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Upstream changes:
1.34 2017-04-07
- Don't pack .*~ temporary files.
- Add MANIFEST.SKIP .
1.33 2017-04-07
- Hopefully fix the tests with "." gone from @INC :
- http://www.cpantesters.org/cpan/report/873193f8-15df-11e7-a7e6-820fe85ef7bd
- Thanks to DCOLLINS for the report.
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No functional change since the previous release 3.98-1.5.
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* Guard use of rl_catch_signals variable with "#if HAVE_RL_CATCH_SIGNALS".
Add comment in patch/patch-aa quote from last commit message.
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- Fixed bugs in numeral systems.
- Fixed bugs related to infinity (Inf).
- Fixed bugs related to Not a Number (NaN).
- Updated and cleanup documentation.
- Cleaned up code structure.
- OpenLibm support.
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Detailed changes are not known and not clear (besides regular cleanup).
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string, otherwise the result is somewhat random. Bump revision again.
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mirror.
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NumPy 1.12.1 supports Python 2.7 and 3.4 - 3.6 and fixes bugs and regressions
found in NumPy 1.12.0. In particular, the regression in f2py constant parsing
is fixed.
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* Fix license information in gemspec.
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2.1.0.2
- Enhancements
* Support for assigning Ruby Complex types to GSL::Matrix::Complex. (@v0dro)
* Support for 2D interpolation by exposing GSLs interp2d and
spline2d. (@v0dro)
* Support for Ruby 2.4. (@badlamer)
- Fixes
* Fix NArray superclass mismatch problem. (@v0dro)
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Ensure data cache value array is aligned adequately
Data caches are used to store pointers and other potentially long
values. Make sure that the position of the values portion of the cache
is aligned to a suitable address. Fixes a bus error on sparc64 machines.
Building nickle on arm64 now, change package names
built .deb and .rpm files are now amd64 instead of i386
Update to version 2.78
Also depend on bison and flex
newer version of flex doesn't have yyunput
This line was just removing a warning about yyunput unused; newer
versions of flex don't even have that symbol anymore. Better to have a
warning than fail to compile.
Adapt tests to new automake requirements
Automake now has a separate variable for the program to run the test
scripts with, and breaks if you try to embed that in the
TESTS_ENVIRONMENT variable, which used to be how this was done.
Use 'G' format for elements when printing arrays in 'g' format
This restricts array printing to just recurse one level.
When using pointer as hash, first cast to intptr_t
This avoids a compiler warning when pointers are not the same size as
HashValues.
Initialize 'replace' in NewTypedBox
When left uninitialized, undefined results will occur. This caused a
test failure on MIPS when being built with PIE support.
Debian bug 857840.
Reported-by: James Cowgill <jcowgill@debian.org>
Open quote character is a single char, not a string
When checking to see if a string needs to be dequoted, check the first
character of the string against the quote character, rather than
checking the whole string.
Probably using strings for the quote markers wasn't the best API
choice as this would have been caught by typechecking had the quote
characters been an int instead.
Define release date in configure.ac and use that instead of build date
This avoids encoding the current date into the resulting output so
that it can be reproduced.
Add JSON input/output code
Reverse data written in linked FileChains
FileChains are linked in newest-in order, so they need to be written
last-first.
Add is_hash primitive
Checks whether a value is a hash
Abort karatsuba multiply in more places
removed gratuitous -O2 from Makefile.am to let CFLAGS handle it
Added a lightly-optimized choose(n, k) function to math.5c.
The lack of a choose operator has continually bugged me;
I've constantly rewritten it "the bad way". This is a
lightly optimized version of that function that seems to
handle most edge cases reasonably. It has only been tested a
little bit.
added check mode to sudoku solver
cleaned up a bunch of sudoku solver stuff
added edge cache to sudoku example
tutorial: Close a couple of SGML tags
nsgmls found a couple of unclosed tags which may make some versions
of docbook tools unhappy.
Fix release docs to use git log instead of git-log
git-log disappeared a long time ago
actually added Sudoku example
added Sudoku generator example
added sudoku example
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octave is using gnulib for portability, but has an additional wrapper
around it. unfortunately that means that this type signature is no longer
portable. netbsd doesn't have struct tm_zone, others do.
I failed to use gnulib to provide struct tm_zone, using an OS-specific macro
as an ugly hack.
reported by hans
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many new features, numerous bug-fixes, improved test coverage and
better documentation. There have been a number of deprecations and
API changes in this release, which are documented below. All users
are encouraged to upgrade to this release, as there are a large number
of bug-fixes and optimizations. Moreover, our development attention
will now shift to bug-fix releases on the 0.19.x branch, and on adding
new features on the master branch.
