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* The NEWS files have been re-organized.
This file contains news for R >= 3.0.0: news for the 0.x.y, 1.x.y
and 2.x.y releases is in files NEWS.0, NEWS.1 and NEWS.2. The
latter files are now installed when R is installed. An HTML
version of news from 2.10.0 to 2.15.3 is available as
doc/html/NEWS.2.html.
* sum() for integer arguments now uses an integer accumulator of at
least 64 bits and so will be more accurate in the very rare case
that a cumulative sum exceeds 2^53 (necessarily summing more than
4 million elements).
* The example() and tools::Rd2ex() functions now have parameters to
allow them to ignore \dontrun markup in examples. (Suggested by
Peter Solymos.)
* str(x) is considerably faster for very large lists, or factors
with 100,000 levels, the latter as in PR#15337.
* col2rgb() now converts factors to character strings not integer
codes (suggested by Bryan Hanson).
* tail(warnings()) now works, via the new `[` method.
* There is now support for the LaTeX style file zi4.sty which has
in some distributions replaced inconsolata.sty.
* unlist(x) now typically returns all non-list xs unchanged, not
just the "vector" ones. Consequently, format(lst) now also works
when the list lst has non-vector elements.
* The tools::getVignetteInfo() function has been added to give
information about installed vignettes.
* New assertCondition(), etc. utilities in tools, useful for
testing.
* Profiling now records non-inlined calls from byte-compiled code
to BUILTIN functions.
* Various functions in stats and elsewhere that use non-standard
evaluation are now more careful to follow the namespace scoping
rules. E.g. stats::lm() can now find stats::model.frame() even
if stats is not on the search path or if some package defines a
function of that name.
* If an invalid/corrupt .Random.seed object is encountered in the
workspace it is ignored with a warning rather than giving an
error. (This allows R itself to rely on a working RNG, e.g. to
choose a random port.)
* seq() and seq.int() give more explicit error messages if called
with invalid (e.g. NaN) inputs.
* When parse() finds a syntax error, it now makes partial parse
information available up to the location of the error. (Request
of Reijo Sund.)
* Methods invoked by NextMethod() had a different dynamic parent to
the generic. This was causing trouble where S3 methods invoked
via lazy evaluation could lose track of their generic.
(PR#15267)
* Code for the negative binomial distribution now treats the case
size == 0 as a one-point distribution at zero.
* abbreviate() handles without warning non-ASCII input strings
which require no abbreviation.
* read.dcf() no longer has a limit of 8191 bytes per line. (Wish of
PR#15250.)
* formatC(x) no longer copies the class of x to the result, to
avoid misuse creating invalid objects as in PR#15303. A warning
is given if a class is discarded.
* Dataset npk has been copied from MASS to allow more tests to be
run without recommended packages being installed.
* The initialization of the regression coefficients for
non-degenerate differenced models in arima() has been changed and
in some examples avoids a local maximum. (PR#15396)
* termplot() now has an argument transform.x to control the display
of individual terms in the plot. (PR#15329)
* format() now supports digits = 0, to display nsmall decimal
places.
* There is a new read-only par() parameter called "page", which
returns a logical value indicating whether the next plot.new()
call will start a new page.
* Processing Sweave and Rd documents to PDF now renders backticks
* utils::modifyList() gets a new argument keep.null allowing NULL
components in the replacement to be retained, instead of causing
corresponding components to be deleted.
* tools::pkgVignettes() gains argument check; if set to TRUE, it
will warn when it appears a vignette requests a non-existent
vignette engine.
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4 years worth of bugfixes/updates.
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--------------------------------------------------------------------------
NEWS for version 1.1 (released on October 28, 2013)
--------------------------------------------------------------------------
New and Changed Features
========================
o Added a new operator on polyhedra: the positive time elapse.
o In the Java language interface:
- The constraint/generator/... system classes now extend the ArrayList
generic container (rather than Vector);
- Variable objects are now built from a long (rather than int) value,
thereby matching the type used elsewhere for space dimensions;
- added new static method to Variable class
void setStringifier(Variable_Stringifier)
where Variable_Stringifier is an interface allowing for
customization of the output routine for variable's names
(see example in interfaces/Java/tests/Variable_Output_test1.java);
- added value NOT_EQUAL to enumeration Relation_Symbol.
Bugfixes
========
o Portability improved.
o Fixed a precision regression in Polyhedron method
void drop_some_non_integer_points(const Variables_Set&,
Complexity_Class);
o In the Java language interface, fixed a C++/Java conversion error
whereby the construction of a valid Variable object in JNI code
was leading to an exception being thrown. The bug has only been
observed on 32-bit builds.
o In the Java interface, fixed declaration of methods
void drop_some_non_integer_points(...);
so as to accept a Complexity_Class enum value.
o Fixed an issue in method MIP_Problem::OK() whereby the method
was trying to enforce a non-invariant condition.
--------------------------------------------------------------------------
NEWS for version 1.0 (released on June 28, 2012)
--------------------------------------------------------------------------
New and Changed Features
========================
o Significant improvements have been obtained in both time and space
resource usage by the definition of data structures and algorithms
for the case of "sparse rows", i.e., sequences of coefficients
where most of the values are zero.
o The library fully supports two different representations for rows:
the "dense" representation is an array-like representation tailored
to sequences having most of their coefficients different from zero;
the "sparse" representation saves memory space (as well as CPU
cycles) when most of the coefficients in the sequence are zero.
o A generic interface allows for a seamless interaction between the
dense and the sparse row representation. Most library entities
(linear expressions, constraints, generators, congruences, and
their systems) can be built using either representation, specified
as a constructor's argument.
o As a by-product of this sparse/dense refactoring work, efficiency
improvements have been obtained even for those computations that
are still based on the dense row representation.
o Reasonable default values for the row representation are provided
for each library entity, automatically leading to significant
memory space savings even in old client/library code, e.g., when
dealing with constraint systems describing weakly relational
abstractions such as boxes and octagonal shapes.
o If desired, these default values can be customized to user's needs
by changing just a few lines of library code. For instance, the
constraint systems stored inside C_Polyhedron and NNC_Polyhedron
objects can be made to use the sparse representation by just
changing the following line in Polyhedron.defs.hh:
static const Representation default_con_sys_repr = DENSE;
to become
static const Representation default_con_sys_repr = SPARSE;
Bugfixes
========
o Fixed a bug affecting methods
bool BD_Shape<T>::contains(const BD_Shape& y) const;
bool Octagonal_Shape<T>::contains(const Octagonal_Shape& y) const;
whereby the wrong result was obtained when *this is an empty
weakly-relational shape and y is not empty.
o Fixed a bug affecting the PIP solver whereby a wrong result could have
been obtained if the input constraint system contained multiple linear
equality constraints.
