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CVS commit: pkgsrc/math/py-scipy
Module Name: pkgsrc
Committed By: adam
Date: Fri Aug 25 15:19:19 UTC 2023
Modified Files:
pkgsrc/math/py-scipy: Makefile PLIST distinfo
Log Message:
py-scipy: updated to 1.11.2
SciPy 1.11.2
Issues closed for 1.11.2
special.jn_zeros(281, 6) hangs
Complex matrix square root of positive semi-definite matrix
BUG: \`loadmat\` fails to load matlab structures with anonymous...
BUG: Floating point CSC with int64 indices doesn't work with...
BUG: \`scipy.optimize.minimize\` fails when \`dtype=float32\`...
DOC: Broken link to installation instructions in README.rst
BUG: Build failure with Cython 3.0.0b3 if scipy is already installed
BUG: optimize.least_squares with method='trf' yields wrong result...
BUG: cKDtree.query no longer accepts DataFrame as input
Spalde error with scipy 1.10: 0-th dimension must be fixed
BUG: <Compilation of scipy 1.11 falls with python3.12>
BUG: Compilation of scipy 1.10.1 and 1.11.1 fails with Python...
Pull requests for 1.11.2
BUG: Fix error in linalg/_matfuncs_sqrtm.py
BUG: sparse.linalg: Cast index arrays to intc before calling...
Allow johnsonsu parameters to be floats
MAINT: stats: fix NumPy DeprecationWarnings
REL, MAINT: prep for 1.11.2
DOC: Fix broken link to installation guide in README
BUG: Ensure cKDtree.query does not pass Pandas DataFrame to np.isfinite
CI, MAINT: 32-bit Pillow pin
BLD: copy \`cython_optimize.pxd\` to build dir
BUG: make \`L-BFGS-B\` optimizer work with single precision gradient
BUG: io/matlab: Fix loading of mat files containing fn handles...
BUG: make Bessel-roots function not hang and not skip roots
DOC: linking interp1d docstring to tutorial
BUG: lsq trf gives x=1e-10 if x0 is near a bound
CI/BLD: create cp312 wheels
DOC: Fix installation instructions using venv/pip
CI: move the musllinux Cirrus job to GHA, optimize other jobs
CI: reduce Cirrus CI usage during wheel builds
BUG: interpolate: fix spalde with len(c) < len(t)
BUG: pass unused xrtol in fmin_bfgs to _minimize_bfgs
BLD: rename \`setup.py\` to \`_setup.py\` to signal it should...
MAINT: NumPy 1.25.x deprecations
MAINT: ensure cobyla objective returns scalar
To generate a diff of this commit:
cvs rdiff -u -r1.67 -r1.68 pkgsrc/math/py-scipy/Makefile
cvs rdiff -u -r1.25 -r1.26 pkgsrc/math/py-scipy/PLIST
cvs rdiff -u -r1.46 -r1.47 pkgsrc/math/py-scipy/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-scipy/Makefile
diff -u pkgsrc/math/py-scipy/Makefile:1.67 pkgsrc/math/py-scipy/Makefile:1.68
--- pkgsrc/math/py-scipy/Makefile:1.67 Wed Jul 12 16:26:29 2023
+++ pkgsrc/math/py-scipy/Makefile Fri Aug 25 15:19:19 2023
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.67 2023/07/12 16:26:29 adam Exp $
+# $NetBSD: Makefile,v 1.68 2023/08/25 15:19:19 adam Exp $
-DISTNAME= scipy-1.11.1
+DISTNAME= scipy-1.11.2
PKGNAME= ${PYPKGPREFIX}-${DISTNAME}
CATEGORIES= math python
MASTER_SITES= ${MASTER_SITE_PYPI:=s/scipy/}
@@ -10,8 +10,11 @@ HOMEPAGE= https://www.scipy.org/
COMMENT= Scientific Algorithms Library for Python
LICENSE= modified-bsd
-DEPENDS+= ${PYPKGPREFIX}-pybind11-[0-9]*:../../devel/py-pybind11
-DEPENDS+= ${PYPKGPREFIX}-pythran>=0.9.11:../../math/py-pythran
+TOOL_DEPENDS+= ${PYPKGPREFIX}-cython>=0.29.35:../../devel/py-cython
