bottleneck

Bottleneck 1.4.0

Release date: in development

Bug Fixes

Contributors

Bottleneck 1.3.2

Release date: 2020-02-20

Bug Fixes

• Explicitly declare numpy version dependency in pyproject.toml for Python 3.8, fixing certain cases where pip install would fail. Thanks to @goggle, @astrofrog, and @0xb0b for reporting. (277)

Contributors

Bottleneck 1.3.1

Release date: 2019-11-18

Bug Fixes

• Fix memory leak in bottleneck.nanmedian with the default argument of axis=None. Thanks to @jsmodic for reporting! (276, 278)

• Add regression test for memory leak case (279)

Contributors

Bottleneck 1.3.0

Release date: 2019-11-12

Project Updates

• Bottleneck has a new maintainer, Christopher Whelan (@qwhelan on GitHub).

• Documentation now hosted at https://bottleneck.readthedocs.io

• 1.3.x will be the last release to support Python 2.7

• Bottleneck now supports and is tested against Python 3.7 and 3.8. (211, 268)

• The LICENSE file has been restructured to only include the license for the Bottleneck project to aid license audit tools. There has been no change to the licensing of Bottleneck.

  • Licenses for other projects incorporated by Bottleneck are now reproduced in full in separate files in the LICENSES/ directory (eg, LICENSES/NUMPY_LICENSE)

  • All licenses have been updated. Notably, setuptools is now MIT licensed and no longer under the ambiguous dual PSF/Zope license.

• Bottleneck now uses 518 for specifying build dependencies, with per Python version specifications (247)

Enhancements

• Remove numpydoc package from Bottleneck source distribution

• bottleneck.slow.reduce.nansum and bottleneck.slow.reduce.ss now longer coerce output to have the same dtype as input

• Test (tox, travis, appveyor) against latest numpy (in conda)

• Performance benchmarking also available via asv

• versioneer now used for versioning (213)

• Test suite now uses pytest as nose is deprecated (222)

• python setup.py build_ext --inplace is now incremental (224)

• python setup.py clean now cleans all artifacts (226)

• Compiler feature support now identified by testing rather than hardcoding (227)

• The BN_OPT_3 macro allows selective use of -O3 at the function level (223)

• Contributors are now automatically cited in the release notes (244)

Performance

• Speed up bottleneck.reduce.anynan and bottleneck.reduce.allnan by 2x via BN_OPT_3 (223)

• All functions covered by asv benchmarks

• bottleneck.nonreduce.replace speedup of 4x via more explicit typing (239)

• bottleneck.reduce.median up to 2x faster for Fortran-ordered arrays (248)

Bug Fixes

• Documentation fails to build on Python 3 (170)

• bottleneck.benchmark.bench crashes on python 3.6.3, numpy 1.13.3 (175)

• bottleneck.nonreduce_axis.push raises when n=None is explicitly passed (178)

• bottleneck.reduce.nansum wrong output when a = np.ones((2, 2))[..., np.newaxis] same issue of other reduce functions (183)

• Silenced FutureWarning from NumPy in the slow version of move functions (194)

• Installing bottleneck onto a system that does not already have Numpy (195)

• Memory leaked when input was not a NumPy array (201)

• Tautological comparison in bottleneck.move.move_rank removed (207, 212)

Cleanup

• The ez_setup.py module is no longer packaged (211)

• Building documentation is now self-contained in make doc (214)

• Codebase now flake8 compliant and run on every commit

• Codebase now uses black for autoformatting (253)

Contributors

Bottleneck 1.2.1

Release date: 2017-05-15

This release adds support for NumPy's relaxed strides checking and fixes a few bugs.

Bug Fixes

• Installing bottleneck when two versions of NumPy are present (156)

• Compiling on Ubuntu 14.04 inside a Windows 7 WMware (157)

• Occasional segmentation fault in bn.nanargmin, nanargmax, median, and nanmedian when all of the following conditions are met: axis is None, input array is 2d or greater, and input array is not C contiguous. (159)

• Reducing np.array([2**31], dtype=np.int64) overflows on Windows (163)

Contributors

Bottleneck 1.2.0

Release date: 2016-10-20

This release is a complete rewrite of Bottleneck.

Port to C

• Bottleneck is now written in C

• Cython is no longer a dependency

• Source tarball size reduced by 80%

• Build time reduced by 66%

• Install size reduced by 45%

Redesign

• Besides porting to C, much of bottleneck has been redesigned to be simpler and faster. For example, bottleneck now uses its own N-dimensional array iterators, reducing function call overhead.

New features

• The new function bench_detailed runs a detailed performance benchmark on a single bottleneck function.

• Bottleneck can be installed on systems that do not yet have NumPy installed. Previously that only worked on some systems.

Beware

• Functions partsort and argpartsort have been renamed to partition and argpartition to match NumPy. Additionally the meaning of the input arguments have changed: bn.partsort(a, n) is now equivalent to bn.partition(a, kth=n-1). Similarly for bn.argpartition.

• The keyword for array input has been changed from arr to a in all functions. It now matches NumPy.