--------------------------------------------------------------------------
NEWS for version 0.12.1 (released on April 16, 2012)
--------------------------------------------------------------------------
New and Changed Features
========================
o In the C, Java, OCaml and Prolog interfaces, modified the signature
of the function/method/predicate for setting the deterministic timeout
threshold. The new interfaces take two input values, named `unscaled'
and `scale', that are used to compute the threshold value as
`unscaled * 2^scale'.
o Added new Box<ITV> methods
bool has_upper_bound(Variable var,
Coefficient& n, Coefficient& d, bool& closed) const;
bool has_lower_bound(Variable var,
Coefficient& n, Coefficient& d, bool& closed) const;
to query a non-empty box for the existence and value of its upper/lower
bound on variable `var'. The methods have been also added to all the
available language interfaces.
o Two BibTeX databases of papers related to the Parma Polyhedra Library
have been added to the distribution (in the `doc' directory).
Bugfixes
========
o Restored the support for deterministic timeouts in the PIP solver
(it was removed by accident in PPL 0.12).
o Minor documentation fixes.
o Portability improved.
--------------------------------------------------------------------------
NEWS for version 0.12 (released on February 27, 2012)
--------------------------------------------------------------------------
New and Changed Features
========================
o New configure options `--with-gmp=DIR', `--with-gmp-include=DIR' and
`--with-gmp-lib=DIR' supersede the (now removed) option
`--with-gmp-prefix'. (The old option never really worked; hopefully
this is the last change in this area.)
o New configuration option `--disable-documentation'. When specified
no new documentation is built: only the documentation already present
in the source tree is installed upon `make install'.
o The resolution process for PIP_Problem now better exploits the
integrality of parameters to simplify the newly generated tautological
constraints, the splitting constraints of decision nodes, and the
expressions defining artificial parameters.
o The implementations of the MIP and PIP solvers are based on a new
data structure leading to significant space and time savings when
the tableau matrix is sparse; the benchmarks of the ppl_lpsol demo
show an improvement on the average case, that grows when the toughest
tests in the benchmark suite are considered.
o When the `--check' option is used, the input data for demo ppl_lpsol
is perturbed the same way as GLPK does, thereby allowing for a
meaningful comparison of the results obtained.
o The input routine for PPL numeric datatypes has been extended to
accept the ISO9899 (C99) hexadecimal floating constant syntax.
o The Parma Watchdog Library has been merged into the
Parma Polyhedra Library.
Bugfixes
========
o Corrected a precision bug in methods
Box<ITV>::upper_bound_assign(const Box&)
Box<ITV>::upper_bound_assign_if_exact(const Box&)
whereby, provided any argument is an empty box and under other rather
specific conditions, the computed result was correct but unnecessarily
imprecise.
o Corrected a bug in method
Grid::relation_with(const Constraint&) const
whereby, under specific conditions, the method was creating invalid
Grid_Generator objects and providing an incorrect result.
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### 0.9.7 / 04.02.2014
* Avoid exception when reading text objects
* Add test for drawings with text (currenty broken)
* Restore xlsopcodes script which had been mangled in previous commits
* Remove ruby 1.9 from roadmap, it's already working fine
* Fix excel file format documentation which had been mangled in previous commits
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bug fixes
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gcalctool ported to vala and renamed gnome-calculator.
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either because they themselves are not ready or because a
dependency isn't. This is annotated by
PYTHON_VERSIONS_INCOMPATIBLE= 33 # not yet ported as of x.y.z
or
PYTHON_VERSIONS_INCOMPATIBLE= 33 # py-foo, py-bar
respectively, please use the same style for other packages,
and check during updates.
Use versioned_dependencies.mk where applicable.
Use REPLACE_PYTHON instead of handcoded alternatives, where applicable.
Reorder Makefile sections into standard order, where applicable.
Remove PYTHON_VERSIONS_INCLUDE_3X lines since that will be default
with the next commit.
Whitespace cleanups and other nits corrected, where necessary.
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currently in pkgsrc).
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into options.mk.
Changes from 2.4 to 3.0
=======================
New features
------------
- Since this release PyTables provides full support to Python_ 3
(closes :issue:`188`).
- The entire code base is now more compliant with coding style guidelines
describe in the PEP8_ (closes :issue:`103` and :issue:`224`).
See `API changes`_ for more details.
- Basic support for HDF5 drivers. Now it is possible to open/create an
HDF5 file using one of the SEC2, DIRECT, LOG, WINDOWS, STDIO or CORE
drivers. Users can also set the main driver parameters (closes
:issue:`166`).
Thanks to Michal Slonina.
- Basic support for in-memory image files. An HDF5 file can be set from or
copied into a memory buffer (thanks to Michal Slonina). This feature is
only available if PyTables is built against HDF5 1.8.9 or newer.
Closes :issue:`165` and :issue:`173`.
- New :meth:`File.get_filesize` method for retrieving the HDF5 file size.
- Implemented methods to get/set the user block size in a HDF5 file
(closes :issue:`123`)
- Improved support for PyInstaller_. Now it is easier to pack frozen
applications that use the PyTables package (closes: :issue:`177`).
Thanks to Stuart Mentzer and Christoph Gohlke.
- All read methods now have an optional *out* argument that allows to pass a
pre-allocated array to store data (closes :issue:`192`)
- Added support for the floating point data types with extended precision
(Float96, Float128, Complex192 and Complex256). This feature is only
available if numpy_ provides it as well.
