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[pkgsrc/trunk]: pkgsrc/math/py-scipy py-scipy: updated to 1.4.1
details: https://anonhg.NetBSD.org/pkgsrc/rev/7bd45e4cc6e3
branches: trunk
changeset: 428465:7bd45e4cc6e3
user: adam <adam%pkgsrc.org@localhost>
date: Tue Apr 28 09:45:27 2020 +0000
description:
py-scipy: updated to 1.4.1
SciPy 1.4.1 is a bug-fix release with no new features
compared to 1.4.0. Importantly, it aims to fix a problem
where an older version of pybind11 may cause a segmentation
fault when imported alongside incompatible libraries.
SciPy 1.4.0 is the culmination of 6 months of hard work. It contains
many new features, numerous bug-fixes, improved test coverage and better
documentation. There have been a number of deprecations and API changes
in this release, which are documented below. All users are encouraged to
upgrade to this release, as there are a large number of bug-fixes and
optimizations. Before upgrading, we recommend that users check that
their own code does not use deprecated SciPy functionality (to do so,
run your code with ``python -Wd`` and check for ``DeprecationWarning`` s).
Our development attention will now shift to bug-fix releases on the
1.4.x branch, and on adding new features on the master branch.
diffstat:
math/py-scipy/Makefile | 21 +++----
math/py-scipy/PLIST | 123 ++++++++++++++++++++++++++++++++++++++++++++++--
math/py-scipy/distinfo | 10 +-
3 files changed, 131 insertions(+), 23 deletions(-)
diffs (truncated from 407 to 300 lines):
diff -r 6886265ff541 -r 7bd45e4cc6e3 math/py-scipy/Makefile
--- a/math/py-scipy/Makefile Tue Apr 28 09:45:26 2020 +0000
+++ b/math/py-scipy/Makefile Tue Apr 28 09:45:27 2020 +0000
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.40 2019/11/04 17:47:30 rillig Exp $
+# $NetBSD: Makefile,v 1.41 2020/04/28 09:45:27 adam Exp $
-DISTNAME= scipy-1.3.0
+DISTNAME= scipy-1.4.1
PKGNAME= ${PYPKGPREFIX}-${DISTNAME}
CATEGORIES= math python
MASTER_SITES= ${MASTER_SITE_PYPI:=s/scipy/}
@@ -10,17 +10,18 @@
COMMENT= Scientific Algorithms Library for Python
LICENSE= modified-bsd
+DEPENDS+= ${PYPKGPREFIX}-pybind11-[0-9]*:../../devel/py-pybind11
+TEST_DEPENDS+= ${PYPKGPREFIX}-nose-[0-9]*:../../devel/py-nose
+TEST_DEPENDS+= ${PYPKGPREFIX}-test-[0-9]*:../../devel/py-test
+
USE_LANGUAGES+= c c++ fortran
MAKE_ENV+= ATLAS=None
# XXX Avoid picking up other compilers when installed
.include "../../mk/compiler.mk"
-.if defined(PKGSRC_FORTRAN) && ${PKGSRC_FORTRAN} == "g95"
-PYSETUPBUILDARGS+= --fcompiler=g95
-.elif defined(PKGSRC_FORTRAN) && ${PKGSRC_FORTRAN} == "gfortran"
+.if defined(PKGSRC_FORTRAN) && ${PKGSRC_FORTRAN} == "gfortran"
PYSETUPBUILDARGS+= --fcompiler=gnu95
-LDFLAGS.Darwin+= -undefined dynamic_lookup
.else
BROKEN= "Requires fortran 95"
