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[pkgsrc/trunk]: pkgsrc/math/py-scipy py-scipy: updated to 1.7.1
details: https://anonhg.NetBSD.org/pkgsrc/rev/785506910f26
branches: trunk
changeset: 768885:785506910f26
user: adam <adam%pkgsrc.org@localhost>
date: Tue Nov 02 18:51:02 2021 +0000
description:
py-scipy: updated to 1.7.1
SciPy 1.7.1 is a bug-fix release with no new features compared to 1.7.0.
1.7.0:
A new submodule for quasi-Monte Carlo, scipy.stats.qmc, was added
The documentation design was updated to use the same PyData-Sphinx theme as NumPy and other ecosystem libraries.
We now vendor and leverage the Boost C++ library to enable numerous improvements for long-standing weaknesses in scipy.stats
scipy.stats has six new distributions, eight new (or overhauled) hypothesis tests, a new function for bootstrapping, a class that enables fast random variate sampling and percentile point function
evaluation, and many other enhancements.
cdist and pdist distance calculations are faster for several metrics, especially weighted cases, thanks to a rewrite to a new C++ backend framework
A new class for radial basis function interpolation, RBFInterpolator, was added to address issues with the Rbf class.
diffstat:
math/py-scipy/Makefile | 18 ++-
math/py-scipy/PLIST | 109 +++++++++++++++++++++-
math/py-scipy/distinfo | 9 +-
math/py-scipy/patches/patch-scipy_stats_setup.py | 15 +++
4 files changed, 132 insertions(+), 19 deletions(-)
diffs (truncated from 458 to 300 lines):
diff -r de32d4a239ed -r 785506910f26 math/py-scipy/Makefile
--- a/math/py-scipy/Makefile Tue Nov 02 18:48:28 2021 +0000
+++ b/math/py-scipy/Makefile Tue Nov 02 18:51:02 2021 +0000
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.49 2021/05/03 17:55:01 adam Exp $
+# $NetBSD: Makefile,v 1.50 2021/11/02 18:51:02 adam Exp $
-DISTNAME= scipy-1.6.3
+DISTNAME= scipy-1.7.1
PKGNAME= ${PYPKGPREFIX}-${DISTNAME}
CATEGORIES= math python
MASTER_SITES= ${MASTER_SITE_PYPI:=s/scipy/}
@@ -11,6 +11,7 @@
LICENSE= modified-bsd
DEPENDS+= ${PYPKGPREFIX}-pybind11-[0-9]*:../../devel/py-pybind11
+DEPENDS+= ${PYPKGPREFIX}-pythran>=0.9.11:../../math/py-pythran
TEST_DEPENDS+= ${PYPKGPREFIX}-nose-[0-9]*:../../devel/py-nose
TEST_DEPENDS+= ${PYPKGPREFIX}-test-[0-9]*:../../devel/py-test
@@ -31,15 +32,16 @@
LDFLAGS.Darwin+= -headerpad_max_install_names
-PYTHON_VERSIONS_INCOMPATIBLE= 36 27
+PYTHON_VERSIONS_INCOMPATIBLE= 27 36
REPLACE_PYTHON+= scipy/sparse/linalg/isolve/tests/test_gcrotmk.py
-.include "../../mk/bsd.prefs.mk"
+# Prefer boost-headers from PkgSrc which are properly patched.