Closes :issue:`51` and :issue:`214`. Many thanks to Andrea Bedini.
- Consistent ``create_xxx()`` signatures. Now it is possible to create all
data sets :class:`Array`, :class:`CArray`, :class:`EArray`,
:class:`VLArray`, and :class:`Table` from existing Python objects (closes
:issue:`61` and :issue:`249`). See also the `API changes`_ section.
- Complete rewrite of the :mod:`nodes.filenode` module. Now it is fully
compliant with the interfaces defined in the standard :mod:`io` module.
Only non-buffered binary I/O is supported currently.
See also the `API changes`_ section. Closes :issue:`244`.
- New :program:`pt2to3` tool is provided to help users to port their
applications to the new API (see `API changes`_ section).
Improvements
------------
- Improved runtime checks on dynamic loading of libraries: meaningful error
messages are generated in case of failure.
Also, now PyTables no more alters the system PATH.
Closes :issue:`178` and :issue:`179` (thanks to Christoph Gohlke).
- Improved list of search paths for libraries as suggested by Nicholaus
Halecky (see :issue:`219`).
- Removed deprecated Cython_ include (.pxi) files. Contents of
:file:`convtypetables.pxi` have been moved in :file:`utilsextension.pyx`.
Closes :issue:`217`.
- The internal Blosc_ library has been upgraded to version 1.2.3.
- Pre-load the bzip2_ library on windows (closes :issue:`205`)
- The :meth:`File.get_node` method now accepts unicode paths
(closes :issue:`203`)
- Improved compatibility with Cython_ 0.19 (see :issue:`220` and
:issue:`221`)
- Improved compatibility with numexpr_ 2.1 (see also :issue:`199` and
:issue:`241`)
- Improved compatibility with development versions of numpy_
(see :issue:`193`)
- Packaging: since this release the standard tar-ball package no more includes
the PDF version of the "PyTables User Guide", so it is a little bit smaller
now. The complete and pre-build version of the documentation both in HTML
and PDF format is available on the file `download area`_ on SourceForge.net.
Closes: :issue:`172`.
- Now PyTables also uses `Travis-CI`_ as continuous integration service.
All branches and all pull requests are automatically tested with different
Python_ versions. Closes :issue:`212`.
Other changes
-------------
- PyTables now requires Python 2.6 or newer.
- Minimum supported version of Numexpr_ is now 2.0.
API changes
-----------
The entire PyTables API as been made more PEP8_ compliant (see :issue:`224`).
This means that many methods, attributes, module global variables and also
keyword parameters have been renamed to be compliant with PEP8_ style
guidelines (e.g. the ``tables.hdf5Version`` constant has been renamed into
``tables.hdf5_version``).
We made the best effort to maintain compatibility to the old API for existing
applications. In most cases, the old 2.x API is still available and usable
even if it is now deprecated (see the Deprecations_ section).
The only important backwards incompatible API changes are for names of
function/methods arguments. All uses of keyword arguments should be
checked and fixed to use the new naming convention.
The new :program:`pt2to3` tool can be used to port PyTables based applications
to the new API.
Many deprecated features and support for obsolete modules has been dropped:
- The deprecated :data:`is_pro` module constant has been removed
- The nra module and support for the obsolete numarray module has been removed.
The *numarray* flavor is no more supported as well (closes :issue:`107`).
- Support for the obsolete Numeric module has been removed.
The *numeric* flavor is no longer available (closes :issue:`108`).
- The tables.netcdf3 module has been removed (closes :issue:`68`).
- The deprecated :exc:`exceptions.Incompat16Warning` exception has been
removed
- The :meth:`File.create_external_link` method no longer has a keyword
parameter named *warn16incompat*. It was deprecated in PyTables 2.4.
Moreover:
- The :meth:`File.create_array`, :meth:`File.create_carray`,
:meth:`File.create_earray`, :meth:`File.create_vlarray`, and
:meth:`File.create_table` methods of the :class:`File` objects gained a
new (optional) keyword argument named ``obj``. It can be used to initialize
the newly created dataset with an existing Python object, though normally
these are numpy_ arrays.
The *atom*/*descriptor* and *shape* parameters are now optional if the
*obj* argument is provided.
- The :mod:`nodes.filenode` has been completely rewritten to be fully
compliant with the interfaces defined in the :mod:`io` module.
The FileNode classes currently implemented are intended for binary I/O.
Main changes:
* the FileNode base class is no more available,
* the new version of :class:`nodes.filenode.ROFileNode` and
:class:`nodes.filenode.RAFileNode` objects no more expose the *offset*
attribute (the *seek* and *tell* methods can be used instead),
* the *lineSeparator* property is no more available end the ``\n``
character is always used as line separator.
- The `__version__` module constants has been removed from almost all the
modules (it was not used after the switch to Git). Of course the package
level constant (:data:`tables.__version__`) still remains.
Closes :issue:`112`.
- The :func:`lrange` has been dropped in favor of xrange (:issue:`181`)
- The :data:`parameters.MAX_THREADS` configuration parameter has been dropped
in favor of :data:`parameters.MAX_BLOSC_THREADS` and
:data:`parameters.MAX_NUMEXPR_THREADS` (closes :issue:`147`).
- The :func:`conditions.compile_condition` function no more has a *copycols*
argument, it was no more necessary since Numexpr_ 1.3.1.
Closes :issue:`117`.
- The *expectedsizeinMB* parameter of the :meth:`File.create_vlarray` and of
the :meth:`VLArrsy.__init__` methods has been replaced by *expectedrows*.
See also (:issue:`35`).
- The :meth:`Table.whereAppend` method has been renamed into
:meth:`Table.append_where` (closes :issue:`248`).
Please refer to the :doc:`../MIGRATING_TO_3.x` document for more details about
API changes and for some useful hint about the migration process from the 2.X
API to the new one.
Other possibly incompatible changes
-----------------------------------
- All methods of the :class:`Table` class that take *start*, *stop* and
*step* parameters (including :meth:`Table.read`, :meth:`Table.where`,
:meth:`Table.iterrows`, etc) have been redesigned to have a consistent
behaviour. The meaning of the *start*, *stop* and *step* and their default
values now always work exactly like in the standard :class:`slice` objects.