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Upstream changes:
Changes in Version 1.7-14
o Several convenience interfaces to read.zoo() have been added:
read.table.zoo(), read.csv.zoo(), read.csv2.zoo(), read.delim.zoo(),
read.delim2.zoo(). All of these first call the corresponding read.*()
function to read the data from a text file (with the respective default
settings) and subsequently call read.zoo() to turn the data into
a zoo series.
o na.approx.default() did not properly process the "maxgap" argument
if y did not contain any NAs but NAs were only created implicitly
by xout being different from x (pointed out by Stefan Metzger).
A suitable fix has been added that merges x and xout first.
o aggregate.zoo() and rollapply.zoo() gained the argument coredata=TRUE
which can control whether only the coredata is passed to each subset
(previous behavior) or the full zoo series.
o The "its" package has been archived on CRAN and hence removed from
the list of zoo's suggested packages. However, various methods for
objects of class "its" continue to be available in zoo in case someone
still uses the legacy code.
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Upstream changes:
CHANGES IN R 3.3.3
NEW FEATURES
Changes when redirection of a http:// URL to a https:// URL is encountered:
The internal methods of download.file() and url() now report that they cannot follow this (rather than failing silently).
(Unix-alike) download.file(method = "auto") (the default) re-tries with method = "libcurl".
(Unix-alike) url(method = "default") with an explicit open argument re-tries with method = "libcurl". This covers many of the usages, e.g. readLines() with a URL argument.
INSTALLATION on a UNIX-ALIKE
The configure check for the zlib version is now robust to versions longer than 5 characters, including 1.2.11.
UTILITIES
Environmental variable _R_CHECK_TESTS_NLINES_ controls how R CMD check reports failing tests (see §8 of the ‘R Internals’ manual).
DEPRECATED AND DEFUNCT
(C-level Native routine registration.) The undocumented styles field of the components of R_CMethodDef and R_FortranMethodDef is deprecated.
BUG FIXES
vapply(x, *) now works with long vectors x. (PR#17174)
isS3method("is.na.data.frame") and similar are correct now. (PR#17171)
grepRaw(<long>, <short>, fixed = TRUE) now works, thanks to a patch by Mikko Korpela. (PR#17132)
Package installation into a library where the package exists via symbolic link now should work wherever Sys.readlink() works, resolving PR#16725.
"Cincinnati" was missing an "n" in the precip dataset.
Fix buffer overflow vulnerability in pdf() when loading an encoding file. Reported by Talos (TALOS-2016-0227).
getDLLRegisteredRoutines() now produces its warning correctly when multiple DLLs match, thanks to Matt Dowle's PR#17184.
Sys.timezone() now returns non-NA also on platforms such as Ubuntu 14.04.5 LTS, thanks to Mikko Korpela's PR#17186.
format(x) for an illegal "POSIXlt" object x no longer segfaults.
methods(f) now also works for f "(" or "{".
(Windows only) dir.create() did not check the length of the path to create, and so could overflow a buffer and crash R. (PR#17206)
On some systems, very small hexadecimal numbers in hex notation would underflow to zero. (PR#17199)
pmin() and pmax() now work again for ordered factors and 0-length S3 classed objects, thanks to Suharto Anggono's PR#17195 and PR#17200.
bug.report() did not do any validity checking on a package's BugReports field. It now ignores an empty field, removes leading whitespace and only attempts to open http:// and https:// URLs, falling back to emailing the maintainer.
Bandwidth selectors bw.ucv() and bw.SJ() gave incorrect answers or incorrectly reported an error (because of integer overflow) for inputs longer than 46341. Similarly for bw.bcv() at length 5793.
Another possible integer overflow is checked and may result in an error report (rather than an incorrect result) for much longer inputs (millions for a smooth distribution).
findMethod() failed if the active signature had expanded beyond what a particular package used. (Example with packages XR and XRJulia on CRAN.)
qbeta() underflowed too early in some very asymmetric cases. (PR#17178)
R CMD Rd2pdf had problems with packages with non-ASCII titles in ‘.Rd’ files (usually the titles were omitted).
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Upstream changes:
0.70 - 02 Mar 2017, H.Merijn Brand
* Add label functionality to ::Sheet
* Add ->column and ->cellcolumn for ::Sheet
* Add col2label sub/method
* Sanitize xls2csv export filenames
* Fix sorting in xlscat for un-aligned columns
* It's 2017
* Be overly verbose about maxrow and maxcol being 1-based (RT#120476)
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Up the version to 0.12.2.
Update the CHANGELOG.
Fix lexer tokenizer to get R1C1 addresses properly parsed.
For now, a lexer name that contains a '[' and ']' pair can have any
characters in-between, in order to have e.g. 'R[-5]C' properly
parsed as a name.