+post-configure:
+ ${RM} -f -r ${WRKSRC}/scipy/_lib/boost/boost
+ ${LN} -s ${BUILDLINK_DIR}/include/boost ${WRKSRC}/scipy/_lib/boost/boost
-post-extract:
- ${CHMOD} -R g-w ${WRKSRC}
- ${CHMOD} 0644 ${WRKSRC}/scipy/optimize/_shgo_lib/sobol_vec.gz
+.include "../../mk/bsd.prefs.mk"
.if ${OPSYS} == "Darwin"
.PHONY: fix-darwin-install-name
@@ -60,6 +62,7 @@
cd ${WRKDIR} && \
${PYTHONBIN} -c "import scipy; scipy.test('full')"
+.include "../../devel/boost-headers/buildlink3.mk"
.include "../../devel/py-cython/buildlink3.mk"
.include "../../devel/py-pybind11/buildlink3.mk"
.include "../../lang/python/application.mk"
@@ -67,4 +70,5 @@
.include "../../math/fftw/buildlink3.mk"
BUILDLINK_API_DEPENDS.py-numpy+= ${PYPKGPREFIX}-numpy>=1.17.3
.include "../../math/py-numpy/buildlink3.mk"
+.include "../../math/py-pythran/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
diff -r de32d4a239ed -r 785506910f26 math/py-scipy/PLIST
--- a/math/py-scipy/PLIST Tue Nov 02 18:48:28 2021 +0000
+++ b/math/py-scipy/PLIST Tue Nov 02 18:51:02 2021 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.18 2021/04/05 19:26:07 tnn Exp $
+@comment $NetBSD: PLIST,v 1.19 2021/11/02 18:51:02 adam Exp $
${PYSITELIB}/${EGG_FILE}/PKG-INFO
${PYSITELIB}/${EGG_FILE}/SOURCES.txt
${PYSITELIB}/${EGG_FILE}/dependency_links.txt
@@ -28,6 +28,9 @@
${PYSITELIB}/scipy/_build_utils/system_info.py
${PYSITELIB}/scipy/_build_utils/system_info.pyc
${PYSITELIB}/scipy/_build_utils/system_info.pyo
+${PYSITELIB}/scipy/_build_utils/tempita.py
+${PYSITELIB}/scipy/_build_utils/tempita.pyc
+${PYSITELIB}/scipy/_build_utils/tempita.pyo
${PYSITELIB}/scipy/_build_utils/tests/__init__.py
${PYSITELIB}/scipy/_build_utils/tests/test_scipy_version.py
${PYSITELIB}/scipy/_distributor_init.py
@@ -36,6 +39,9 @@
${PYSITELIB}/scipy/_lib/__init__.py
${PYSITELIB}/scipy/_lib/__init__.pyc
${PYSITELIB}/scipy/_lib/__init__.pyo
+${PYSITELIB}/scipy/_lib/_boost_utils.py
+${PYSITELIB}/scipy/_lib/_boost_utils.pyc
+${PYSITELIB}/scipy/_lib/_boost_utils.pyo
${PYSITELIB}/scipy/_lib/_bunch.py
${PYSITELIB}/scipy/_lib/_bunch.pyc
${PYSITELIB}/scipy/_lib/_bunch.pyo
@@ -102,7 +108,6 @@
${PYSITELIB}/scipy/_lib/tests/test_ccallback.py
${PYSITELIB}/scipy/_lib/tests/test_deprecation.py
${PYSITELIB}/scipy/_lib/tests/test_import_cycles.py
-${PYSITELIB}/scipy/_lib/tests/test_linear_assignment.py
${PYSITELIB}/scipy/_lib/tests/test_tmpdirs.py
${PYSITELIB}/scipy/_lib/tests/test_warnings.py
${PYSITELIB}/scipy/_lib/uarray.py
@@ -146,6 +151,7 @@
${PYSITELIB}/scipy/constants/tests/__init__.py
${PYSITELIB}/scipy/constants/tests/test_codata.py
${PYSITELIB}/scipy/constants/tests/test_constants.py
+${PYSITELIB}/scipy/doc_requirements.txt
${PYSITELIB}/scipy/fft/__init__.py
${PYSITELIB}/scipy/fft/__init__.pyc
${PYSITELIB}/scipy/fft/__init__.pyo
@@ -158,6 +164,9 @@
${PYSITELIB}/scipy/fft/_debug_backends.py
${PYSITELIB}/scipy/fft/_debug_backends.pyc
${PYSITELIB}/scipy/fft/_debug_backends.pyo
+${PYSITELIB}/scipy/fft/_fftlog.py
+${PYSITELIB}/scipy/fft/_fftlog.pyc