Closes :issue:`44` and :issue:`255`.
- Unicode attributes are not stored in the HDF5 file as pickled string.
They are now saved on the HDF5 file as UTF-8 encoded strings.
Although this does not introduce any API breakage, files produced are
different (for unicode attributes) from the ones produced by earlier
versions of PyTables.
- System attributes are now stored in the HDF5 file using the character set
that reflects the native string behaviour: ASCII for Python 2 and UTF8 for
Python 3. In any case, system attributes are represented as Python string.
- The :meth:`iterrows` method of :class:`*Array` and :class:`Table` as well
as the :meth:`Table.itersorted` now behave like functions in the standard
:mod:`itertools` module.
If the *start* parameter is provided and *stop* is None then the
array/table is iterated from *start* to the last line.
In PyTables < 3.0 only one element was returned.
Deprecations
------------
- As described in `API changes`_, all functions, methods and attribute names
that was not compliant with the PEP8_ guidelines have been changed.
Old names are still available but they are deprecated.
- The use of upper-case keyword arguments in the :func:`open_file` function
and the :class:`File` class initializer is now deprecated. All parameters
defined in the :file:`tables/parameters.py` module can still be passed as
keyword argument to the :func:`open_file` function just using a lower-case
version of the parameter name.
Bugs fixed
----------
- Better check access on closed files (closes :issue:`62`)
- Fix for :meth:`File.renameNode` where in certain cases
:meth:`File._g_updateLocation` was wrongly called (closes :issue:`208`).
Thanks to Michka Popoff.
- Fixed ptdump failure on data with nested columns (closes :issue:`213`).
Thanks to Alexander Ford.
- Fixed an error in :func:`open_file` when *filename* is a :class:`numpy.str_`
(closes :issue:`204`)
- Fixed :issue:`119`, :issue:`230` and :issue:`232`, where an index on
:class:`Time64Col` (only, :class:`Time32Col` was ok) hides the data on
selection from a Tables. Thanks to Jeff Reback.
- Fixed ``tables.tests.test_nestedtypes.ColsTestCase.test_00a_repr`` test
method. Now the ``repr`` of of cols on big-endian platforms is correctly
handled (closes :issue:`237`).
- Fixes bug with completely sorted indexes where *nrowsinbuf* must be equal
to or greater than the *chunksize* (thanks to Thadeus Burgess).
Closes :issue:`206` and :issue:`238`.
- Fixed an issue of the :meth:`Table.itersorted` with reverse iteration
(closes :issue:`252` and :issue:`253`).
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Changes from 2.2.1 to 2.2.2
===========================
* The `copy_args` argument of `NumExpr` function has been brought
back. This has been mainly necessary for compatibility with
PyTables < 3.0, which I decided to continue to support. Fixed #115.
* The `__nonzero__` method in `ExpressionNode` class has been
commented out. This is also for compatibility with PyTables < 3.0.
See #24 for details.
* Fixed the type of some parameters in the C extension so that s390
architecture compiles. Fixes #116. Thank to Antonio Valentino for
reporting and the patch.
Changes from 2.2 to 2.2.1
=========================
* Fixes a secondary effect of "from numpy.testing import `*`", where
division is imported now too, so only then necessary functions from
there are imported now. Thanks to Christoph Gohlke for the patch.
Changes from 2.1 to 2.2
=======================
* [LICENSE] Fixed a problem with the license of the
numexpr/win32/pthread.{c,h} files emulating pthreads on Windows
platforms. After persmission from the original authors is granted,
these files adopt the MIT license and can be redistributed without
problems. See issue #109 for details
(https://code.google.com/p/numexpr/issues/detail?id=110).
* [ENH] Improved the algorithm to decide the initial number of threads
to be used. This was necessary because by default, numexpr was
using a number of threads equal to the detected number of cores, and
this can be just too much for moder systems where this number can be
too high (and counterporductive for performance in many cases).
Now, the 'NUMEXPR_NUM_THREADS' environment variable is honored, and
in case this is not present, a maximum number of *8* threads are
setup initially. The new algorithm is fully described in the Users
Guide now in the note of 'General routines' section:
https://code.google.com/p/numexpr/wiki/UsersGuide#General_routines.
Closes #110.
* [ENH] numexpr.test() returns `TestResult` instead of None now.
Closes #111.
* [FIX] Modulus with zero with integers no longer crashes the
interpreter. It nows puts a zero in the result. Fixes #107.
* [API CLEAN] Removed `copy_args` argument of `evaluate`. This should
only be used by old versions of PyTables (< 3.0).
* [DOC] Documented the `optimization` and `truediv` flags of
`evaluate` in Users Guide
(https://code.google.com/p/numexpr/wiki/UsersGuide).
Changes from 2.0.1 to 2.1
===========================
* Dropped compatibility with Python < 2.6.
* Improve compatibiity with Python 3:
- switch from PyString to PyBytes API (requires Python >= 2.6).
- fixed incompatibilities regarding the int/long API
- use the Py_TYPE macro
- use the PyVarObject_HEAD_INIT macro instead of PyObject_HEAD_INIT
* Fixed several issues with different platforms not supporting
multithreading or subprocess properly (see tickets #75 and #77).
* Now, when trying to use pure Python boolean operators, 'and',
'or' and 'not', an error is issued suggesting that '&', '|' and
'~' should be used instead (fixes #24).
Changes from 2.0 to 2.0.1
=========================
* Added compatibility with Python 2.5 (2.4 is definitely not supported
anymore).
* `numexpr.evaluate` is fully documented now, in particular the new
`out`, `order` and `casting` parameters.
* Reduction operations are fully documented now.
* Negative axis in reductions are not supported (they have never been
actually), and a `ValueError` will be raised if they are used.
Changes from 1.x series to 2.0
==============================
- Added support for the new iterator object in NumPy 1.6 and later.
This allows for better performance with operations that implies
broadcast operations, fortran-ordered or non-native byte orderings.
