py-scipy: update to 1.6.2

Highlights of this release

scipy.ndimage improvements: Fixes and ehancements to boundary extension
  modes for interpolation functions. Support for complex-valued inputs in many
  filtering and interpolation functions. New grid_mode option for
  scipy.ndimage.zoom to enable results consistent with scikit-image's
  rescale.
scipy.optimize.linprog has fast, new methods for large, sparse problems
  from the HiGHS library.
scipy.stats improvements including new distributions, a new test, and
  enhancements to existing distributions and tests

Deprecated features

scipy.spatial changes
  Calling KDTree.query with k=None to find all neighbours is deprecated.
  Use KDTree.query_ball_point instead.
distance.wminkowski was deprecated; use distance.minkowski and supply
  weights with the w keyword instead.
Backwards incompatible changes
  Using scipy.fft as a function aliasing numpy.fft.fft was removed after
  being deprecated in SciPy 1.4.0. As a result, the scipy.fft submodule
  must be explicitly imported now, in line with other SciPy subpackages.
  scipy.signal changes
The output of decimate, lfilter_zi, lfiltic, sos2tf, and
  sosfilt_zi have been changed to match numpy.result_type of their inputs.
The window function slepian was removed.
The frechet_l and frechet_r distributions were removed.

3 files changed, 74 insertions, 18 deletions

diff --git a/math/py-scipy/Makefile b/math/py-scipy/Makefile
index 95cb45cebe6..bf2785fb46c 100644
--- a/math/py-scipy/Makefile
+++ b/math/py-scipy/Makefile
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.43 2020/10/12 21:52:04 bacon Exp $
+# $NetBSD: Makefile,v 1.44 2021/04/05 19:26:07 tnn Exp $
 
-DISTNAME=	scipy-1.5.2
+DISTNAME=	scipy-1.6.2
 PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
-PKGREVISION=	1
 CATEGORIES=	math python
 MASTER_SITES=	${MASTER_SITE_PYPI:=s/scipy/}
 