Thanks

• Moritz E. Beber: continuous integration with AppVeyor

• Christoph Gohlke: Windows compatibility

• Jennifer Olsen: comments and suggestions

• A special thanks to the Cython developers. The quickest way to appreciate their work is to remove Cython from your project. It is not easy.

Contributors

Bottleneck 1.1.0

Release date: 2016-06-22

This release makes Bottleneck more robust, releases GIL, adds new functions.

More Robust

• bn.move_median can now handle NaNs and min_count parameter

• bn.move_std is slower but numerically more stable

• Bottleneck no longer crashes on byte-swapped input arrays

Faster

• All Bottleneck functions release the GIL

• median is faster if the input array contains NaN

• move_median is faster for input arrays that contain lots of NaNs

• No speed penalty for median, nanmedian, nanargmin, nanargmax for Fortran ordered input arrays when axis is None

• Function call overhead cut in half for reduction along all axes (axis=None) if the input array satisfies at least one of the following properties: 1d, C contiguous, F contiguous

• Reduction along all axes (axis=None) is more than twice as fast for long, narrow input arrays such as a (1000000, 2) C contiguous array and a (2, 1000000) F contiguous array

New Functions

• move_var

• move_argmin

• move_argmax

• move_rank

• push

Beware

• bn.median now returns NaN for a slice that contains one or more NaNs

• Instead of using the distutils default, the '-O2' C compiler flag is forced

• bn.move_std output changed when mean is large compared to standard deviation

• Fixed: Non-accelerated moving window functions used min_count incorrectly

• bn.move_median is a bit slower for float input arrays that do not contain NaN

Thanks

Alphabeticaly by last name

• Alessandro Amici worked on setup.py

• Pietro Battiston modernized bottleneck installation

• Moritz E. Beber set up continuous integration with Travis CI

• Jaime Frio improved the numerical stability of move_std

• Christoph Gohlke revived Windows compatibility

• Jennifer Olsen added NaN support to move_median

Contributors

Bottleneck 1.0.0

Release date: 2015-02-06

This release is a complete rewrite of Bottleneck.

Faster

• "python setup.py build" is 18.7 times faster

• Function-call overhead cut in half---a big speed up for small input arrays

• Arbitrary ndim input arrays accelerated; previously only 1d, 2d, and 3d

• bn.nanrankdata is twice as fast for float input arrays

• bn.move_max, bn.move_min are faster for int input arrays

• No speed penalty for reducing along all axes when input is Fortran ordered

Smaller

• Compiled binaries 14.1 times smaller

• Source tarball 4.7 times smaller

• 9.8 times less C code

• 4.3 times less Cython code

• 3.7 times less Python code

Beware

• Requires numpy 1.9.1

• Single API, e.g.: bn.nansum instead of bn.nansum and nansum_2d_float64_axis0

• On 64-bit systems bn.nansum(int32) returns int32 instead of int64

• bn.nansum now returns 0 for all NaN slices (as does numpy 1.9.1)

• Reducing over all axes returns, e.g., 6.0; previously np.float64(6.0)

• bn.ss() now has default axis=None instead of axis=0

• bn.nn() is no longer in bottleneck

min_count

• Previous releases had moving window function pairs: move_sum, move_nansum

• This release only has half of the pairs: move_sum

• Instead a new input parameter, min_count, has been added

• min_count=None same as old move_sum; min_count=1 same as old move_nansum

• If # non-NaN values in window < min_count, then NaN assigned to the window

• Exception: move_median does not take min_count as input

Bug Fixes

• Can now install bottleneck with pip even if numpy is not already installed

• bn.move_max, bn.move_min now return float32 for float32 input

Contributors

Bottleneck 0.8.0

Release date: 2014-01-21

This version of Bottleneck requires NumPy 1.8.

Breaks from 0.7.0

• This version of Bottleneck requires NumPy 1.8

• nanargmin and nanargmax behave like the corresponding functions in NumPy 1.8

Bug fixes

• nanargmax/nanargmin wrong for redundant max/min values in 1d int arrays

Contributors

Bottleneck 0.7.0

Release date: 2013-09-10

Enhancements

• bn.rankdata() is twice as fast (with input a = np.random.rand(1000000))

• C files now included in github repo; cython not needed to try latest

• C files are now generated with Cython 0.19.1 instead of 0.16

• Test bottleneck across multiple python/numpy versions using tox

• Source tarball size cut in half

Bug fixes

• move_std, move_nanstd return inappropriate NaNs (sqrt of negative #) (50)

• make test fails on some computers (52)

• scipy optional yet some unit tests depend on scipy (57)

• now works on Mac OS X 10.8 using clang compiler (49, 55)

• nanstd([1.0], ddof=1) and nanvar([1.0], ddof=1) crash (60)

Contributors

Bottleneck 0.6.0

Release date: 2012-06-04

Thanks to Dougal Sutherland, Bottleneck now runs on Python 3.2.