Performance for other scenarios is preserved (except for very small
arrays).
- Division in numexpr is consistent now with Python/NumPy. Fixes #22
and #58.
- Constants like "2." or "2.0" must be evaluated as float, not
integer. Fixes #59.
- `evaluate()` function has received a new parameter `out` for storing
the result in already allocated arrays. This is very useful when
dealing with large arrays, and a allocating new space for keeping
the result is not acceptable. Closes #56.
- Maximum number of threads raised from 256 to 4096. Machines with a
higher number of cores will still be able to import numexpr, but
limited to 4096 (which is an absurdly high number already).
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0.7.4.1
These are the release notes for SymPy 0.7.4.1, which was released
on December 15, 2013.
This version of SymPy has been tested on Python 2.6, 2.7, 3.2, 3.3,
and PyPy.
This was a small bugfix release to fix an import issue on Windows
(https://github.com/sympy/sympy/issues/2681).
0.7.4
These are the release notes for SymPy 0.7.4, which was released on
December 9, 2013.
This version of SymPy has been tested on Python 2.6, 2.7, 3.2, 3.3,
and PyPy.
Major changes
Python 3
SymPy now uses a single code-base for Python 2 and Python 3.
Geometric Algebra
The internal representation of a multivector has been changes to
more fully use the inherent capabilities of SymPy. A multivector
is now represented by a linear combination of real commutative
SymPy expressions and a collection of non-commutative SymPy symbols.
Each non-commutative symbol represents a base in the geometric
algebra of an N-dimensional vector space. The total number of
non-commutative bases is 2**N - 1 (N of which are a basis for the
vector space) which when including scalars give a dimension for
the geometric algebra of 2**N. The different products of geometric
algebra are implemented as functions that take pairs of bases
symbols and return a multivector for each pair of bases.
The LaTeX printing module for multivectors has been rewritten to
simply extend the existing sympy LaTeX printing module and the
sympy LaTeX module is now used to print the bases coefficients in
the multivector representation instead of writing an entire LaTeX
printing module from scratch.
The main change in the geometric algebra module from the viewpoint
of the user is the inteface for the gradient operator and the
implementation of vector manifolds:
The gradient operator is now implemented as a special vector (the
user can name it grad if they wish) so the if F is a multivector
field all the operations of grad on F can be written grad*F, F*grad,
grad^F, F^grad, grad|F, F|grad, grad<F, F<grad, grad>F, and F>grad
where **, ^, |, <, and > are the geometric product, outer product,
inner product, left contraction, and right contraction, respectively.
The vector manifold is defined as a parametric vector field in an
embedding vector space. For example a surface in a 3-dimensional
space would be a vector field as a function of two parameters. Then
multivector fields can be defined on the manifold. The operations
available to be performed on these fields are directional derivative,
gradient, and projection. The weak point of the current manifold
representation is that all fields on the manifold are represented
in terms of the bases of the embedding vector space.
Classical Cryptography
Implements:
Affine ciphers
Vigenere ciphers
Bifid ciphers
Hill ciphers
RSA and "kid RSA"
linear feedback shift registers.
Common Subexpression Elimination (CSE)
Major changes have been done in cse internals resulting in a big
speedup for larger expressions. Some changes reflect on the user
side:
Adds and Muls are now recursively matched ([w*x, w*x*y, w*x*y*z]
ǹow turns into [(x0, w*x), (x1, x0*y)], [x0, x1, x1*z])
CSE is now not performed on the non-commutative parts of
multiplications (it avoids some bugs).
Pre and post optimizations are not performed by default anymore.
The optimizations parameter still exists and optimizations='basic'
can be used to apply previous default optimizations. These
optimizations could really slow down cse on larger expressions
and are no guarantee of better results.
An order parameter has been introduced to control whether Adds
and Muls terms are ordered independently of hashing implementation.
The default order='canonical' will independently order the
terms. order='none' will not do any ordering (hashes order is
used) and will represent a major performance improvement for
really huge expressions.
In general, the output of cse will be slightly different from
the previous implementation.
Diophantine Equation Module
This is a new addition to SymPy as a result of a GSoC project. With
the current release, following five types of equations are supported.
Linear Diophantine equation, a_{1}x_{1} + a_{2}x_{2} + . . .
+ a_{n}x_{n} = b
General binary quadratic equation, ax^2 + bxy + cy^2 + dx + ey
+ f = 0
Homogeneous ternary quadratic equation, ax^2 + by^2 + cz^2 +
dxy + eyz + fzx = 0
Extended Pythagorean equation, a_{1}x_{1}^2 + a_{2}x_{2}^2 +
. . . + a_{n}x_{n}^2 = a_{n+1}x_{n+1}^2
General sum of squares, x_{1}^2 + x_{2}^2 + . . . + x_{n}^2 =
k
Unification of Sum, Product, and Integral classes
A new superclass has been introduced to unify the treatments of
indexed expressions, such as Sum, Product, and Integral. This
enforced common behavior accross the objects, and provides more
robust support for a number of operations. For example, Sums and
Integrals can now be factored or expanded. S.subs() can be used to
substitute for expressions inside a Sum/Integral/Product that are
independent of the index variables, including unknown functions,
for instance, Integral(f(x), (x, 1, 3)).subs(f(x), x**2), while
Sum.change_index() or Integral.transform are now used for other
changes of summation or integration variables. Support for finite
and infinite sequence products has also been restored.
In addition there were a number of fixes to the evaluation of nested
sums and sums involving Kronecker delta functions, see issue 3924
and issue 3987.
Series
The Order object used to represent the growth of a function in
series expansions as a variable tend to zero can now also
represent growth as a variable tend to infinity. This also
fixed a number of issues with limits. See issue 234 and issue
2670.
Division by Order is disallowed, see issue 1756.
Addition of Order object is now commutative, see issue 1180.
Physics
Initial work on gamma matrices, depending on the tensor module.
Logic
New objects true and false which are Basic versions of the
Python builtins True and False.
