values from the tree on write. This
fixes a long-standing issue where the tree structure is not preserved
on write, but will break ``ExtensionType`` subclasses that depend on
this behavior. Extension developers will need to modify their
``to_tree`` methods to check for ``None`` before adding a key to
the tree (or modify the schema to permit nulls, if that is the
intention).
- Deprecated the ``auto_inline`` argument to ``AsdfFile.write_to`` and
``AsdfFile.update`` and added ``AsdfConfig.array_inline_threshold``.
- Add ``edit`` subcommand to asdftool for efficient editing of
the YAML portion of an ASDF file.
- Increase limit on integer literals to signed 64-bit.
- Remove the ``asdf.test`` method and ``asdf.__githash__`` attribute.
- Add support for custom compression via extensions.
- Remove unnecessary ``.tree`` from search result paths.
- Drop support for bugs in older operating systems and Python versions.
- Add argument to ``asdftool diff`` that ignores tree nodes that match
a JMESPath expression.
- Fix behavior of ``exception`` argument to ``GenericFile.seek_until``.
- Fix issues in file type detection to allow non-seekable input and
filenames without recognizable extensions. Remove the ``asdf.asdf.is_asdf_file``
function.
- Update ``asdftool extensions`` and ``asdftool tags`` to incorporate
the new extension API.
- Add ``AsdfSearchResult.replace`` method for assigning new values to
search results.
- Search for block index starting from end of file. Fixes rare bug when
a data block contains a block index.
- Update asdf-standard to 1.6.0 tag.
2.7.5 (2021-06-09)
------------------
- Fix bug in ``asdf.schema.check_schema`` causing relative references in
metaschemas to be resolved incorrectly.
- Fix bug in block manager when a new block is added to an existing
file without a block index.
2.7.4 (2021-04-30)
------------------
- Fix pytest plugin failure under older versions of pytest.
- Copy array views when the base array is non-contiguous.
- Prohibit views over FITS arrays that change dtype.
- Add support for HTTPS URLs and following redirects.
- Prevent astropy warnings in tests when opening known bad files.
What's new in 1.3.5 (December 12, 2021)
---------------------------------------
Fixed regressions
~~~~~~~~~~~~~~~~~
- Fixed regression in :meth:`Series.equals` when comparing floats with dtype object to None (:issue:`44190`)
- Fixed regression in :func:`merge_asof` raising error when array was supplied as join key (:issue:`42844`)
- Fixed regression when resampling :class:`DataFrame` with :class:`DateTimeIndex` with empty groups and ``uint8``, ``uint16`` or ``uint32`` columns incorrectly raising ``RuntimeError`` (:issue:`43329`)
- Fixed regression in creating a :class:`DataFrame` from a timezone-aware :class:`Timestamp` scalar near a Daylight Savings Time transition (:issue:`42505`)
- Fixed performance regression in :func:`read_csv` (:issue:`44106`)
- Fixed regression in :meth:`Series.duplicated` and :meth:`Series.drop_duplicates` when Series has :class:`Categorical` dtype with boolean categories (:issue:`44351`)
- Fixed regression in :meth:`.GroupBy.sum` with ``timedelta64[ns]`` dtype containing ``NaT`` failing to treat that value as NA (:issue:`42659`)
- Fixed regression in :meth:`.RollingGroupby.cov` and :meth:`.RollingGroupby.corr` when ``other`` had the same shape as each group would incorrectly return superfluous groups in the result (:issue:`42915`)
v0.20.2
This is a bugfix release to resolve (:issue:`3391`, :issue:`5715`). It also
includes performance improvements in unstacking to a ``sparse`` array and a
number of documentation improvements.
Breaking changes
- Use complex nan when interpolating complex values out of bounds by default (instead of real nan) (:pull:`6019`).
Performance
- Significantly faster unstacking to a ``sparse`` array. :pull:`5577`
Bug fixes
- :py:func:`xr.map_blocks` and :py:func:`xr.corr` now work when dask is not installed (:issue:`3391`, :issue:`5715`, :pull:`5731`).
- Fix plot.line crash for data of shape ``(1, N)`` in _title_for_slice on format_item (:pull:`5948`).
- Fix a regression in the removal of duplicate backend entrypoints (:issue:`5944`, :pull:`5959`)
Documentation
- Better examples in docstrings for groupby and resampling reductions (:pull:`5871`).
Internal Changes
- Use ``importlib`` to replace functionality of ``pkg_resources`` in
backend plugins tests. (:pull:`5959`).