+${PYSITELIB}/scipy/fft/_fftlog.pyo
${PYSITELIB}/scipy/fft/_helper.py
${PYSITELIB}/scipy/fft/_helper.pyc
${PYSITELIB}/scipy/fft/_helper.pyo
@@ -190,6 +199,7 @@
${PYSITELIB}/scipy/fft/tests/mock_backend.py
${PYSITELIB}/scipy/fft/tests/test_backend.py
${PYSITELIB}/scipy/fft/tests/test_fft_function.py
+${PYSITELIB}/scipy/fft/tests/test_fftlog.py
${PYSITELIB}/scipy/fft/tests/test_helper.py
${PYSITELIB}/scipy/fft/tests/test_multithreading.py
${PYSITELIB}/scipy/fft/tests/test_numpy.py
@@ -319,6 +329,13 @@
${PYSITELIB}/scipy/interpolate/_pade.pyc
${PYSITELIB}/scipy/interpolate/_pade.pyo
${PYSITELIB}/scipy/interpolate/_ppoly.so
+${PYSITELIB}/scipy/interpolate/_rbfinterp.py
+${PYSITELIB}/scipy/interpolate/_rbfinterp.pyc
+${PYSITELIB}/scipy/interpolate/_rbfinterp.pyo
+${PYSITELIB}/scipy/interpolate/_rbfinterp_pythran.py
+${PYSITELIB}/scipy/interpolate/_rbfinterp_pythran.pyc
+${PYSITELIB}/scipy/interpolate/_rbfinterp_pythran.pyo
+${PYSITELIB}/scipy/interpolate/_rbfinterp_pythran.so
${PYSITELIB}/scipy/interpolate/dfitpack.so
${PYSITELIB}/scipy/interpolate/fitpack.py
${PYSITELIB}/scipy/interpolate/fitpack.pyc
@@ -358,6 +375,7 @@
${PYSITELIB}/scipy/interpolate/tests/test_pade.py
${PYSITELIB}/scipy/interpolate/tests/test_polyint.py
${PYSITELIB}/scipy/interpolate/tests/test_rbf.py
+${PYSITELIB}/scipy/interpolate/tests/test_rbfinterp.py
${PYSITELIB}/scipy/interpolate/tests/test_regression.py
${PYSITELIB}/scipy/io/__init__.py
${PYSITELIB}/scipy/io/__init__.pyc
@@ -647,6 +665,7 @@
${PYSITELIB}/scipy/io/tests/data/test-8000Hz-le-1ch-10S-20bit-extra.wav
${PYSITELIB}/scipy/io/tests/data/test-8000Hz-le-1ch-1byte-ulaw.wav
${PYSITELIB}/scipy/io/tests/data/test-8000Hz-le-2ch-1byteu.wav
+${PYSITELIB}/scipy/io/tests/data/test-8000Hz-le-3ch-5S-24bit-inconsistent.wav
${PYSITELIB}/scipy/io/tests/data/test-8000Hz-le-3ch-5S-24bit.wav
${PYSITELIB}/scipy/io/tests/data/test-8000Hz-le-3ch-5S-36bit.wav
${PYSITELIB}/scipy/io/tests/data/test-8000Hz-le-3ch-5S-45bit.wav
@@ -791,6 +810,7 @@
${PYSITELIB}/scipy/linalg/tests/test_lapack.py
${PYSITELIB}/scipy/linalg/tests/test_matfuncs.py
${PYSITELIB}/scipy/linalg/tests/test_matmul_toeplitz.py
+${PYSITELIB}/scipy/linalg/tests/test_misc.py
${PYSITELIB}/scipy/linalg/tests/test_procrustes.py
${PYSITELIB}/scipy/linalg/tests/test_sketches.py
${PYSITELIB}/scipy/linalg/tests/test_solve_toeplitz.py
@@ -882,6 +902,7 @@
${PYSITELIB}/scipy/optimize/__init__.py
${PYSITELIB}/scipy/optimize/__init__.pyc
${PYSITELIB}/scipy/optimize/__init__.pyo
+${PYSITELIB}/scipy/optimize/__nnls.pyi
${PYSITELIB}/scipy/optimize/__nnls.so
${PYSITELIB}/scipy/optimize/_basinhopping.py
${PYSITELIB}/scipy/optimize/_basinhopping.pyc
@@ -900,6 +921,9 @@
${PYSITELIB}/scipy/optimize/_dual_annealing.py
${PYSITELIB}/scipy/optimize/_dual_annealing.pyc
${PYSITELIB}/scipy/optimize/_dual_annealing.pyo
+${PYSITELIB}/scipy/optimize/_group_columns.py
+${PYSITELIB}/scipy/optimize/_group_columns.pyc
+${PYSITELIB}/scipy/optimize/_group_columns.pyo
${PYSITELIB}/scipy/optimize/_group_columns.so