Other
Arbitrary comparisons between expressions (like x < y) no longer
have a boolean truth value. This means code like if x < y or
sorted(exprs) will raise TypeError if x < y is symbolic. A
typical fix of the former is if (x < y) is True (assuming the
if block should be skipped if x < y is symbolic), and of the
latter is sorted(exprs, key=default_sort_key), which will order
the expressions in an arbitrary, but consistent way, even across
platforms and Python versions. See issue 2832.
Arbitrary comparisons between complex numbers (for example, I
> 1) now raise TypeError as well (see PR #2510).
minpoly now works with algebraic functions, like minpoly(sqrt(x)
+ sqrt(x + 1), y).
exp can now act on any matrix, even those which are not
diagonalizable. It is also more comfortable to call it, exp(m)
instead of just m.exp(), as was required previously.
sympify now has an option evaluate=False that will not
automatically simplify expressions like x+x.
Deep processing of cancel and simplify functions. simplify is
now recursive through the expression tree. See e.g. issue 3923.
Improved the modularity of the codebase for potential subclasses,
see issue 3652.
The SymPy cheatsheet was cleaned up.
Backwards compatibility breaks and deprecations
Removed deprecated Real class and is_Real property of Basic,
see issue 1721.
Removed deprecated 'each_char' option for symbols(), see issue
1919.
The viewer="StringIO" option to preview() has been deprecated.
Use viewer="BytesIO" instead. See issue 3984.
TransformationSet has been renamed to ImageSet. Added public
facing imageset function.
0.7.3
These are the release notes for SymPy 0.7.3, which was released on
July 13, 2013. It can be downloaded from
https://github.com/sympy/sympy/releases/tag/sympy-0.7.3.
This version of SymPy has been tested on Python 2.5, 2.6, 2.7, 3.2,
3.3, and PyPy.
Major changes
Integration
This release includes Risch integration algorithm from Aaron Meurer's
2010 Google Summer of Code project. This makes integrate much more
powerful and much faster for the supported functions. The algorithm
is called automatically from integrate(). For now, only transcendental
elementary functions containing exp or log are supported. To access
the algorithm directly, use integrate(expr, x, risch=True). The
algorithm has the ability to prove that integrals are nonelementary.
To determine if a function is nonelementary, integrate using
risch=True. If the resulting Integral class is an instance of
NonElementaryIntegral, then it is not elementary (otherwise, that
part of the algorithm has just not been implemented yet).
Here is an example integral that could not be computed before:
>>> f = x*(x + 1)*(2*x*(x - (2*x**3 + 2*x**2 + x + 1)*log(x +
1))*exp(3*x**2) + (x**2*exp(2*x**2) - log(x + 1)**2)**2)/((x +
1)*log(x + 1)**2 - (x**3 + x**2)*exp(2*x**2))**2
>>> integrate(f, x)
x + x*exp(x**2)*log(x + 1)/(x**2*exp(2*x**2) - log(x + 1)**2) -
log(x + 1) - log(exp(x**2) - log(x + 1)/x)/2 + log(exp(x**2) +
log(x + 1)/x)/2
ODE
Built basic infrastructure of the PDE module (PR #1970)
Theano Interaction
SymPy expressions can now be translated into Theano expressions
for numeric evaluation. This includes most standard scalar operations
(e.g. sin, exp, gamma, but not beta or MeijerG) and matrices. This
system generally outperforms lambdify and autowrap but does require
Theano to be installed.
Matrix Expressions
Assumptions
Matrix expressions now support inference using the new assumptions
system. New predicates include invertible, symmetric, positive_definite,
orthogonal, ....
New Operators
New operators include Adjoint, HadamardProduct, Determinant,
MatrixSlice, DFT. Also, preliminary support exists for factorizations
like SVD and LU.
Context manager for New Assumptions
Added the with assuming(*facts) context manager for new assumptions.
See blogpost
Backwards compatibility breaks and deprecations
This is the last version of SymPy to support Python 2.5.
The IPython extension, i.e., %load_ext
sympy.interactive.ipythonprinting is deprecated. Use from sympy
import init_printing; init_printing() instead. See issue 3914.
The viewer='file' option to preview without a file name is
deprecated. Use filename='name' in addition to viewer='file'.
See issue 3919.
The deprecated syntax Symbol('x', dummy=True), which had been
deprecated since 0.7.0, has been removed. Use Dummy('x') or
symbols('x', cls=Dummy) instead. See issue 3378.
The deprecated Expr methods as_coeff_terms and as_coeff_factors,
which have been deprecated in favor of as_coeff_mul and
as_coeff_add, respectively (see also as_coeff_Mul and as_coeff_Add),
were removed. The methods had been deprecated since SymPy 0.7.0.
See issue 3377.
The spherical harmonics have been completely rewritten. See PR
#1510.
Minor changes
Solvers
Added enhancements and improved the methods of solving exact
differential equation ((PR #1955)) and ((PR #1823))
Support for differential equations with linear coefficients
and those that can be reduced to separable and linear form ((PR
#1940), (PR #1864), (PR #1883))
Support for first order linear general PDE's with constant
coefficients ((PR #2109))
Return all found independent solutions for underdetermined
systems.
Handle recursive problems for which y(0) = 0.
Handle matrix equations.
Integration
integrate will split out integrals into Piecewise expressions
when conditions must hold for the answer to be true. For example,
integrate(x**n, x) now gives Piecewise((log(x), Eq(n, -1),
(x**(n + 1)/(n + 1), True)) (previously it just gave x**(n +
1)/(n + 1))
Calculate Gauss-Legendre and Gauss-Laguerre points and weights
(PR #1497)
Various new error and inverse error functions (PR #1703)
Use in heurisch for more symmetric and nicer results
Gruntz for expintegrals and all new erf*
Li, li logarithmic integrals (PR #1708)
Integration of li/Li by heurisch (PR #1712)
elliptic integrals, complete and incomplete
Integration of complete elliptic integrals by meijerg
Integration of Piecewise with symbolic conditions.
Fixed many wrong results of DiracDelta integrals.
Logic
Addition of SOPform and POSform functions to sympy.logic to
generate boolean expressions from truth tables.