.endif
@@ -48,9 +49,6 @@
done
.endif
-TEST_DEPENDS+= ${PYPKGPREFIX}-nose-[0-9]*:../../devel/py-nose
-TEST_DEPENDS+= ${PYPKGPREFIX}-test-[0-9]*:../../devel/py-test
-
# self test failures for 1.1.0 reported at
# https://github.com/scipy/scipy/issues/9196
# needs 'make install' first!
@@ -58,12 +56,13 @@
cd ${WRKDIR} && \
${PYTHONBIN} -c "import scipy; scipy.test('full')"
+.include "../../devel/py-cython/buildlink3.mk"
+.include "../../devel/py-pybind11/buildlink3.mk"
.include "../../lang/python/application.mk"
.include "../../lang/python/distutils.mk"
-.include "../../devel/py-cython/buildlink3.mk"
.include "../../math/blas/buildlink3.mk"
.include "../../math/fftw/buildlink3.mk"
.include "../../math/lapack/buildlink3.mk"
-BUILDLINK_API_DEPENDS.py-numpy+= ${PYPKGPREFIX}-numpy>=1.8.2
+BUILDLINK_API_DEPENDS.py-numpy+= ${PYPKGPREFIX}-numpy>=1.17.3
.include "../../math/py-numpy/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
diff -r 6886265ff541 -r 7bd45e4cc6e3 math/py-scipy/PLIST
--- a/math/py-scipy/PLIST Tue Apr 28 09:45:26 2020 +0000
+++ b/math/py-scipy/PLIST Tue Apr 28 09:45:27 2020 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.15 2019/06/14 14:53:29 adam Exp $
+@comment $NetBSD: PLIST,v 1.16 2020/04/28 09:45:27 adam Exp $
${PYSITELIB}/${EGG_FILE}/PKG-INFO
${PYSITELIB}/${EGG_FILE}/SOURCES.txt
${PYSITELIB}/${EGG_FILE}/dependency_links.txt
@@ -19,9 +19,18 @@
${PYSITELIB}/scipy/_build_utils/_fortran.py
${PYSITELIB}/scipy/_build_utils/_fortran.pyc
${PYSITELIB}/scipy/_build_utils/_fortran.pyo
+${PYSITELIB}/scipy/_build_utils/compiler_helper.py
+${PYSITELIB}/scipy/_build_utils/compiler_helper.pyc
+${PYSITELIB}/scipy/_build_utils/compiler_helper.pyo
+${PYSITELIB}/scipy/_build_utils/setup.py
+${PYSITELIB}/scipy/_build_utils/setup.pyc
+${PYSITELIB}/scipy/_build_utils/setup.pyo
${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
${PYSITELIB}/scipy/_distributor_init.pyo
@@ -39,6 +48,9 @@
${PYSITELIB}/scipy/_lib/_numpy_compat.py
${PYSITELIB}/scipy/_lib/_numpy_compat.pyc
${PYSITELIB}/scipy/_lib/_numpy_compat.pyo
+${PYSITELIB}/scipy/_lib/_pep440.py
+${PYSITELIB}/scipy/_lib/_pep440.pyc
+${PYSITELIB}/scipy/_lib/_pep440.pyo
${PYSITELIB}/scipy/_lib/_test_ccallback.so
${PYSITELIB}/scipy/_lib/_testutils.py
${PYSITELIB}/scipy/_lib/_testutils.pyc
@@ -49,6 +61,17 @@
${PYSITELIB}/scipy/_lib/_tmpdirs.py
${PYSITELIB}/scipy/_lib/_tmpdirs.pyc
${PYSITELIB}/scipy/_lib/_tmpdirs.pyo
+${PYSITELIB}/scipy/_lib/_uarray/LICENSE
+${PYSITELIB}/scipy/_lib/_uarray/__init__.py
+${PYSITELIB}/scipy/_lib/_uarray/__init__.pyc
+${PYSITELIB}/scipy/_lib/_uarray/__init__.pyo
+${PYSITELIB}/scipy/_lib/_uarray/_backend.py
+${PYSITELIB}/scipy/_lib/_uarray/_backend.pyc
+${PYSITELIB}/scipy/_lib/_uarray/_backend.pyo