@@ -32,7 +31,7 @@ FFLAGS+=	-fPIC
 
 LDFLAGS.Darwin+=	-headerpad_max_install_names
 
-PYTHON_VERSIONS_INCOMPATIBLE=	27
+PYTHON_VERSIONS_INCOMPATIBLE=	36 27
 
 REPLACE_PYTHON+=	scipy/sparse/linalg/isolve/tests/test_gcrotmk.py
 
diff --git a/math/py-scipy/PLIST b/math/py-scipy/PLIST
index 3193ec761d5..2408e436e72 100644
--- a/math/py-scipy/PLIST
+++ b/math/py-scipy/PLIST
@@ -1,12 +1,12 @@
-@comment $NetBSD: PLIST,v 1.17 2020/08/04 01:16:19 tnn Exp $
+@comment $NetBSD: PLIST,v 1.18 2021/04/05 19:26:07 tnn Exp $
 ${PYSITELIB}/${EGG_FILE}/PKG-INFO
 ${PYSITELIB}/${EGG_FILE}/SOURCES.txt
 ${PYSITELIB}/${EGG_FILE}/dependency_links.txt
+${PYSITELIB}/${EGG_FILE}/requires.txt
 ${PYSITELIB}/${EGG_FILE}/top_level.txt
 ${PYSITELIB}/scipy/HACKING.rst.txt
 ${PYSITELIB}/scipy/INSTALL.rst.txt
 ${PYSITELIB}/scipy/LICENSE.txt
-${PYSITELIB}/scipy/THANKS.txt
 ${PYSITELIB}/scipy/__config__.py
 ${PYSITELIB}/scipy/__config__.pyc
 ${PYSITELIB}/scipy/__config__.pyo
@@ -29,7 +29,6 @@ ${PYSITELIB}/scipy/_build_utils/system_info.py
 ${PYSITELIB}/scipy/_build_utils/system_info.pyc
 ${PYSITELIB}/scipy/_build_utils/system_info.pyo
 ${PYSITELIB}/scipy/_build_utils/tests/__init__.py
-${PYSITELIB}/scipy/_build_utils/tests/test_circular_imports.py
 ${PYSITELIB}/scipy/_build_utils/tests/test_scipy_version.py
 ${PYSITELIB}/scipy/_distributor_init.py
 ${PYSITELIB}/scipy/_distributor_init.pyc
@@ -37,10 +36,16 @@ ${PYSITELIB}/scipy/_distributor_init.pyo
 ${PYSITELIB}/scipy/_lib/__init__.py
 ${PYSITELIB}/scipy/_lib/__init__.pyc
 ${PYSITELIB}/scipy/_lib/__init__.pyo
+${PYSITELIB}/scipy/_lib/_bunch.py
+${PYSITELIB}/scipy/_lib/_bunch.pyc
+${PYSITELIB}/scipy/_lib/_bunch.pyo
 ${PYSITELIB}/scipy/_lib/_ccallback.py
 ${PYSITELIB}/scipy/_lib/_ccallback.pyc
 ${PYSITELIB}/scipy/_lib/_ccallback.pyo
 ${PYSITELIB}/scipy/_lib/_ccallback_c.so
+${PYSITELIB}/scipy/_lib/_disjoint_set.py
+${PYSITELIB}/scipy/_lib/_disjoint_set.pyc
+${PYSITELIB}/scipy/_lib/_disjoint_set.pyo
 ${PYSITELIB}/scipy/_lib/_fpumode.so
 ${PYSITELIB}/scipy/_lib/_gcutils.py
 ${PYSITELIB}/scipy/_lib/_gcutils.pyc
@@ -93,9 +98,11 @@ ${PYSITELIB}/scipy/_lib/tests/test__pep440.py
 ${PYSITELIB}/scipy/_lib/tests/test__testutils.py
 ${PYSITELIB}/scipy/_lib/tests/test__threadsafety.py
 ${PYSITELIB}/scipy/_lib/tests/test__util.py
+${PYSITELIB}/scipy/_lib/tests/test_bunch.py
 ${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
@@ -115,6 +122,7 @@ ${PYSITELIB}/scipy/cluster/setup.pyc
 ${PYSITELIB}/scipy/cluster/setup.pyo
 ${PYSITELIB}/scipy/cluster/tests/__init__.py
 ${PYSITELIB}/scipy/cluster/tests/hierarchy_test_data.py
+${PYSITELIB}/scipy/cluster/tests/test_disjoint_set.py
 ${PYSITELIB}/scipy/cluster/tests/test_hierarchy.py
 ${PYSITELIB}/scipy/cluster/tests/test_vq.py
 ${PYSITELIB}/scipy/cluster/vq.py
@@ -254,6 +262,11 @@ ${PYSITELIB}/scipy/integrate/_ivp/radau.pyo
 ${PYSITELIB}/scipy/integrate/_ivp/rk.py
 ${PYSITELIB}/scipy/integrate/_ivp/rk.pyc
 ${PYSITELIB}/scipy/integrate/_ivp/rk.pyo
+${PYSITELIB}/scipy/integrate/_ivp/setup.py
+${PYSITELIB}/scipy/integrate/_ivp/setup.pyc
+${PYSITELIB}/scipy/integrate/_ivp/setup.pyo
+${PYSITELIB}/scipy/integrate/_ivp/tests/test_ivp.py
+${PYSITELIB}/scipy/integrate/_ivp/tests/test_rk.py
 ${PYSITELIB}/scipy/integrate/_ode.py
 ${PYSITELIB}/scipy/integrate/_ode.pyc
 ${PYSITELIB}/scipy/integrate/_ode.pyo
@@ -370,6 +383,7 @@ ${PYSITELIB}/scipy/io/arff/tests/data/quoted_nominal.arff
 ${PYSITELIB}/scipy/io/arff/tests/data/quoted_nominal_spaces.arff
 ${PYSITELIB}/scipy/io/arff/tests/data/test1.arff
 ${PYSITELIB}/scipy/io/arff/tests/data/test10.arff