+TOOL_DEPENDS+= ${PYPKGPREFIX}-meson_python-[0-9]*:../../devel/py-meson_python
+TOOL_DEPENDS+= ${PYPKGPREFIX}-wheel-[0-9]*:../../devel/py-wheel
+DEPENDS+= ${PYPKGPREFIX}-pybind11>=2.10.4:../../devel/py-pybind11
+DEPENDS+= ${PYPKGPREFIX}-pythran>=0.12.0:../../math/py-pythran
TEST_DEPENDS+= ${PYPKGPREFIX}-mpmath-[0-9]*:../../math/py-mpmath
TEST_DEPENDS+= ${PYPKGPREFIX}-nose-[0-9]*:../../devel/py-nose
TEST_DEPENDS+= ${PYPKGPREFIX}-pooch-[0-9]*:../../devel/py-pooch
@@ -21,10 +24,17 @@ TEST_DEPENDS+= ${PYPKGPREFIX}-test-timeo
TEST_DEPENDS+= ${PYPKGPREFIX}-test-xdist-[0-9]*:../../devel/py-test-xdist
USE_LANGUAGES+= c99 c++11 fortran
+USE_TOOLS+= pkg-config
MAKE_ENV+= ATLAS=None
GCC_REQD+= 8
EGG_NAME= ${DISTNAME:S/scipy/SciPy/}
+SUBST_CLASSES+= pythran
+SUBST_STAGE.pythran= pre-configure
+SUBST_MESSAGE.pythran= Fixing pythran binary name.
+SUBST_FILES.pythran= meson.build
+SUBST_SED.pythran= -e "s,'pythran','pythran-${PYVERSSUFFIX}',"
+
# XXX Avoid picking up other compilers when installed
.include "../../mk/compiler.mk"
@@ -65,8 +75,9 @@ do-test:
.include "../../devel/py-cython/buildlink3.mk"
.include "../../devel/py-pybind11/buildlink3.mk"
.include "../../lang/python/application.mk"
-.include "../../lang/python/egg.mk"
+.include "../../lang/python/wheel.mk"
.include "../../math/fftw/buildlink3.mk"
+.include "../../math/openblas/buildlink3.mk"
BUILDLINK_API_DEPENDS.py-numpy+= ${PYPKGPREFIX}-numpy>=1.21.6
.include "../../math/py-numpy/buildlink3.mk"
.include "../../math/py-pythran/buildlink3.mk"
Index: pkgsrc/math/py-scipy/PLIST
diff -u pkgsrc/math/py-scipy/PLIST:1.25 pkgsrc/math/py-scipy/PLIST:1.26
--- pkgsrc/math/py-scipy/PLIST:1.25 Wed Jul 12 16:26:29 2023
+++ pkgsrc/math/py-scipy/PLIST Fri Aug 25 15:19:19 2023
@@ -1,531 +1,403 @@
-@comment $NetBSD: PLIST,v 1.25 2023/07/12 16:26:29 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
-${PYSITELIB}/scipy/LICENSE.txt
-${PYSITELIB}/scipy/LICENSES_bundled.txt
+@comment $NetBSD: PLIST,v 1.26 2023/08/25 15:19:19 adam Exp $
+${PYSITELIB}/${WHEEL_INFODIR}/INSTALLER
+${PYSITELIB}/${WHEEL_INFODIR}/LICENSE.txt
+${PYSITELIB}/${WHEEL_INFODIR}/METADATA
+${PYSITELIB}/${WHEEL_INFODIR}/RECORD
+${PYSITELIB}/${WHEEL_INFODIR}/REQUESTED
+${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
+${PYSITELIB}/${WHEEL_INFODIR}/direct_url.json
${PYSITELIB}/scipy/__config__.py
${PYSITELIB}/scipy/__config__.pyc
-${PYSITELIB}/scipy/__config__.pyo
${PYSITELIB}/scipy/__init__.py
${PYSITELIB}/scipy/__init__.pyc
-${PYSITELIB}/scipy/__init__.pyo
-${PYSITELIB}/scipy/_build_utils/__init__.py
-${PYSITELIB}/scipy/_build_utils/__init__.pyc
-${PYSITELIB}/scipy/_build_utils/__init__.pyo
-${PYSITELIB}/scipy/_build_utils/_fortran.py
-${PYSITELIB}/scipy/_build_utils/_fortran.pyc
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-${PYSITELIB}/scipy/_build_utils/compiler_helper.py
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${PYSITELIB}/scipy/special/tests/test_zeta.py
+${PYSITELIB}/scipy/special/tests/test_zeta.pyc
${PYSITELIB}/scipy/stats/__init__.py
${PYSITELIB}/scipy/stats/__init__.pyc
-${PYSITELIB}/scipy/stats/__init__.pyo
${PYSITELIB}/scipy/stats/_axis_nan_policy.py
${PYSITELIB}/scipy/stats/_axis_nan_policy.pyc
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${PYSITELIB}/scipy/stats/_biasedurn.pxd