+${PYSITELIB}/scipy/_lib/_uarray/_uarray.so
+${PYSITELIB}/scipy/_lib/_uarray/setup.py
+${PYSITELIB}/scipy/_lib/_uarray/setup.pyc
+${PYSITELIB}/scipy/_lib/_uarray/setup.pyo
${PYSITELIB}/scipy/_lib/_util.py
${PYSITELIB}/scipy/_lib/_util.pyc
${PYSITELIB}/scipy/_lib/_util.pyo
@@ -58,6 +81,9 @@
${PYSITELIB}/scipy/_lib/decorator.py
${PYSITELIB}/scipy/_lib/decorator.pyc
${PYSITELIB}/scipy/_lib/decorator.pyo
+${PYSITELIB}/scipy/_lib/deprecation.py
+${PYSITELIB}/scipy/_lib/deprecation.pyc
+${PYSITELIB}/scipy/_lib/deprecation.pyo
${PYSITELIB}/scipy/_lib/doccer.py
${PYSITELIB}/scipy/_lib/doccer.pyc
${PYSITELIB}/scipy/_lib/doccer.pyo
@@ -78,6 +104,9 @@
${PYSITELIB}/scipy/_lib/tests/test_import_cycles.py
${PYSITELIB}/scipy/_lib/tests/test_tmpdirs.py
${PYSITELIB}/scipy/_lib/tests/test_warnings.py
+${PYSITELIB}/scipy/_lib/uarray.py
+${PYSITELIB}/scipy/_lib/uarray.pyc
+${PYSITELIB}/scipy/_lib/uarray.pyo
${PYSITELIB}/scipy/cluster/__init__.py
${PYSITELIB}/scipy/cluster/__init__.pyc
${PYSITELIB}/scipy/cluster/__init__.pyo
@@ -115,10 +144,57 @@
${PYSITELIB}/scipy/constants/tests/__init__.py
${PYSITELIB}/scipy/constants/tests/test_codata.py
${PYSITELIB}/scipy/constants/tests/test_constants.py
+${PYSITELIB}/scipy/fft/__init__.py
+${PYSITELIB}/scipy/fft/__init__.pyc
+${PYSITELIB}/scipy/fft/__init__.pyo
+${PYSITELIB}/scipy/fft/_backend.py
+${PYSITELIB}/scipy/fft/_backend.pyc
+${PYSITELIB}/scipy/fft/_backend.pyo
+${PYSITELIB}/scipy/fft/_basic.py
+${PYSITELIB}/scipy/fft/_basic.pyc
+${PYSITELIB}/scipy/fft/_basic.pyo
+${PYSITELIB}/scipy/fft/_debug_backends.py
+${PYSITELIB}/scipy/fft/_debug_backends.pyc
+${PYSITELIB}/scipy/fft/_debug_backends.pyo
+${PYSITELIB}/scipy/fft/_helper.py
+${PYSITELIB}/scipy/fft/_helper.pyc
+${PYSITELIB}/scipy/fft/_helper.pyo
+${PYSITELIB}/scipy/fft/_pocketfft/LICENSE.md
+${PYSITELIB}/scipy/fft/_pocketfft/__init__.py
+${PYSITELIB}/scipy/fft/_pocketfft/__init__.pyc
+${PYSITELIB}/scipy/fft/_pocketfft/__init__.pyo
+${PYSITELIB}/scipy/fft/_pocketfft/basic.py
+${PYSITELIB}/scipy/fft/_pocketfft/basic.pyc
+${PYSITELIB}/scipy/fft/_pocketfft/basic.pyo
+${PYSITELIB}/scipy/fft/_pocketfft/helper.py
+${PYSITELIB}/scipy/fft/_pocketfft/helper.pyc
+${PYSITELIB}/scipy/fft/_pocketfft/helper.pyo
+${PYSITELIB}/scipy/fft/_pocketfft/pypocketfft.so
+${PYSITELIB}/scipy/fft/_pocketfft/realtransforms.py
+${PYSITELIB}/scipy/fft/_pocketfft/realtransforms.pyc
+${PYSITELIB}/scipy/fft/_pocketfft/realtransforms.pyo
+${PYSITELIB}/scipy/fft/_pocketfft/setup.py
+${PYSITELIB}/scipy/fft/_pocketfft/setup.pyc
+${PYSITELIB}/scipy/fft/_pocketfft/setup.pyo
+${PYSITELIB}/scipy/fft/_pocketfft/tests/__init__.py
+${PYSITELIB}/scipy/fft/_pocketfft/tests/test_basic.py