Fix a range address parsing error.
It previously failed to parse 'R[-5]C:R[-1]C'.
Add a test case that ixion currently fails to parse.
Export these hash::operator(...) symbols.
add CI config
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It supports both python 2 and 3 nowadays.
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While here, drop maintainership - I haven't used the thing in years,
and definitely not since its conversion to a CMake build (of which I
know nothing).
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as likely intended. Bump revision.
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-----------------------------------------
- 1.14 G7UM6iSk Sat Jul 30 06:44:28:46 -0500 2016
* synchronized README and Changes to updated POD
- 1.12 G7OMKBCn Sun Jul 24 20:11:12:49 -0500 2016
* added digit set 'b96' as a reordering of 'asc'
- 1.10 G7OMF3ZT Sun Jul 24 15:03:35:29 -0500 2016
* added new digit sets from Math::Base::Convert
* switched all old hex() to distinct new heX() and updated POD to
reflect
* fixed META license to match POD and resolve issue:
<HTTPS://RT.CPAN.Org/Public/Bug/Display.html?id=60122> (Thanks again
xenoterracide.)
* removed PT from VERSION to resolve issue:
<HTTPS://RT.CPAN.Org/Public/Bug/Display.html?id=60275> (Thanks
Alexandr.)
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----------------------------------------
0.69 - 02 Dec 2016, H.Merijn Brand
* Several OO fixes, more tests, more docs
0.68 - 29 Nov 2016, H.Merijn Brand
* List non-core modules/version used on very verbose in xlscat
* Option to export all sheets in a spreadsheet to CSV (UTF-8 only)
* Add OO interface
* Feature: add new spreadsheets to existing book (even of different types)
0.67 - 17 Jun 2016, H.Merijn Brand
* CPANTESTERS showed that some versions really messed op numeric/percentage
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---------------------------------------
Changes in v2.13 - Jonathan "Duke" Leto
September 2015
--------------------------
* Fix bug where as_list() did not work correctly for non-square matrices.
Reported by Elia Liitiäinen in RT #116968
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-------------------------------------
2.14 2017-02-01 Shlomif
- Hopefully fix the GPG signature.
- https://rt.cpan.org/Ticket/Display.html?id=120062
- Thanks to Pavel Mateja for the report.
2.13 2016-11-18 Shlomif
- Fix the tests on older libgmps.
- See https://rt.cpan.org/Ticket/Display.html?id=118816
- Thanks to Hugo van der Sanden for the patches.
- Refactoring of the test suite.
2.12 2016-11-09 Shlomif
- Add support for testing methods that return lists.
- Add broot, brootrem, bsqrtrem, is_perfect_power, is_perfect_square
- Thanks to Hugo van der Sanden for the patches
- https://rt.cpan.org/Ticket/Display.html?id=118677
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-----------------------------------------
2017-02-05 v1.6004 pjacklam
* Fix typos in POD.
* Update link in SUPPORT section.
* Minor improvements to the documentation (POD).
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---------------------------------------
2017-02-10 v1.999809 pjacklam
* When a new method is added to Math::BigInt or Math::BigFloat, and this new
method requires a new backend library method, die with a suitable error
message if the installed backend library does not support this new method.
The error message says that the method requires a newer version of the
backend library.
* Fix typos in Math::BigFloat and Math::BigInt.
* Add bfib() and blucas() to Math::BigInt. They return Fibonacci and Lucas
numbers, respectively. The actual computation of the numbers is done by the
backend library. Documented both methods in POD. Add test files bfib-mbi.t
and blucas-mbi.t.
* Add _fib() and _lucas() to Math::BigInt::Lib. They return Fibonacci and
Lucas numbers, respectively. Document both methods in POD. Add test files
author-lib-arithmetic-unary-_fib.t and author-lib-arithmetic-unary-_lucas.t.
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-------------------------------------
From: https://cran.r-project.org/web/packages/quantreg/ChangeLog
5.21
1. Allowed ... to be passed in plot.summary.crqs.
2. Fixed namespace bug in dynrq, and added an Edgeworth wacky AR(1) example
to dynrq.Rd.
3. Fixed rqss bug about length of residual vector
5.23
1. Added a "cluster" option for summary.rq() when using the bootstrap option
this option implements the wild gradient bootstrap method of Hagemann (2016).
See boot.rq for further details. [Needs further testing.]
2. Added a sfn method for rq models, and in the process modified somewhat
the return object for both rq.fit.sfn and rq.fit.sfnc so that it is compatible
with other rq.fit objects.