Addition of simplify_logic function and enabling simplify() to
reduce logic expressions to their simplest forms.
Addition of bool_equals function to check equality of boolean
expressions and return a mapping of variables from one expr to
other that leads to the equality.
Addition of disjunctive normal form methods - to_dnf, is_dnf
Others
gmpy version 2 is now supported
Added is_algebraic_expr() method (PR #2176)
Many improvements to the handling of noncommutative symbols:
Better support in simplification functions, e.g. factor,
trigsimp
Better integration with Order()
Better pattern matching
Improved pattern matching including matching the identity.
normalizes Jacobi polynomials
Quadrature rules for orthogonal polynomials in arbitrary
precision (hermite, laguerre, legendre, gen_legendre, jacobi)
summation of harmonic numbers
Many improvements of the polygamma functions
evaluation at special arguments
Connections to harmonic numbers
structured full partial fraction decomposition (mainly interesting
for developers)
besselsimp improvements
Karr summation convention
New spherical harmonics
improved minimal_polynomial using composition of algebraic
numbers (PR #2038)
faster integer polynomial factorization (PR #2148)
Euler-Descartes method for quartic equations (PR #1947)
algebraic operations on tensors (PR #1700)
tensor canonicalization (PR #1644)
Handle the simplification of summations and products over a
KroneckerDelta.
Implemented LaTeX printing of DiracDelta, Heaviside, KroneckerDelta
and LeviCivita, also many Matrix expressions.
Improved LaTeX printing of fractions, Mul in general.
IPython integration and printing issues have been ironed out.
Stats now supports discrete distributions (e.g. Poisson) by
relying on Summation objects
Added DOT printing for visualization of expression trees
Added information about solvability and nilpotency of named
groups.
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PyEphem provides scientific-grade astronomical computations for the Python
programming language. Given a date and location on the Earth's surface, it can
compute the positions of the Sun and Moon, of the planets and their moons, and
of any asteroids, comets, or earth satellites whose orbital elements the user
can provide. Additional functions are provided to compute the angular
separation between two objects in the sky, to determine the constellation in
which an object lies, and to find the times at which an object rises, transits,
and sets on a particular day.
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Mark as not for python-3.x.
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Release 2.3.0
=============
New Features
------------
:mod:`rpy2.rinterface`:
- C-level API, allowing other C-level modules to make use of utilities
without going through the Python level. The exact definition of
the API is not yet fixed. For now there is
PyRinteractive_IsInitialized() to assess whether R was initialized
(through :mod:`rpy2.rinterface` or not).
- C-module _rpy_device, allowing one to implement R graphical devices
in Python [(very) experimental]
- Tracking of R objects kept protected from garbage collection by rpy2
is now possible.
- New method :meth:`Sexp.rid` to return the identifier of the R object
represented by a Python/rpy2 object
:mod:`rpy2.rinteractive`:
- Dynamic build of Python docstrings out of the R manual pages
:mod:`rpy2.robjects.help`:
- Build dynamic help
:mod:`rpy2.robjects.packages:
- Build anonymous R packages from strings
- When using :func:`importr`, the datasets are added as an attribute
:attr:`data`, itself an instance of a new class :class:`PackageData`.
It no longer possible to access datasets are regular objects from
a code package (because of changes in R), and the new system is
more robust against quirks.
Changes
-------
:mod:`rpy2.rinterface`:
- :attr:`SexpClosure.env` to replace the method `closureenv`.
Release 2.2.6
=============
Bugs fixed
----------
- Newest R-2.15 and ggplot2 0.9 broke the ggplot2 interaface
in :mod:`rpy2.robjects.lib.ggplot2`
Release 2.2.5
=============
Bugs fixed
----------
- install process: Library location for some of the R installations
- should compile on win32 (thanks to a patch from Evgeny Cherkashin),
a work to a limited extend
Release 2.2.4
=============
Bugs fixed
----------
- Memory leak when creating R vectors from Python (issue #82)
Release 2.2.3
=============
Bugs fixed
----------
- Dynamic construction of S4 classes was looking for R help as 'class.<class>'
rather than '<class>-class'
- The cleanup of temporary directories created by R was not happening if
the Python process terminated without calline :func:`rpy2.rinterface.endr()`
(issue #68, and proof-of-principle fix by chrish42)
Release 2.2.2
=============
Bugs fixed
----------
- With the robjects layer, repr() on a list containing non-vector elements
was failing
Release 2.2.1
=============
Bugs fixed
----------
- MANIFEST.in was missing from MANIFEST.in, required with Python 3
Release 2.2.0
=============
New Features
------------
- Support for Python 3, and for some of its features ported to Python 2.7
:mod:`rpy2.robjects`:
- :meth:`Environment.keys` to list the keys
- classes :class:`robjects.vectors.POSIXlt` and
:class:`robjects.vectors.POSIXlt` to represent vectors of R
dates/time
- :func:`packages.get_packagepath` to get the path to an R package
- module :mod:`rpy2.robjects.help` to expose the R help system to Python
- Metaclass utilities in :mod:`rpy2.robjects.methods`, allowing to reflect
automatically R S4 classes as Python classes.
- :meth:`rpy2.robjects.vectors.FactorVector.iter_labels` to iterate over the labels
- :class:`rpy2.robjects.vectors.ListVector` to represent R lists.
- Constructor for :class:`rpy2.robjects.vectors.ListVector` and
:class:`rpy2.robjects.vectors.DataFrame` accept any iterable at the condition
that the elements iterated through also valid subscripts for it (e.g., given
an iterable v, the following is valid:
.. code-block:: python
x[k] for x in v
:mod:`rpy2.rinterface`:
- :data:`NA_Complex` and :class:`NAComplexType` for missing complex values.
- :class:`SexpExtPtr` to represent R objects of type EXTPTR (external pointers).
- :func:`rpy2.rinterface.parse` to parse a string a R code
- :func:`rpy2.rinterface.rternalise` to wrap Python function as :class:`SexpClosure` that can
be called by R just as it was a function of its own.