+${PYSITELIB}/scipy/io/arff/tests/data/test11.arff
 ${PYSITELIB}/scipy/io/arff/tests/data/test2.arff
 ${PYSITELIB}/scipy/io/arff/tests/data/test3.arff
 ${PYSITELIB}/scipy/io/arff/tests/data/test4.arff
@@ -623,13 +637,23 @@ ${PYSITELIB}/scipy/io/tests/data/struct_scalars_replicated.sav
 ${PYSITELIB}/scipy/io/tests/data/struct_scalars_replicated_3d.sav
 ${PYSITELIB}/scipy/io/tests/data/test-44100Hz-2ch-32bit-float-be.wav
 ${PYSITELIB}/scipy/io/tests/data/test-44100Hz-2ch-32bit-float-le.wav
+${PYSITELIB}/scipy/io/tests/data/test-44100Hz-be-1ch-4bytes.wav
 ${PYSITELIB}/scipy/io/tests/data/test-44100Hz-le-1ch-4bytes-early-eof-no-data.wav
 ${PYSITELIB}/scipy/io/tests/data/test-44100Hz-le-1ch-4bytes-early-eof.wav
 ${PYSITELIB}/scipy/io/tests/data/test-44100Hz-le-1ch-4bytes-incomplete-chunk.wav
 ${PYSITELIB}/scipy/io/tests/data/test-44100Hz-le-1ch-4bytes.wav
 ${PYSITELIB}/scipy/io/tests/data/test-48000Hz-2ch-64bit-float-le-wavex.wav
+${PYSITELIB}/scipy/io/tests/data/test-8000Hz-be-3ch-5S-24bit.wav
+${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.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
+${PYSITELIB}/scipy/io/tests/data/test-8000Hz-le-3ch-5S-53bit.wav
+${PYSITELIB}/scipy/io/tests/data/test-8000Hz-le-3ch-5S-64bit.wav
+${PYSITELIB}/scipy/io/tests/data/test-8000Hz-le-4ch-9S-12bit.wav
+${PYSITELIB}/scipy/io/tests/data/test-8000Hz-le-5ch-9S-5bit.wav
 ${PYSITELIB}/scipy/io/tests/data/various_compressed.sav
 ${PYSITELIB}/scipy/io/tests/test_fortran.py
 ${PYSITELIB}/scipy/io/tests/test_idl.py
@@ -679,6 +703,7 @@ ${PYSITELIB}/scipy/linalg/_matfuncs_inv_ssq.pyo
 ${PYSITELIB}/scipy/linalg/_matfuncs_sqrtm.py
 ${PYSITELIB}/scipy/linalg/_matfuncs_sqrtm.pyc
 ${PYSITELIB}/scipy/linalg/_matfuncs_sqrtm.pyo
+${PYSITELIB}/scipy/linalg/_matfuncs_sqrtm_triu.so
 ${PYSITELIB}/scipy/linalg/_procrustes.py
 ${PYSITELIB}/scipy/linalg/_procrustes.pyc
 ${PYSITELIB}/scipy/linalg/_procrustes.pyo
@@ -765,6 +790,7 @@ ${PYSITELIB}/scipy/linalg/tests/test_fblas.py
 ${PYSITELIB}/scipy/linalg/tests/test_interpolative.py
 ${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_procrustes.py
 ${PYSITELIB}/scipy/linalg/tests/test_sketches.py
 ${PYSITELIB}/scipy/linalg/tests/test_solve_toeplitz.py
@@ -793,7 +819,6 @@ ${PYSITELIB}/scipy/ndimage/__init__.py
 ${PYSITELIB}/scipy/ndimage/__init__.pyc
 ${PYSITELIB}/scipy/ndimage/__init__.pyo
 ${PYSITELIB}/scipy/ndimage/_ctest.so
-${PYSITELIB}/scipy/ndimage/_ctest_oldapi.so
 ${PYSITELIB}/scipy/ndimage/_cytest.so
 ${PYSITELIB}/scipy/ndimage/_nd_image.so
 ${PYSITELIB}/scipy/ndimage/_ni_docstrings.py
@@ -830,10 +855,10 @@ ${PYSITELIB}/scipy/ndimage/tests/dots.png
 ${PYSITELIB}/scipy/ndimage/tests/test_c_api.py
 ${PYSITELIB}/scipy/ndimage/tests/test_datatypes.py
 ${PYSITELIB}/scipy/ndimage/tests/test_filters.py
+${PYSITELIB}/scipy/ndimage/tests/test_fourier.py
+${PYSITELIB}/scipy/ndimage/tests/test_interpolation.py
 ${PYSITELIB}/scipy/ndimage/tests/test_measurements.py
 ${PYSITELIB}/scipy/ndimage/tests/test_morphology.py
-${PYSITELIB}/scipy/ndimage/tests/test_ndimage.py
-${PYSITELIB}/scipy/ndimage/tests/test_regression.py
 ${PYSITELIB}/scipy/ndimage/tests/test_splines.py
 ${PYSITELIB}/scipy/odr/__init__.py
 ${PYSITELIB}/scipy/odr/__init__.pyc
@@ -879,10 +904,38 @@ ${PYSITELIB}/scipy/optimize/_group_columns.so
 ${PYSITELIB}/scipy/optimize/_hessian_update_strategy.py
 ${PYSITELIB}/scipy/optimize/_hessian_update_strategy.pyc
 ${PYSITELIB}/scipy/optimize/_hessian_update_strategy.pyo
+${PYSITELIB}/scipy/optimize/_highs/__init__.py
+${PYSITELIB}/scipy/optimize/_highs/__init__.pyc
