Release Notes¶

titlesonly:

These are the major changes made in each release. For details of the changes see the commit log at https://github.com/pydata/bottleneck

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¶

A total of 1 people contributed patches to this release. People with a “+” by their names contributed a patch for the first time.

Christopher Whelan

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¶

A total of 1 people contributed patches to this release. People with a “+” by their names contributed a patch for the first time.

Christopher Whelan

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 PEP 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¶

A total of 9 people contributed patches to this release. People with a “+” by their names contributed a patch for the first time.

Ales Erjavec +
Christoph Gohlke
Christopher Whelan +
Daniel Hakimi +
Ghislain Antony Vaillant +
Keith Goodman
Stephan Hoyer
Thomas Robitaille +
kwgoodman

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¶

A total of 1 people contributed patches to this release. People with a “+” by their names contributed a patch for the first time.

Keith Goodman

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¶

A total of 3 people contributed patches to this release. People with a “+” by their names contributed a patch for the first time.

Keith Goodman
Moritz E. Beber +
kwgoodman

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¶

A total of 10 people contributed patches to this release. People with a “+” by their names contributed a patch for the first time.

Alessandro Amici +
Christoph Gohlke
Jaime Fernandez +
Jenn Olsen +
Keith Goodman
Midnighter +
Pietro Battiston +
jaimefrio +
jennolsen84 +
kwgoodman

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¶

A total of 4 people contributed patches to this release. People with a “+” by their names contributed a patch for the first time.

Keith Goodman
Lev Givon +
Stephan Hoyer
kwgoodman

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¶

A total of 4 people contributed patches to this release. People with a “+” by their names contributed a patch for the first time.

Christoph Gohlke +
Keith Goodman
Stephan Hoyer +
kwgoodman

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¶

A total of 5 people contributed patches to this release. People with a “+” by their names contributed a patch for the first time.

Jens Hedegaard Nielsen +
John Benediktsson +
Keith Goodman
jmcloughlin +
kwgoodman

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¶

A total of 4 people contributed patches to this release. People with a “+” by their names contributed a patch for the first time.

Ben Root +
Dougal Sutherland +
Keith Goodman
kwgoodman +

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¶

A total of 1 people contributed patches to this release. People with a “+” by their names contributed a patch for the first time.

Keith Goodman

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¶

A total of 1 people contributed patches to this release. People with a “+” by their names contributed a patch for the first time.

Keith Goodman

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¶

A total of 1 people contributed patches to this release. People with a “+” by their names contributed a patch for the first time.

Keith Goodman

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¶

A total of 1 people contributed patches to this release. People with a “+” by their names contributed a patch for the first time.

Keith Goodman

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¶

A total of 1 people contributed patches to this release. People with a “+” by their names contributed a patch for the first time.

Keith Goodman

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¶

A total of 1 people contributed patches to this release. People with a “+” by their names contributed a patch for the first time.

Keith Goodman

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¶

A total of 0 people contributed patches to this release. People with a “+” by their names contributed a patch for the first time.

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