5.24
1. Reverted to the old fortran versions of srqfn.f and srqfnc.f, ie removed
Martin Maechler's C versions, in preparation for some new sparse forms of the
bootstrapping functions. Made a couple of slight changes in the return object
for these functions.
2. Fixed a sihttps://cran.r-project.org/web/packages/quantreg/ChangeLoggn error in the cluster option pointed out in an email of
Andreas on May 9 2016.
3. Added jackknife option to boot.rq for the proposal of Portnoy.
4. Adapted boot.rq and friends so that when there are multiple taus
summary.rqs reuses the same randomization for each of the taus to facilitate
joint inference with the bootstrap realizations.
5.25
1. When method = "sfn" store model$x in sparse form. Then when
bootstrapping use method = "sfn" rather than the usual "br" method.
2. When using the "cluster" option for bootstrap allow "sfn" as above.
3. When na.action = "omit" and length(fit$na.action) > 0, then omit
these values from the strata indicator "cluster". This would seem to
help bring together the survey package and quantreg as desired by
email correspondance with donald706.
5.26
1. Fixed long line per Kurt's suggestion.
2. Added some comments about method "sfn" in the man page for rq.
5.27
1. removed lines that cat'd taus from rqprocess in the khmal.R
2. fixed environment problem in nlrq, according to suggestion of
Vaidotas Zemlys-Balevicius email August 9 2016.
5.28
1. Cleaned up the fortran source a bit in accordance with Kurt's mandate
of late August 2016. There are still some offensive items mainly in crq.f
that should be dealt with, but I wasn't able to dig into this at the moment.
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Since arpack installs a dynamic library, its BUILDLINK_DEPMETHOD
shouldn't be set to "build" by default.
Bump PKGREVISION of octave for its runtime dependency change.
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Otherwise, the library refers to a nonexistent lib in /usr/lib on Darwin.
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Features a case sensitive command line interface, internal IEEE 754
calculations with 15 significant digits, calculations with real and
complex numbers, variables and user defined functions, logarithmic
and exponential functions, trigonometric and hyperbolic function
and selected mathematical constants and rounding functions.
Packaged by Carsten Larsen via PR pkg/51922
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* Linear Least Squares / Minimum Norm solution
* Symmetric-indefinite Factorization: Aasen’s tridiagonalization
* Symmetric-indefinite Factorization: New storage format for L factor in Rook Pivoting and Bunch Kaufman of LDLT
* Symmetric eigenvalue problem: Two-stage algorithm for reduction to tridiagonal form
* Improved Complex Jacobi SVD
* LAPACKE interfaces
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The following modules were renamed to simplify maintenance.
* src/prob.h RENAMED -> src/api/prob.h
* src/glpapi01.c RENAMED -> src/api/prob1.c
* src/glpapi02.c RENAMED -> src/api/prob2.c
* src/glpapi03.c RENAMED -> src/api/prob3.c
* src/glpapi04.c RENAMED -> src/api/prob4.c
* src/glpapi05.c RENAMED -> src/api/prob5.c
* src/env/tls.c
TLS (thread local storage class specifier) option was added;
see comments in tls.c for details.
* configure.ac, config.h.in
Test for TLS was added.
* src/env/tls.c
Dll support was added.
The following modules were changed to add __cdecl specifier
for functions passed to qsort (this is needed only on compiling
GLPK with MSVC to run under MS Windows).
* src/api/cpxbas.c
* src/cglib/cfg1.c
* src/cglib/gmigen.c
* src/cglib/mirgen.c
* src/misc/wclique1.c
* src/simplex/spychuzc.c
* src/glpios10.c
* src/glpios11.c
* examples/glpsol.c
* src/glpk.h, src/env/env.c
The API routine glp_version was changed to avoid initialization
of the GLPK environment. The new API routine glp_config was
added (but not documented yet).
* INSTALL
Description of the configure option '--with-zlib' was removed.
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more convenient.
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FFTW 3.3.6-pl1:
* Bugfix: FFTW 3.3.6 had the wrong libtool version number, and generated
shared libraries of the form libfftw3.so.2.6.6 instead of
libfftw3.so.3.*.
FFTW 3.3.6:
* The fftw_make_planner_thread_safe() API introduced in 3.3.5 didn't
work, and this 3.3.6 fixes it. Sorry about that.
* compilation fixes for IBM XLC
* compilation fixes for threads on Windows
* fix SIMD autodetection on amd64 when (_MSC_VER > 1500)
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FAILED (KNOWNFAIL=8, SKIP=9, errors=1, failures=1)
==========================
NumPy 1.12.0 Release Notes
==========================
This release supports Python 2.7 and 3.4 - 3.6.