+${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
+${PYSITELIB}/scipy/optimize/_highs/cython/src/HighsRuntimeOptions.pxd
+${PYSITELIB}/scipy/optimize/_highs/cython/src/HighsStatus.pxd
+${PYSITELIB}/scipy/optimize/_highs/cython/src/SimplexConst.pxd
+${PYSITELIB}/scipy/optimize/_highs/cython/src/highs_c_api.pxd
+${PYSITELIB}/scipy/optimize/_highs/setup.py
+${PYSITELIB}/scipy/optimize/_highs/setup.pyc
+${PYSITELIB}/scipy/optimize/_highs/setup.pyo
 ${PYSITELIB}/scipy/optimize/_lbfgsb.so
 ${PYSITELIB}/scipy/optimize/_linprog.py
 ${PYSITELIB}/scipy/optimize/_linprog.pyc
 ${PYSITELIB}/scipy/optimize/_linprog.pyo
+${PYSITELIB}/scipy/optimize/_linprog_doc.py
+${PYSITELIB}/scipy/optimize/_linprog_doc.pyc
+${PYSITELIB}/scipy/optimize/_linprog_doc.pyo
+${PYSITELIB}/scipy/optimize/_linprog_highs.py
+${PYSITELIB}/scipy/optimize/_linprog_highs.pyc
+${PYSITELIB}/scipy/optimize/_linprog_highs.pyo
 ${PYSITELIB}/scipy/optimize/_linprog_ip.py
 ${PYSITELIB}/scipy/optimize/_linprog_ip.pyc
 ${PYSITELIB}/scipy/optimize/_linprog_ip.pyo
@@ -937,6 +990,9 @@ ${PYSITELIB}/scipy/optimize/_nnls.pyo
 ${PYSITELIB}/scipy/optimize/_numdiff.py
 ${PYSITELIB}/scipy/optimize/_numdiff.pyc
 ${PYSITELIB}/scipy/optimize/_numdiff.pyo
+${PYSITELIB}/scipy/optimize/_qap.py
+${PYSITELIB}/scipy/optimize/_qap.pyc
+${PYSITELIB}/scipy/optimize/_qap.pyo
 ${PYSITELIB}/scipy/optimize/_remove_redundancy.py
 ${PYSITELIB}/scipy/optimize/_remove_redundancy.pyc
 ${PYSITELIB}/scipy/optimize/_remove_redundancy.pyo
@@ -1084,6 +1140,7 @@ ${PYSITELIB}/scipy/optimize/tests/test_minpack.py
 ${PYSITELIB}/scipy/optimize/tests/test_nnls.py
 ${PYSITELIB}/scipy/optimize/tests/test_nonlin.py
 ${PYSITELIB}/scipy/optimize/tests/test_optimize.py
+${PYSITELIB}/scipy/optimize/tests/test_quadratic_assignment.py
 ${PYSITELIB}/scipy/optimize/tests/test_regression.py
 ${PYSITELIB}/scipy/optimize/tests/test_slsqp.py
 ${PYSITELIB}/scipy/optimize/tests/test_tnc.py
@@ -1160,6 +1217,7 @@ ${PYSITELIB}/scipy/signal/tests/test_fir_filter_design.py
 ${PYSITELIB}/scipy/signal/tests/test_ltisys.py
 ${PYSITELIB}/scipy/signal/tests/test_max_len_seq.py
 ${PYSITELIB}/scipy/signal/tests/test_peak_finding.py
+${PYSITELIB}/scipy/signal/tests/test_result_type.py
 ${PYSITELIB}/scipy/signal/tests/test_savitzky_golay.py
 ${PYSITELIB}/scipy/signal/tests/test_signaltools.py
 ${PYSITELIB}/scipy/signal/tests/test_spectral.py
@@ -1477,9 +1535,7 @@ ${PYSITELIB}/scipy/spatial/transform/_rotation_groups.pyo
 ${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.py
-${PYSITELIB}/scipy/spatial/transform/rotation.pyc
-${PYSITELIB}/scipy/spatial/transform/rotation.pyo
+${PYSITELIB}/scipy/spatial/transform/rotation.so
 ${PYSITELIB}/scipy/spatial/transform/setup.py
 ${PYSITELIB}/scipy/spatial/transform/setup.pyc
 ${PYSITELIB}/scipy/spatial/transform/setup.pyo
@@ -1719,6 +1775,7 @@ ${PYSITELIB}/scipy/stats/tests/test_discrete_basic.py
 ${PYSITELIB}/scipy/stats/tests/test_discrete_distns.py
 ${PYSITELIB}/scipy/stats/tests/test_distributions.py
 ${PYSITELIB}/scipy/stats/tests/test_fit.py
+${PYSITELIB}/scipy/stats/tests/test_hypotests.py
 ${PYSITELIB}/scipy/stats/tests/test_kdeoth.py
 ${PYSITELIB}/scipy/stats/tests/test_morestats.py
 ${PYSITELIB}/scipy/stats/tests/test_mstats_basic.py
diff --git a/math/py-scipy/distinfo b/math/py-scipy/distinfo
index 80f679ee81f..0c5e199b43b 100644
--- a/math/py-scipy/distinfo
+++ b/math/py-scipy/distinfo
@@ -1,7 +1,7 @@
-$NetBSD: distinfo,v 1.22 2020/08/04 01:16:19 tnn Exp $
+$NetBSD: distinfo,v 1.23 2021/04/05 19:26:07 tnn Exp $
 
