CVS commit: pkgsrc/math/py-bottleneck

["Adam Ciarcinski" <adam%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   adam
Date:           Mon Apr 27 08:06:41 UTC 2020

Modified Files:
        pkgsrc/math/py-bottleneck: Makefile PLIST distinfo

Log Message:
py-bottleneck: updated to 1.3.2

Bottleneck 1.3.2

Bug Fixes
- Explicitly declare numpy version dependency in ``pyproject.toml`` for Python 3.8, fixing
  certain cases where ``pip install`` would fail.
  and ``@0xb0b`` for reporting.

Bottleneck 1.3.1

Bug Fixes
- Fix memory leak in :func:`bottleneck.nanmedian` with the default argument of ``axis=None``.
- Add regression test for memory leak case

Bottleneck 1.3.0

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.
- 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

Enhancements
- Remove ``numpydoc`` package from Bottleneck source distribution
- :func:`bottleneck.slow.reduce.nansum` and :func:`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
- Test suite now uses ``pytest`` as ``nose`` is deprecated
- ``python setup.py build_ext --inplace`` is now incremental
- ``python setup.py clean`` now cleans all artifacts
- Compiler feature support now identified by testing rather than hardcoding
- The ``BN_OPT_3`` macro allows selective use of ``-O3`` at the function level
- Contributors are now automatically cited in the release notes

Performance
- Speed up :func:`bottleneck.reduce.anynan` and :func:`bottleneck.reduce.allnan` by 2x via ``BN_OPT_3``
- All functions covered by ``asv`` benchmarks
- :func:`bottleneck.nonreduce.replace` speedup of 4x via more explicit typing
- :func:`bottleneck.reduce.median` up to 2x faster for Fortran-ordered arrays

Bug Fixes
- Documentation fails to build on Python 3
- :func:`bottleneck.benchmark.bench` crashes on python 3.6.3, numpy 1.13.3
- :func:`bottleneck.nonreduce_axis.push` raises when :code:`n=None` is explicitly passed
- :func:`bottleneck.reduce.nansum` wrong output when :code:`a = np.ones((2, 2))[..., np.newaxis]`
  same issue of other reduce functions
- Silenced FutureWarning from NumPy in the slow version of move functions
- Installing bottleneck onto a system that does not already have Numpy
- Memory leaked when input was not a NumPy array
- Tautological comparison in :func:`bottleneck.move.move_rank` removed

Cleanup
- The ``ez_setup.py`` module is no longer packaged
- Building documentation is now self-contained in ``make doc``
- Codebase now ``flake8`` compliant and run on every commit
- Codebase now uses ``black`` for autoformatting


To generate a diff of this commit:
cvs rdiff -u -r1.2 -r1.3 pkgsrc/math/py-bottleneck/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/math/py-bottleneck/PLIST \
    pkgsrc/math/py-bottleneck/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/py-bottleneck/Makefile
diff -u pkgsrc/math/py-bottleneck/Makefile:1.2 pkgsrc/math/py-bottleneck/Makefile:1.3
--- pkgsrc/math/py-bottleneck/Makefile:1.2      Sat Nov  2 16:16:21 2019
+++ pkgsrc/math/py-bottleneck/Makefile  Mon Apr 27 08:06:41 2020
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.2 2019/11/02 16:16:21 rillig Exp $
+# $NetBSD: Makefile,v 1.3 2020/04/27 08:06:41 adam Exp $
 
-DISTNAME=      Bottleneck-1.2.1
+DISTNAME=      Bottleneck-1.3.2
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME:tl}
 CATEGORIES=    math python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=B/Bottleneck/}
@@ -10,11 +10,10 @@ HOMEPAGE=   https://github.com/kwgoodman/b
 COMMENT=       Collection of fast NumPy array functions written in C
 LICENSE=       2-clause-bsd
 
-#DEPENDS+=             ${PYPKGPREFIX}-dateutil-[0-9]*:../../time/py-dateutil
-#BUILD_DEPENDS+=       ${PYPKGPREFIX}-nose-[0-9]*:../../devel/py-nose
+TEST_DEPENDS+= ${PYPKGPREFIX}-test-runner-[0-9]*:../../devel/py-test-runner
 