${PYSITELIB}/scipy/optimize/_hessian_update_strategy.py
${PYSITELIB}/scipy/optimize/_hessian_update_strategy.pyc
@@ -909,14 +933,12 @@
${PYSITELIB}/scipy/optimize/_highs/__init__.pyo
${PYSITELIB}/scipy/optimize/_highs/_highs_constants.so
${PYSITELIB}/scipy/optimize/_highs/_highs_wrapper.so
-${PYSITELIB}/scipy/optimize/_highs/_mpswriter.so
${PYSITELIB}/scipy/optimize/_highs/cython/src/HConst.pxd
${PYSITELIB}/scipy/optimize/_highs/cython/src/Highs.pxd
${PYSITELIB}/scipy/optimize/_highs/cython/src/HighsIO.pxd
${PYSITELIB}/scipy/optimize/_highs/cython/src/HighsInfo.pxd
${PYSITELIB}/scipy/optimize/_highs/cython/src/HighsLp.pxd
${PYSITELIB}/scipy/optimize/_highs/cython/src/HighsLpUtils.pxd
-${PYSITELIB}/scipy/optimize/_highs/cython/src/HighsMipSolver.pxd
${PYSITELIB}/scipy/optimize/_highs/cython/src/HighsModelUtils.pxd
${PYSITELIB}/scipy/optimize/_highs/cython/src/HighsOptions.pxd
${PYSITELIB}/scipy/optimize/_highs/cython/src/HighsRuntimeOptions.pxd
@@ -1008,10 +1030,6 @@
${PYSITELIB}/scipy/optimize/_shgo_lib/__init__.py
${PYSITELIB}/scipy/optimize/_shgo_lib/__init__.pyc
${PYSITELIB}/scipy/optimize/_shgo_lib/__init__.pyo
-${PYSITELIB}/scipy/optimize/_shgo_lib/sobol_seq.py
-${PYSITELIB}/scipy/optimize/_shgo_lib/sobol_seq.pyc
-${PYSITELIB}/scipy/optimize/_shgo_lib/sobol_seq.pyo
-${PYSITELIB}/scipy/optimize/_shgo_lib/sobol_vec.gz
${PYSITELIB}/scipy/optimize/_shgo_lib/triangulation.py
${PYSITELIB}/scipy/optimize/_shgo_lib/triangulation.pyc
${PYSITELIB}/scipy/optimize/_shgo_lib/triangulation.pyo
@@ -1087,6 +1105,9 @@
${PYSITELIB}/scipy/optimize/cython_optimize/_zeros.pxd
${PYSITELIB}/scipy/optimize/cython_optimize/_zeros.so
${PYSITELIB}/scipy/optimize/cython_optimize/c_zeros.pxd
+${PYSITELIB}/scipy/optimize/cython_optimize/setup.py
+${PYSITELIB}/scipy/optimize/cython_optimize/setup.pyc
+${PYSITELIB}/scipy/optimize/cython_optimize/setup.pyo
${PYSITELIB}/scipy/optimize/lbfgsb.py
${PYSITELIB}/scipy/optimize/lbfgsb.pyc
${PYSITELIB}/scipy/optimize/lbfgsb.pyo
@@ -1166,6 +1187,9 @@
${PYSITELIB}/scipy/signal/_max_len_seq.py
${PYSITELIB}/scipy/signal/_max_len_seq.pyc
${PYSITELIB}/scipy/signal/_max_len_seq.pyo
+${PYSITELIB}/scipy/signal/_max_len_seq_inner.py
+${PYSITELIB}/scipy/signal/_max_len_seq_inner.pyc
+${PYSITELIB}/scipy/signal/_max_len_seq_inner.pyo
${PYSITELIB}/scipy/signal/_max_len_seq_inner.so
${PYSITELIB}/scipy/signal/_peak_finding.py
${PYSITELIB}/scipy/signal/_peak_finding.pyc
@@ -1175,6 +1199,9 @@
${PYSITELIB}/scipy/signal/_savitzky_golay.pyc
${PYSITELIB}/scipy/signal/_savitzky_golay.pyo
${PYSITELIB}/scipy/signal/_sosfilt.so
+${PYSITELIB}/scipy/signal/_spectral.py
+${PYSITELIB}/scipy/signal/_spectral.pyc
+${PYSITELIB}/scipy/signal/_spectral.pyo
${PYSITELIB}/scipy/signal/_spectral.so
${PYSITELIB}/scipy/signal/_upfirdn.py
${PYSITELIB}/scipy/signal/_upfirdn.pyc
@@ -1457,6 +1484,7 @@
${PYSITELIB}/scipy/spatial/__init__.py
${PYSITELIB}/scipy/spatial/__init__.pyc
${PYSITELIB}/scipy/spatial/__init__.pyo
+${PYSITELIB}/scipy/spatial/_distance_pybind.so
${PYSITELIB}/scipy/spatial/_distance_wrap.so