- :class:`rpy2.rinterface.RNULLType` for R's C-level NULL value and
:class:`rpy2.rinterface.UnboundValueType` for R's C-level R_UnboundValue
(both singletons).
- :meth:`rinterface.SexpVector.index`, of similar behaviour to :meth:`list.index`.
- :meth:`rpy2.rinterface.Sexp.list_attrs` to list the names of all R attributes
for a given object.
- :class:`rpy2.rinterface.ByteSexpVector` to represent R 'raw' vectors.
- constant `R_LEN_T_MAX` to store what is the maximum length for a vector in R.
- tuple `R_VERSION_BUILD` to store the version of R rpy2 was built against
- getter :attr:`Sexp.rclass` to return the R class associated with an object
:mod:`rpy2.rlike`:
- :class:`container.OrdDict` get proper methods :meth:`keys` and `get`
:mod:`rpy2.interactive`:
- A new sub-package to provide utilities for interactive work, either for
handling R interactive events or use Python for interactive programming
(as often done with the R console)
Changes
-------
:mod:`rpy2.robjects`:
- NA_bool, NA_real, NA_integer, NA_character and NA_complex are now
deprecated (and removed).
NA_Logical, NA_Real, NA_Integer, NA_Character, NA_Complex should be used.
- :class:`rpy2.robjects.packages.Package` now inherits from :class:`types.ModuleType`
- classes representing R vector also inherit their type-specific
rinterface-level counterpart.
- Importing the :class:`rpy2.robjects.numpy2ri` is no longer sufficient
to active the conversion. Explicit activation is now needed; the function
`activate` can do that.
:mod:`rpy2.rinterface`:
- :class:`IntSexpVector`, :class:`FloatSexpVector`,
:class:`StrSexpVector`, :class:`BoolSexpVector`, :class:`ComplexSexpVector`
are now defined at the C level, improving performances
and memory footprint whenever a lot of instances are created.
Bugs fixed
----------
- Better and more explicit detection system for needed libraries when
compiling rpy2 (ported to release 2.1.6)
- Long-standing issue with readline fixed (issue #10)
Release 2.1.9
=============
Bugs fixed
----------
- The R class in rpy2.robjects is now truly a singleton
- When using numpy 1.5 and Python >= 2.7, the exposed buffer for R numerical (double)
vectors or arrays was wrong.
Release 2.1.8
=============
Bugs fixed
----------
- Fixed issue with R arrays with more than 2 dimensions and numpy arrays
(issue #47 - backported from the branch 2.2.x).
Release 2.1.7
=============
Bugs fixed
----------
- More fixes for the automated detection of include and libraries at build time.
Release 2.1.6
=============
Bugs fixed
----------
- Further fixes in the automatic detection of includes and libraries
needed to compile rpy2 against R. The detection code has
been refactored (backport from the 2.2.x branch)
Release 2.1.5
=============
Bugs fixed
----------
- fixes the automatic detection of R_HOME/lib during building/compiling
when R_HOME/lib is not in lib/ (issue #54)
Release 2.1.4
=============
New features
------------
- :mod:`rpy2.robjects.lib.ggplot2` now has the functions :func:`limits`,
:func:`xlim`, :func:`ylim` exposed (patch contributed anonymously)
Bugs fixed
----------
- Install script when the BLAS library used by R is specified as a library
file (patch by Michael Kuhn)
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changes:
-additions to builtins and library
-minor fixes
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libraries when previously preferring libraries from pkgsrc causes conflicts.
Fixes build on SmartOS where the platform /usr/lib/libgcc_s.so.1 for legacy
applications conflicts with GCC libraries from pkgsrc.
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Gnumeric 1.12.9
Jean
* Implement double click for graph sheets. [#712216]
Morten:
* Minor improvement to history dialog.
* Fix drop-down sizing (gtk+ regression). [#710749]
* Improve accuracy of R.QCAUCHY.
* Acquire more special function test cases.
* Improve accuracy of R.QGAMMA and thus R.QCHISQ.
* Improve accuracy of R.QBETA, R.QF, R.QTUKEY, R.QSNORM, and R.QST.
* Improve accuracy of COMBIN, PERMUT, POCHHAMMER, FACT, GAMMA.
* Improve accuracy of bessel functions with large non-integer alpha.
* Improve accuracy of ACOTH.
* Fix fuzzed file problems. [#708091] [#712662] [#712685] [#712700]
[#712708] [#712772] [#712788] [#712731] [#715003]
* Restore sheet reordering by drag.
* Fix BETA on win32.
* Fix win32 registry initialization.
* Fix win32 gdk-pixbuf install heisen-crash.
* Incorporate new tests from crlibm.
* New functions SINPI and COSPI.
* Improve accuracy of SIN/COS/TAN on win32.
* Work around GTK+ ABI break. [Redhat #1033827]
Xabier Rodríguez Calvar:
* Fix dialog button order. [#710378]
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BROKEN and explicitly scheduled to be removed after 2013Q4.
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Calculator.cpp, but it was enough to push it over 2GB. So disable
optimisation for now.
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This is a major release from 0.11.0 and includes several new features
and enhancements along with a large number of bug fixes.
Highlites include a consistent I/O API naming scheme, routines to read
html, write multi-indexes to csv files, read & write STATA data files,
read & write JSON format files, Python 3 support for HDFStore, filtering
of groupby expressions via filter, and a revamped replace routine that
accepts regular expressions.
For detailed changes see:
http://pandas.pydata.org/pandas-docs/stable/whatsnew.html
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Bump PKGREVISION for runtime dependency pattern changed packages.
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### 0.9.6 / 02.12.2013
Author: Malcolm Blyth <trashbat@co.ck>
Date: Mon Dec 2 11:44:25 2013 +0000
* Fixed issue whereby object author being null caused a gross failure.
* Now returns object author as an empty string
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### 0.9.5 / 20.11.2013
Author: Malcolm Blyth <trashbat@co.ck>
Date: Tue Nov 19 15:14:31 2013 +0000
* Bumped revision
* Fixed author stringname error (damn this 1 based counting)
* Updating integration test to check for comments contained within the cells.
* Checking also for multiple comments in a sheet
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