Highlights
==========
The NumPy 1.12.0 release contains a large number of fixes and improvements, but
few that stand out above all others. That makes picking out the highlights
somewhat arbitrary but the following may be of particular interest or indicate
areas likely to have future consequences.
* Order of operations in ``np.einsum`` can now be optimized for large speed improvements.
* New ``signature`` argument to ``np.vectorize`` for vectorizing with core dimensions.
* The ``keepdims`` argument was added to many functions.
* New context manager for testing warnings
* Support for BLIS in numpy.distutils
* Much improved support for PyPy (not yet finished)
Dropped Support
===============
* Support for Python 2.6, 3.2, and 3.3 has been dropped.
Added Support
=============
* Support for PyPy 2.7 v5.6.0 has been added. While not complete (nditer
``updateifcopy`` is not supported yet), this is a milestone for PyPy's
C-API compatibility layer.
Build System Changes
====================
* Library order is preserved, instead of being reordered to match that of
the directories.
Deprecations
============
Assignment of ndarray object's ``data`` attribute
-------------------------------------------------
Assigning the 'data' attribute is an inherently unsafe operation as pointed
out in gh-7083. Such a capability will be removed in the future.
Unsafe int casting of the num attribute in ``linspace``
-------------------------------------------------------
``np.linspace`` now raises DeprecationWarning when num cannot be safely
interpreted as an integer.
Insufficient bit width parameter to ``binary_repr``
---------------------------------------------------
If a 'width' parameter is passed into ``binary_repr`` that is insufficient to
represent the number in base 2 (positive) or 2's complement (negative) form,
the function used to silently ignore the parameter and return a representation
using the minimal number of bits needed for the form in question. Such behavior
is now considered unsafe from a user perspective and will raise an error in the
future.
Future Changes
==============
* In 1.13 NAT will always compare False except for ``NAT != NAT``,
which will be True. In short, NAT will behave like NaN
* In 1.13 np.average will preserve subclasses, to match the behavior of most
other numpy functions such as np.mean. In particular, this means calls which
returned a scalar may return a 0-d subclass object instead.
Multiple-field manipulation of structured arrays
------------------------------------------------
In 1.13 the behavior of structured arrays involving multiple fields will change
in two ways:
First, indexing a structured array with multiple fields (eg,
``arr[['f1', 'f3']]``) will return a view into the original array in 1.13,
instead of a copy. Note the returned view will have extra padding bytes
corresponding to intervening fields in the original array, unlike the copy in
1.12, which will affect code such as ``arr[['f1', 'f3']].view(newdtype)``.
Second, for numpy versions 1.6 to 1.12 assignment between structured arrays
occurs "by field name": Fields in the destination array are set to the
identically-named field in the source array or to 0 if the source does not have
a field::
>>> a = np.array([(1,2),(3,4)], dtype=[('x', 'i4'), ('y', 'i4')])
>>> b = np.ones(2, dtype=[('z', 'i4'), ('y', 'i4'), ('x', 'i4')])
>>> b[:] = a
>>> b
array([(0, 2, 1), (0, 4, 3)],
dtype=[('z', '<i4'), ('y', '<i4'), ('x', '<i4')])
In 1.13 assignment will instead occur "by position": The Nth field of the
destination will be set to the Nth field of the source regardless of field
name. The old behavior can be obtained by using indexing to reorder the fields
before
assignment, e.g., ``b[['x', 'y']] = a[['y', 'x']]``.
Compatibility notes
===================
DeprecationWarning to error
---------------------------
* Indexing with floats raises ``IndexError``,
e.g., a[0, 0.0].
* Indexing with non-integer array_like raises ``IndexError``,
e.g., ``a['1', '2']``
* Indexing with multiple ellipsis raises ``IndexError``,
e.g., ``a[..., ...]``.
* Non-integers used as index values raise ``TypeError``,
e.g., in ``reshape``, ``take``, and specifying reduce axis.
FutureWarning to changed behavior
---------------------------------
* ``np.full`` now returns an array of the fill-value's dtype if no dtype is
given, instead of defaulting to float.
* np.average will emit a warning if the argument is a subclass of ndarray,
as the subclass will be preserved starting in 1.13. (see Future Changes)
``power`` and ``**`` raise errors for integer to negative integer powers
------------------------------------------------------------------------
The previous behavior depended on whether numpy scalar integers or numpy
integer arrays were involved.
For arrays
* Zero to negative integer powers returned least integral value.
* Both 1, -1 to negative integer powers returned correct values.
* The remaining integers returned zero when raised to negative integer powers.
For scalars
* Zero to negative integer powers returned least integral value.
* Both 1, -1 to negative integer powers returned correct values.
* The remaining integers sometimes returned zero, sometimes the
correct float depending on the integer type combination.