-USE_LANGUAGES= c
+PYSETUPTESTTARGET=     pytest
 
-.include "../../lang/python/egg.mk"
 .include "../../math/py-numpy/buildlink3.mk"
+.include "../../lang/python/egg.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/math/py-bottleneck/PLIST
diff -u pkgsrc/math/py-bottleneck/PLIST:1.1 pkgsrc/math/py-bottleneck/PLIST:1.2
--- pkgsrc/math/py-bottleneck/PLIST:1.1 Wed Jun  7 08:12:47 2017
+++ pkgsrc/math/py-bottleneck/PLIST     Mon Apr 27 08:06:41 2020
@@ -1,13 +1,19 @@
-@comment $NetBSD: PLIST,v 1.1 2017/06/07 08:12:47 adam Exp $
+@comment $NetBSD: PLIST,v 1.2 2020/04/27 08:06:41 adam Exp $
 ${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
 ${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
 ${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/not-zip-safe
 ${PYSITELIB}/${EGG_INFODIR}/requires.txt
 ${PYSITELIB}/${EGG_INFODIR}/top_level.txt
-${PYSITELIB}/bottleneck/LICENSE
 ${PYSITELIB}/bottleneck/__init__.py
 ${PYSITELIB}/bottleneck/__init__.pyc
 ${PYSITELIB}/bottleneck/__init__.pyo
+${PYSITELIB}/bottleneck/_pytesttester.py
+${PYSITELIB}/bottleneck/_pytesttester.pyc
+${PYSITELIB}/bottleneck/_pytesttester.pyo
+${PYSITELIB}/bottleneck/_version.py
+${PYSITELIB}/bottleneck/_version.pyc
+${PYSITELIB}/bottleneck/_version.pyo
 ${PYSITELIB}/bottleneck/benchmark/__init__.py
 ${PYSITELIB}/bottleneck/benchmark/__init__.pyc
 ${PYSITELIB}/bottleneck/benchmark/__init__.pyo
@@ -42,18 +48,24 @@ ${PYSITELIB}/bottleneck/slow/reduce.pyo
 ${PYSITELIB}/bottleneck/src/__init__.py
 ${PYSITELIB}/bottleneck/src/__init__.pyc
 ${PYSITELIB}/bottleneck/src/__init__.pyo
-${PYSITELIB}/bottleneck/src/template.py
-${PYSITELIB}/bottleneck/src/template.pyc
-${PYSITELIB}/bottleneck/src/template.pyo
+${PYSITELIB}/bottleneck/src/bn_config.py
+${PYSITELIB}/bottleneck/src/bn_config.pyc
+${PYSITELIB}/bottleneck/src/bn_config.pyo
+${PYSITELIB}/bottleneck/src/bn_template.py
+${PYSITELIB}/bottleneck/src/bn_template.pyc
+${PYSITELIB}/bottleneck/src/bn_template.pyo
 ${PYSITELIB}/bottleneck/tests/__init__.py
 ${PYSITELIB}/bottleneck/tests/__init__.pyc
 ${PYSITELIB}/bottleneck/tests/__init__.pyo
-${PYSITELIB}/bottleneck/tests/input_modifcation_test.py
-${PYSITELIB}/bottleneck/tests/input_modifcation_test.pyc
-${PYSITELIB}/bottleneck/tests/input_modifcation_test.pyo
+${PYSITELIB}/bottleneck/tests/input_modification_test.py
+${PYSITELIB}/bottleneck/tests/input_modification_test.pyc
+${PYSITELIB}/bottleneck/tests/input_modification_test.pyo
 ${PYSITELIB}/bottleneck/tests/list_input_test.py
 ${PYSITELIB}/bottleneck/tests/list_input_test.pyc
 ${PYSITELIB}/bottleneck/tests/list_input_test.pyo
+${PYSITELIB}/bottleneck/tests/memory_test.py
+${PYSITELIB}/bottleneck/tests/memory_test.pyc
+${PYSITELIB}/bottleneck/tests/memory_test.pyo
 ${PYSITELIB}/bottleneck/tests/move_test.py
 ${PYSITELIB}/bottleneck/tests/move_test.pyc
 ${PYSITELIB}/bottleneck/tests/move_test.pyo
@@ -72,6 +84,3 @@ ${PYSITELIB}/bottleneck/tests/scalar_inp
 ${PYSITELIB}/bottleneck/tests/util.py
 ${PYSITELIB}/bottleneck/tests/util.pyc
 ${PYSITELIB}/bottleneck/tests/util.pyo
-${PYSITELIB}/bottleneck/version.py
-${PYSITELIB}/bottleneck/version.pyc
-${PYSITELIB}/bottleneck/version.pyo
Index: pkgsrc/math/py-bottleneck/distinfo
diff -u pkgsrc/math/py-bottleneck/distinfo:1.1 pkgsrc/math/py-bottleneck/distinfo:1.2
--- pkgsrc/math/py-bottleneck/distinfo:1.1      Wed Jun  7 08:12:47 2017
+++ pkgsrc/math/py-bottleneck/distinfo  Mon Apr 27 08:06:41 2020
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.1 2017/06/07 08:12:47 adam Exp $
+$NetBSD: distinfo,v 1.2 2020/04/27 08:06:41 adam Exp $
 
-SHA1 (Bottleneck-1.2.1.tar.gz) = 3547a3566551525509da4edfdfb502e829d32668
-RMD160 (Bottleneck-1.2.1.tar.gz) = 4afdfb4b31dbe614d1d0c2f4668a78058bdfc0fe
-SHA512 (Bottleneck-1.2.1.tar.gz) = c766999cd1501b9f1dee0177b631ece12824d1f95c33077705f6387c911df583c3556ea22b208e455567f75e6e12e29b95855a6aea316bd1d6113bf47a04cf5a
-Size (Bottleneck-1.2.1.tar.gz) = 105225 bytes
+SHA1 (Bottleneck-1.3.2.tar.gz) = 9d7b334512be667dc9e1ecba7f9b9da479a74863
+RMD160 (Bottleneck-1.3.2.tar.gz) = 965ff15f3525811d075781f44adb77a034f1417b
+SHA512 (Bottleneck-1.3.2.tar.gz) = 78f1a42c9429783c08de22e3c1815e8e8267a633323b7fd520b120ff21a31f9489717a1ca45b81d0b808aa48d0f17fd08b8018be48d8f78bea5f1fbd17d762d1
+Size (Bottleneck-1.3.2.tar.gz) = 88246 bytes