+${PYSITELIB}/scipy/fft/_pocketfft/tests/test_real_transforms.py
+${PYSITELIB}/scipy/fft/_realtransforms.py
+${PYSITELIB}/scipy/fft/_realtransforms.pyc
+${PYSITELIB}/scipy/fft/_realtransforms.pyo
+${PYSITELIB}/scipy/fft/setup.py
+${PYSITELIB}/scipy/fft/setup.pyc
+${PYSITELIB}/scipy/fft/setup.pyo
+${PYSITELIB}/scipy/fft/tests/mock_backend.py
+${PYSITELIB}/scipy/fft/tests/test_backend.py
+${PYSITELIB}/scipy/fft/tests/test_fft_function.py
+${PYSITELIB}/scipy/fft/tests/test_helper.py
+${PYSITELIB}/scipy/fft/tests/test_multithreading.py
+${PYSITELIB}/scipy/fft/tests/test_numpy.py
+${PYSITELIB}/scipy/fft/tests/test_real_transforms.py
${PYSITELIB}/scipy/fftpack/__init__.py
${PYSITELIB}/scipy/fftpack/__init__.pyc
${PYSITELIB}/scipy/fftpack/__init__.pyo
-${PYSITELIB}/scipy/fftpack/_fftpack.so
${PYSITELIB}/scipy/fftpack/basic.py
${PYSITELIB}/scipy/fftpack/basic.pyc
${PYSITELIB}/scipy/fftpack/basic.pyo
@@ -139,6 +215,7 @@
${PYSITELIB}/scipy/fftpack/tests/__init__.py
${PYSITELIB}/scipy/fftpack/tests/fftw_dct.c
${PYSITELIB}/scipy/fftpack/tests/fftw_double_ref.npz
+${PYSITELIB}/scipy/fftpack/tests/fftw_longdouble_ref.npz
${PYSITELIB}/scipy/fftpack/tests/fftw_single_ref.npz
${PYSITELIB}/scipy/fftpack/tests/gen_fftw_ref.py
${PYSITELIB}/scipy/fftpack/tests/gendata.m
@@ -168,6 +245,9 @@
${PYSITELIB}/scipy/integrate/_ivp/common.py
${PYSITELIB}/scipy/integrate/_ivp/common.pyc
${PYSITELIB}/scipy/integrate/_ivp/common.pyo
+${PYSITELIB}/scipy/integrate/_ivp/dop853_coefficients.py
+${PYSITELIB}/scipy/integrate/_ivp/dop853_coefficients.pyc
+${PYSITELIB}/scipy/integrate/_ivp/dop853_coefficients.pyo
${PYSITELIB}/scipy/integrate/_ivp/ivp.py
${PYSITELIB}/scipy/integrate/_ivp/ivp.pyc
${PYSITELIB}/scipy/integrate/_ivp/ivp.pyo
@@ -184,6 +264,9 @@
${PYSITELIB}/scipy/integrate/_ode.pyc
${PYSITELIB}/scipy/integrate/_ode.pyo
${PYSITELIB}/scipy/integrate/_odepack.so
+${PYSITELIB}/scipy/integrate/_quad_vec.py
+${PYSITELIB}/scipy/integrate/_quad_vec.pyc
+${PYSITELIB}/scipy/integrate/_quad_vec.pyo
${PYSITELIB}/scipy/integrate/_quadpack.so
${PYSITELIB}/scipy/integrate/_test_multivariate.so
${PYSITELIB}/scipy/integrate/_test_odeint_banded.so
@@ -203,10 +286,10 @@
${PYSITELIB}/scipy/integrate/tests/__init__.py
${PYSITELIB}/scipy/integrate/tests/_test_multivariate.c
${PYSITELIB}/scipy/integrate/tests/banded5x5.f
+${PYSITELIB}/scipy/integrate/tests/test__quad_vec.py
${PYSITELIB}/scipy/integrate/tests/test_banded_ode_solvers.py
${PYSITELIB}/scipy/integrate/tests/test_bvp.py
${PYSITELIB}/scipy/integrate/tests/test_integrate.py
-${PYSITELIB}/scipy/integrate/tests/test_ivp.py
${PYSITELIB}/scipy/integrate/tests/test_odeint_jac.py
${PYSITELIB}/scipy/integrate/tests/test_quadpack.py
${PYSITELIB}/scipy/integrate/tests/test_quadrature.py