${PYSITELIB}/scipy/spatial/_geometric_slerp.py
${PYSITELIB}/scipy/spatial/_geometric_slerp.pyc
@@ -1477,10 +1505,12 @@
${PYSITELIB}/scipy/spatial/ckdtree.so
${PYSITELIB}/scipy/spatial/distance.py
${PYSITELIB}/scipy/spatial/distance.pyc
+${PYSITELIB}/scipy/spatial/distance.pyi
${PYSITELIB}/scipy/spatial/distance.pyo
${PYSITELIB}/scipy/spatial/kdtree.py
${PYSITELIB}/scipy/spatial/kdtree.pyc
${PYSITELIB}/scipy/spatial/kdtree.pyo
+${PYSITELIB}/scipy/spatial/qhull.pyi
${PYSITELIB}/scipy/spatial/qhull.so
${PYSITELIB}/scipy/spatial/qhull_src/COPYING.txt
${PYSITELIB}/scipy/spatial/setup.py
@@ -1535,6 +1565,7 @@
${PYSITELIB}/scipy/spatial/transform/_rotation_spline.py
${PYSITELIB}/scipy/spatial/transform/_rotation_spline.pyc
${PYSITELIB}/scipy/spatial/transform/_rotation_spline.pyo
+${PYSITELIB}/scipy/spatial/transform/rotation.pyi
${PYSITELIB}/scipy/spatial/transform/rotation.so
${PYSITELIB}/scipy/spatial/transform/setup.py
${PYSITELIB}/scipy/spatial/transform/setup.pyc
@@ -1570,6 +1601,9 @@
${PYSITELIB}/scipy/special/_precompute/__init__.py
${PYSITELIB}/scipy/special/_precompute/__init__.pyc
${PYSITELIB}/scipy/special/_precompute/__init__.pyo
+${PYSITELIB}/scipy/special/_precompute/cosine_cdf.py
+${PYSITELIB}/scipy/special/_precompute/cosine_cdf.pyc
+${PYSITELIB}/scipy/special/_precompute/cosine_cdf.pyo
${PYSITELIB}/scipy/special/_precompute/expn_asy.py
${PYSITELIB}/scipy/special/_precompute/expn_asy.pyc
${PYSITELIB}/scipy/special/_precompute/expn_asy.pyo
@@ -1594,6 +1628,12 @@
${PYSITELIB}/scipy/special/_precompute/utils.py
${PYSITELIB}/scipy/special/_precompute/utils.pyc
${PYSITELIB}/scipy/special/_precompute/utils.pyo
+${PYSITELIB}/scipy/special/_precompute/wright_bessel.py
+${PYSITELIB}/scipy/special/_precompute/wright_bessel.pyc
+${PYSITELIB}/scipy/special/_precompute/wright_bessel.pyo
+${PYSITELIB}/scipy/special/_precompute/wright_bessel_data.py
+${PYSITELIB}/scipy/special/_precompute/wright_bessel_data.pyc
+${PYSITELIB}/scipy/special/_precompute/wright_bessel_data.pyo
${PYSITELIB}/scipy/special/_precompute/wrightomega.py
${PYSITELIB}/scipy/special/_precompute/wrightomega.pyc
${PYSITELIB}/scipy/special/_precompute/wrightomega.pyo
@@ -1643,6 +1683,7 @@
${PYSITELIB}/scipy/special/tests/test_bdtr.py
${PYSITELIB}/scipy/special/tests/test_boxcox.py
${PYSITELIB}/scipy/special/tests/test_cdflib.py
+${PYSITELIB}/scipy/special/tests/test_cosine_distr.py
${PYSITELIB}/scipy/special/tests/test_cython_special.py
${PYSITELIB}/scipy/special/tests/test_data.py
${PYSITELIB}/scipy/special/tests/test_digamma.py
@@ -1662,6 +1703,7 @@
${PYSITELIB}/scipy/special/tests/test_mpmath.py
${PYSITELIB}/scipy/special/tests/test_nan_inputs.py
${PYSITELIB}/scipy/special/tests/test_ndtr.py
+${PYSITELIB}/scipy/special/tests/test_ndtri_exp.py
${PYSITELIB}/scipy/special/tests/test_orthogonal.py
${PYSITELIB}/scipy/special/tests/test_orthogonal_eval.py
${PYSITELIB}/scipy/special/tests/test_owens_t.py
@@ -1678,6 +1720,7 @@
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