All of these cases now raise a ``ValueError`` except for those integer
combinations whose common type is float, for instance uint64 and int8. It was
felt that a simple rule was the best way to go rather than have special
exceptions for the integer units. If you need negative powers, use an inexact
type.
Relaxed stride checking is the default
--------------------------------------
This will have some impact on code that assumed that ``F_CONTIGUOUS`` and
``C_CONTIGUOUS`` were mutually exclusive and could be set to determine the
default order for arrays that are now both.
The ``np.percentile`` 'midpoint' interpolation method fixed for exact indices
-----------------------------------------------------------------------------
The 'midpoint' interpolator now gives the same result as 'lower' and 'higher' when
the two coincide. Previous behavior of 'lower' + 0.5 is fixed.
``keepdims`` kwarg is passed through to user-class methods
----------------------------------------------------------
numpy functions that take a ``keepdims`` kwarg now pass the value
through to the corresponding methods on ndarray sub-classes. Previously the
``keepdims`` keyword would be silently dropped. These functions now have
the following behavior:
1. If user does not provide ``keepdims``, no keyword is passed to the underlying
method.
2. Any user-provided value of ``keepdims`` is passed through as a keyword
argument to the method.
This will raise in the case where the method does not support a
``keepdims`` kwarg and the user explicitly passes in ``keepdims``.
The following functions are changed: ``sum``, ``product``,
``sometrue``, ``alltrue``, ``any``, ``all``, ``amax``, ``amin``,
``prod``, ``mean``, ``std``, ``var``, ``nanmin``, ``nanmax``,
``nansum``, ``nanprod``, ``nanmean``, ``nanmedian``, ``nanvar``,
``nanstd``
``bitwise_and`` identity changed
--------------------------------
The previous identity was 1, it is now -1. See entry in `Improvements`_ for
more explanation.
ma.median warns and returns nan when unmasked invalid values are encountered
----------------------------------------------------------------------------
Similar to unmasked median the masked median `ma.median` now emits a Runtime
warning and returns `NaN` in slices where an unmasked `NaN` is present.
Greater consistancy in ``assert_almost_equal``
----------------------------------------------
The precision check for scalars has been changed to match that for arrays. It
is now::
abs(actual - desired) < 1.5 * 10**(-decimal)
Note that this is looser than previously documented, but agrees with the
previous implementation used in ``assert_array_almost_equal``. Due to the
change in implementation some very delicate tests may fail that did not
fail before.
``NoseTester`` behaviour of warnings during testing
---------------------------------------------------
When ``raise_warnings="develop"`` is given, all uncaught warnings will now
be considered a test failure. Previously only selected ones were raised.
Warnings which are not caught or raised (mostly when in release mode)
will be shown once during the test cycle similar to the default python
settings.
``assert_warns`` and ``deprecated`` decorator more specific
-----------------------------------------------------------
The ``assert_warns`` function and context manager are now more specific
to the given warning category. This increased specificity leads to them
being handled according to the outer warning settings. This means that
no warning may be raised in cases where a wrong category warning is given
and ignored outside the context. Alternatively the increased specificity
may mean that warnings that were incorrectly ignored will now be shown
or raised. See also the new ``suppress_warnings`` context manager.
The same is true for the ``deprecated`` decorator.
C API
-----
No changes.
New Features
============
Writeable keyword argument for ``as_strided``
---------------------------------------------
``np.lib.stride_tricks.as_strided`` now has a ``writeable``
keyword argument. It can be set to False when no write operation
to the returned array is expected to avoid accidental
unpredictable writes.
``axes`` keyword argument for ``rot90``
---------------------------------------
The ``axes`` keyword argument in ``rot90`` determines the plane in which the
array is rotated. It defaults to ``axes=(0,1)`` as in the originial function.
Generalized ``flip``
--------------------
``flipud`` and ``fliplr`` reverse the elements of an array along axis=0 and
axis=1 respectively. The newly added ``flip`` function reverses the elements of
an array along any given axis.
* ``np.count_nonzero`` now has an ``axis`` parameter, allowing
non-zero counts to be generated on more than just a flattened
array object.
BLIS support in ``numpy.distutils``
-----------------------------------
Building against the BLAS implementation provided by the BLIS library is now
supported. See the ``[blis]`` section in ``site.cfg.example`` (in the root of
the numpy repo or source distribution).
Hook in ``numpy/__init__.py`` to run distribution-specific checks
-----------------------------------------------------------------
Binary distributions of numpy may need to run specific hardware checks or load
specific libraries during numpy initialization. For example, if we are
distributing numpy with a BLAS library that requires SSE2 instructions, we
would like to check the machine on which numpy is running does have SSE2 in
order to give an informative error.