@@ -289,6 +372,8 @@
${PYSITELIB}/scipy/io/arff/tests/data/iris.arff
${PYSITELIB}/scipy/io/arff/tests/data/missing.arff
${PYSITELIB}/scipy/io/arff/tests/data/nodata.arff
+${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/test2.arff
@@ -542,6 +627,7 @@
${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-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
@@ -793,9 +879,6 @@
${PYSITELIB}/scipy/optimize/_hessian_update_strategy.py
${PYSITELIB}/scipy/optimize/_hessian_update_strategy.pyc
${PYSITELIB}/scipy/optimize/_hessian_update_strategy.pyo
-${PYSITELIB}/scipy/optimize/_hungarian.py
-${PYSITELIB}/scipy/optimize/_hungarian.pyc
-${PYSITELIB}/scipy/optimize/_hungarian.pyo
${PYSITELIB}/scipy/optimize/_lbfgsb.so
${PYSITELIB}/scipy/optimize/_linprog.py
${PYSITELIB}/scipy/optimize/_linprog.pyc
@@ -812,6 +895,10 @@
${PYSITELIB}/scipy/optimize/_linprog_util.py
${PYSITELIB}/scipy/optimize/_linprog_util.pyc
${PYSITELIB}/scipy/optimize/_linprog_util.pyo
+${PYSITELIB}/scipy/optimize/_lsap.py
+${PYSITELIB}/scipy/optimize/_lsap.pyc
+${PYSITELIB}/scipy/optimize/_lsap.pyo
+${PYSITELIB}/scipy/optimize/_lsap_module.so
${PYSITELIB}/scipy/optimize/_lsq/__init__.py
${PYSITELIB}/scipy/optimize/_lsq/__init__.pyc
${PYSITELIB}/scipy/optimize/_lsq/__init__.pyo
@@ -912,6 +999,7 @@
${PYSITELIB}/scipy/optimize/_trustregion_constr/tests/test_canonical_constraint.py
${PYSITELIB}/scipy/optimize/_trustregion_constr/tests/test_projections.py
${PYSITELIB}/scipy/optimize/_trustregion_constr/tests/test_qp_subproblem.py
+${PYSITELIB}/scipy/optimize/_trustregion_constr/tests/test_report.py
${PYSITELIB}/scipy/optimize/_trustregion_constr/tr_interior_point.py
${PYSITELIB}/scipy/optimize/_trustregion_constr/tr_interior_point.pyc
${PYSITELIB}/scipy/optimize/_trustregion_constr/tr_interior_point.pyo
@@ -984,9 +1072,9 @@
${PYSITELIB}/scipy/optimize/tests/test_cython_optimize.py
${PYSITELIB}/scipy/optimize/tests/test_differentiable_functions.py
${PYSITELIB}/scipy/optimize/tests/test_hessian_update_strategy.py
-${PYSITELIB}/scipy/optimize/tests/test_hungarian.py
${PYSITELIB}/scipy/optimize/tests/test_lbfgsb_hessinv.py
${PYSITELIB}/scipy/optimize/tests/test_least_squares.py
+${PYSITELIB}/scipy/optimize/tests/test_linear_assignment.py
${PYSITELIB}/scipy/optimize/tests/test_linesearch.py
${PYSITELIB}/scipy/optimize/tests/test_linprog.py
${PYSITELIB}/scipy/optimize/tests/test_lsq_common.py
@@ -1029,6 +1117,7 @@
${PYSITELIB}/scipy/signal/_savitzky_golay.py
${PYSITELIB}/scipy/signal/_savitzky_golay.pyc
${PYSITELIB}/scipy/signal/_savitzky_golay.pyo
+${PYSITELIB}/scipy/signal/_sosfilt.so
${PYSITELIB}/scipy/signal/_spectral.so
${PYSITELIB}/scipy/signal/_upfirdn.py
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