New functions

• replace(arr, old, new), e.g, replace(arr, np.nan, 0)

• nn(arr, arr0, axis) nearest neighbor and its index of 1d arr0 in 2d arr

• anynan(arr, axis) faster alternative to np.isnan(arr).any(axis)

• allnan(arr, axis) faster alternative to np.isnan(arr).all(axis)

Enhancements

• Python 3.2 support (may work on earlier versions of Python 3)

• C files are now generated with Cython 0.16 instead of 0.14.1

• Upgrade numpydoc from 0.3.1 to 0.4 to support Sphinx 1.0.1

Breaks from 0.5.0

• Support for Python 2.5 dropped

• Default axis for benchmark suite is now axis=1 (was 0)

Bug fixes

• Confusing error message in partsort and argpartsort (31)

• Update path in MANIFEST.in (32)

• Wrong output for very large (2**31) input arrays (35)

Contributors

Bottleneck 0.5.0

Release date: 2011-06-13

The fifth release of bottleneck adds four new functions, comes in a single source distribution instead of separate 32 and 64 bit versions, and contains bug fixes.

J. David Lee wrote the C-code implementation of the double heap moving window median.

New functions

• move_median(), moving window median

• partsort(), partial sort

• argpartsort()

• ss(), sum of squares, faster version of scipy.stats.ss

Changes

• Single source distribution instead of separate 32 and 64 bit versions

• nanmax and nanmin now follow Numpy 1.6 (not 1.5.1) when input is all NaN

Bug fixes

• Support python 2.5 by importing with statement (14)

• nanmedian wrong for particular ordering of NaN and non-NaN elements (22)

• argpartsort, nanargmin, nanargmax returned wrong dtype on 64-bit Windows (26)

• rankdata and nanrankdata crashed on 64-bit Windows (29)

Contributors

Bottleneck 0.4.3

Release date: 2011-03-17

This is a bug fix release.

Bug fixes

• median and nanmedian modified (partial sort) input array (11)

• nanmedian wrong when odd number of elements with all but last a NaN (12)

Enhancement

• Lazy import of SciPy (rarely used) speeds Bottleneck import 3x

Contributors

Bottleneck 0.4.2

Release date: 2011-03-08

This is a bug fix release.

Same bug fixed in Bottleneck 0.4.1 for nanstd() was fixed for nanvar() in this release. Thanks again to Christoph Gohlke for finding the bug.

Contributors

Bottleneck 0.4.1

Release date: 2011-03-08

This is a bug fix release.

The low-level functions nanstd_3d_int32_axis1 and nanstd_3d_int64_axis1, called by bottleneck.nanstd(), wrote beyond the memory owned by the output array if arr.shape[1] == 0 and arr.shape[0] > arr.shape[2], where arr is the input array.

Thanks to Christoph Gohlke for finding an example to demonstrate the bug.

Contributors

Bottleneck 0.4.0

Release date: 2011-03-08

The fourth release of Bottleneck contains new functions and bug fixes. Separate source code distributions are now made for 32 bit and 64 bit operating systems.

New functions

• rankdata()

• nanrankdata()

Enhancements

• Optionally specify the shapes of the arrays used in benchmark

• Can specify which input arrays to fill with one-third NaNs in benchmark

Breaks from 0.3.0

• Removed group_nanmean() function

• Bump dependency from NumPy 1.4.1 to NumPy 1.5.1

• C files are now generated with Cython 0.14.1 instead of 0.13

Bug fixes

• Some functions gave wrong output dtype for some input dtypes on 32 bit OS (6)

• Some functions choked on size zero input arrays (7)

• Segmentation fault with Cython 0.14.1 (but not 0.13) (8)

Contributors

Bottleneck 0.3.0

Release date: 2010-01-19

The third release of Bottleneck is twice as fast for small input arrays and contains 10 new functions.

Faster

• All functions are faster (less overhead in selector functions)

New functions

• nansum()

• move_sum()

• move_nansum()

• move_mean()

• move_std()

• move_nanstd()

• move_min()

• move_nanmin()

• move_max()

• move_nanmax()

Enhancements

• You can now specify the dtype and axis to use in the benchmark timings

• Improved documentation and more unit tests

Breaks from 0.2.0

• Moving window functions now default to axis=-1 instead of axis=0

• Low-level moving window selector functions no longer take window as input

Bug fix

• int input array resulted in call to slow, non-cython version of move_nanmean

Contributors

Bottleneck 0.2.0

Release date: 2010-12-27

The second release of Bottleneck is faster, contains more functions, and supports more dtypes.

Faster

• All functions faster (less overhead) when output is not a scalar

• Faster nanmean() for 2d, 3d arrays containing NaNs when axis is not None

New functions

• nanargmin()

• nanargmax()

• nanmedian()

Enhancements

• Added support for float32

• Fallback to slower, non-Cython functions for unaccelerated ndim/dtype

• Scipy is no longer a dependency

• Added support for older versions of NumPy (1.4.1)

• All functions are now templated for dtype and axis

• Added a sandbox for prototyping of new Bottleneck functions

• Rewrote benchmarking code

Contributors

Bottleneck 0.1.0

Release date: 2010-12-10

Initial release. The three categories of Bottleneck functions:

• Faster replacement for NumPy and SciPy functions

• Moving window functions

• Group functions that bin calculations by like-labeled elements