Add a hook in ``numpy/__init__.py`` to import a ``numpy/_distributor_init.py``
file that will remain empty (bar a docstring) in the standard numpy source,
but that can be overwritten by people making binary distributions of numpy.
New nanfunctions ``nancumsum`` and ``nancumprod`` added
-------------------------------------------------------
Nan-functions ``nancumsum`` and ``nancumprod`` have been added to
compute ``cumsum`` and ``cumprod`` by ignoring nans.
``np.interp`` can now interpolate complex values
------------------------------------------------
``np.lib.interp(x, xp, fp)`` now allows the interpolated array ``fp``
to be complex and will interpolate at ``complex128`` precision.
New polynomial evaluation function ``polyvalfromroots`` added
-------------------------------------------------------------
The new function ``polyvalfromroots`` evaluates a polynomial at given points
from the roots of the polynomial. This is useful for higher order polynomials,
where expansion into polynomial coefficients is inaccurate at machine
precision.
New array creation function ``geomspace`` added
-----------------------------------------------
The new function ``geomspace`` generates a geometric sequence. It is similar
to ``logspace``, but with start and stop specified directly:
``geomspace(start, stop)`` behaves the same as
``logspace(log10(start), log10(stop))``.
New context manager for testing warnings
----------------------------------------
A new context manager ``suppress_warnings`` has been added to the testing
utils. This context manager is designed to help reliably test warnings.
Specifically to reliably filter/ignore warnings. Ignoring warnings
by using an "ignore" filter in Python versions before 3.4.x can quickly
result in these (or similar) warnings not being tested reliably.
The context manager allows to filter (as well as record) warnings similar
to the ``catch_warnings`` context, but allows for easier specificity.
Also printing warnings that have not been filtered or nesting the
context manager will work as expected. Additionally, it is possible
to use the context manager as a decorator which can be useful when
multiple tests give need to hide the same warning.
New masked array functions ``ma.convolve`` and ``ma.correlate`` added
---------------------------------------------------------------------
These functions wrapped the non-masked versions, but propagate through masked
values. There are two different propagation modes. The default causes masked
values to contaminate the result with masks, but the other mode only outputs
masks if there is no alternative.
New ``float_power`` ufunc
-------------------------
The new ``float_power`` ufunc is like the ``power`` function except all
computation is done in a minimum precision of float64. There was a long
discussion on the numpy mailing list of how to treat integers to negative
integer powers and a popular proposal was that the ``__pow__`` operator should
always return results of at least float64 precision. The ``float_power``
function implements that option. Note that it does not support object arrays.
``np.loadtxt`` now supports a single integer as ``usecol`` argument
-------------------------------------------------------------------
Instead of using ``usecol=(n,)`` to read the nth column of a file
it is now allowed to use ``usecol=n``. Also the error message is
more user friendly when a non-integer is passed as a column index.
Improved automated bin estimators for ``histogram``
---------------------------------------------------
Added 'doane' and 'sqrt' estimators to ``histogram`` via the ``bins``
argument. Added support for range-restricted histograms with automated
bin estimation.
``np.roll`` can now roll multiple axes at the same time
-------------------------------------------------------
The ``shift`` and ``axis`` arguments to ``roll`` are now broadcast against each
other, and each specified axis is shifted accordingly.
The ``__complex__`` method has been implemented for the ndarrays
----------------------------------------------------------------
Calling ``complex()`` on a size 1 array will now cast to a python
complex.
``pathlib.Path`` objects now supported
--------------------------------------
The standard ``np.load``, ``np.save``, ``np.loadtxt``, ``np.savez``, and similar
functions can now take ``pathlib.Path`` objects as an argument instead of a
filename or open file object.
New ``bits`` attribute for ``np.finfo``
---------------------------------------
This makes ``np.finfo`` consistent with ``np.iinfo`` which already has that
attribute.
New ``signature`` argument to ``np.vectorize``
----------------------------------------------
This argument allows for vectorizing user defined functions with core
dimensions, in the style of NumPy's
:ref:`generalized universal functions<c-api.generalized-ufuncs>`. This allows
for vectorizing a much broader class of functions. For example, an arbitrary
distance metric that combines two vectors to produce a scalar could be
vectorized with ``signature='(n),(n)->()'``. See ``np.vectorize`` for full
details.
Emit py3kwarnings for division of integer arrays
------------------------------------------------
To help people migrate their code bases from Python 2 to Python 3, the
python interpreter has a handy option -3, which issues warnings at runtime.
One of its warnings is for integer division::
$ python -3 -c "2/3"
-c:1: DeprecationWarning: classic int division
In Python 3, the new integer division semantics also apply to numpy arrays.