-SHA1 (scipy-1.5.2.tar.gz) = d921aa98f73ea5bc533536df7fa681df52d8b9e2
-RMD160 (scipy-1.5.2.tar.gz) = 84d89d666191a1a2270a03bf4b45b40195615e42
-SHA512 (scipy-1.5.2.tar.gz) = 45463df30a0f6270d9f4cf52235f31607904a6ae1375e12600e7f1ab2d27b1dc25a6211b49dceb71506be22c756890adaf9f81d9e6be7455def86c9caf0dc923
-Size (scipy-1.5.2.tar.gz) = 25423944 bytes
+SHA1 (scipy-1.6.2.tar.gz) = 7ef8a684f9feb4fd24d35e87f9d1f69eb6ec793e
+RMD160 (scipy-1.6.2.tar.gz) = 9255e87c9b0f16028e65469b477ade7a76a5ec17
+SHA512 (scipy-1.6.2.tar.gz) = 18b03f32e8343c5a6c6148ac0bfd4b5f2cc9ff5f74d5d41761ae9e773d6af8774c7b09a3fcc47122864eccce1dbbc17e9325819885d3fc3ab2baf98e7d3befa4
+Size (scipy-1.6.2.tar.gz) = 27187804 bytes
 SHA1 (patch-scipy_special___round.h) = bc05a935e6423ce8395450ad3b30e88826939422