With this version, numpy will emit a similar warning::
$ python -3 -c "import numpy as np; np.array(2)/np.array(3)"
-c:1: DeprecationWarning: numpy: classic int division
numpy.sctypes now includes bytes on Python3 too
-----------------------------------------------
Previously, it included str (bytes) and unicode on Python2, but only str
(unicode) on Python3.
Improvements
============
``bitwise_and`` identity changed
--------------------------------
The previous identity was 1 with the result that all bits except the LSB were
masked out when the reduce method was used. The new identity is -1, which
should work properly on twos complement machines as all bits will be set to
one.
Generalized Ufuncs will now unlock the GIL
------------------------------------------
Generalized Ufuncs, including most of the linalg module, will now unlock
the Python global interpreter lock.
Caches in `np.fft` are now bounded in total size and item count
---------------------------------------------------------------
The caches in `np.fft` that speed up successive FFTs of the same length can no
longer grow without bounds. They have been replaced with LRU (least recently
used) caches that automatically evict no longer needed items if either the
memory size or item count limit has been reached.
Improved handling of zero-width string/unicode dtypes
-----------------------------------------------------
Fixed several interfaces that explicitly disallowed arrays with zero-width
string dtypes (i.e. ``dtype('S0')`` or ``dtype('U0')``, and fixed several
bugs where such dtypes were not handled properly. In particular, changed
``ndarray.__new__`` to not implicitly convert ``dtype('S0')`` to
``dtype('S1')`` (and likewise for unicode) when creating new arrays.
Integer ufuncs vectorized with AVX2
-----------------------------------
If the cpu supports it at runtime the basic integer ufuncs now use AVX2
instructions. This feature is currently only available when compiled with GCC.
Order of operations optimization in ``np.einsum``
--------------------------------------------------
``np.einsum`` now supports the ``optimize`` argument which will optimize the
order of contraction. For example, ``np.einsum`` would complete the chain dot
example ``np.einsum(‘ij,jk,kl->il’, a, b, c)`` in a single pass which would
scale like ``N^4``; however, when ``optimize=True`` ``np.einsum`` will create
an intermediate array to reduce this scaling to ``N^3`` or effectively
``np.dot(a, b).dot(c)``. Usage of intermediate tensors to reduce scaling has
been applied to the general einsum summation notation. See ``np.einsum_path``
for more details.
quicksort has been changed to an introsort
------------------------------------------
The quicksort kind of ``np.sort`` and ``np.argsort`` is now an introsort which
is regular quicksort but changing to a heapsort when not enough progress is
made. This retains the good quicksort performance while changing the worst case
runtime from ``O(N^2)`` to ``O(N*log(N))``.
``ediff1d`` improved performance and subclass handling
------------------------------------------------------
The ediff1d function uses an array instead on a flat iterator for the
subtraction. When to_begin or to_end is not None, the subtraction is performed
in place to eliminate a copy operation. A side effect is that certain
subclasses are handled better, namely astropy.Quantity, since the complete
array is created, wrapped, and then begin and end values are set, instead of
using concatenate.
Improved precision of ``ndarray.mean`` for float16 arrays
---------------------------------------------------------
The computation of the mean of float16 arrays is now carried out in float32 for
improved precision. This should be useful in packages such as Theano
where the precision of float16 is adequate and its smaller footprint is
desireable.
Changes
=======
All array-like methods are now called with keyword arguments in fromnumeric.py
------------------------------------------------------------------------------
Internally, many array-like methods in fromnumeric.py were being called with
positional arguments instead of keyword arguments as their external signatures
were doing. This caused a complication in the downstream 'pandas' library
that encountered an issue with 'numpy' compatibility. Now, all array-like
methods in this module are called with keyword arguments instead.
Operations on np.memmap objects return numpy arrays in most cases
-----------------------------------------------------------------
Previously operations on a memmap object would misleadingly return a memmap
instance even if the result was actually not memmapped. For example,
``arr + 1`` or ``arr + arr`` would return memmap instances, although no memory
from the output array is memmaped. Version 1.12 returns ordinary numpy arrays
from these operations.
Also, reduction of a memmap (e.g. ``.sum(axis=None``) now returns a numpy
scalar instead of a 0d memmap.
stacklevel of warnings increased
--------------------------------
The stacklevel for python based warnings was increased so that most warnings
will report the offending line of the user code instead of the line the
warning itself is given. Passing of stacklevel is now tested to ensure that
new warnings will receive the ``stacklevel`` argument.
This causes warnings with the "default" or "module" filter to be shown once
for every offending user code line or user module instead of only once. On
python versions before 3.4, this can cause warnings to appear that were falsely
ignored before, which may be surprising especially in test suits.
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