${PYSITELIB}/scipy/stats/_biasedurn.so
${PYSITELIB}/scipy/stats/_binned_statistic.py
${PYSITELIB}/scipy/stats/_binned_statistic.pyc
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${PYSITELIB}/scipy/stats/_binomtest.py
${PYSITELIB}/scipy/stats/_binomtest.pyc
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${PYSITELIB}/scipy/stats/_boost/__init__.py
${PYSITELIB}/scipy/stats/_boost/__init__.pyc
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${PYSITELIB}/scipy/stats/_boost/beta_ufunc.so
${PYSITELIB}/scipy/stats/_boost/binom_ufunc.so
${PYSITELIB}/scipy/stats/_boost/hypergeom_ufunc.so
@@ -2181,204 +1855,137 @@ ${PYSITELIB}/scipy/stats/_boost/nbinom_u
${PYSITELIB}/scipy/stats/_boost/ncf_ufunc.so
${PYSITELIB}/scipy/stats/_boost/nct_ufunc.so
${PYSITELIB}/scipy/stats/_boost/ncx2_ufunc.so
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${PYSITELIB}/scipy/stats/_boost/skewnorm_ufunc.so
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${PYSITELIB}/scipy/stats/_common.py
${PYSITELIB}/scipy/stats/_common.pyc
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${PYSITELIB}/scipy/stats/_constants.py
${PYSITELIB}/scipy/stats/_constants.pyc
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${PYSITELIB}/scipy/stats/_continuous_distns.py
${PYSITELIB}/scipy/stats/_continuous_distns.pyc
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${PYSITELIB}/scipy/stats/_covariance.py
${PYSITELIB}/scipy/stats/_covariance.pyc
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${PYSITELIB}/scipy/stats/_crosstab.py
${PYSITELIB}/scipy/stats/_crosstab.pyc
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${PYSITELIB}/scipy/stats/_discrete_distns.py
${PYSITELIB}/scipy/stats/_discrete_distns.pyc
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${PYSITELIB}/scipy/stats/_distn_infrastructure.py
${PYSITELIB}/scipy/stats/_distn_infrastructure.pyc
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${PYSITELIB}/scipy/stats/_distr_params.py
${PYSITELIB}/scipy/stats/_distr_params.pyc
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${PYSITELIB}/scipy/stats/_entropy.py
${PYSITELIB}/scipy/stats/_entropy.pyc
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${PYSITELIB}/scipy/stats/_fit.py
${PYSITELIB}/scipy/stats/_fit.pyc
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${PYSITELIB}/scipy/stats/_generate_pyx.py
${PYSITELIB}/scipy/stats/_generate_pyx.pyc
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${PYSITELIB}/scipy/stats/_hypotests.py
${PYSITELIB}/scipy/stats/_hypotests.pyc
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${PYSITELIB}/scipy/stats/_kde.py
${PYSITELIB}/scipy/stats/_kde.pyc
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${PYSITELIB}/scipy/stats/_ksstats.py
${PYSITELIB}/scipy/stats/_ksstats.pyc
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${PYSITELIB}/scipy/stats/_levy_stable/__init__.py
${PYSITELIB}/scipy/stats/_levy_stable/__init__.pyc
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${PYSITELIB}/scipy/stats/_levy_stable/levyst.so
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${PYSITELIB}/scipy/stats/_mannwhitneyu.py
${PYSITELIB}/scipy/stats/_mannwhitneyu.pyc
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${PYSITELIB}/scipy/stats/_morestats.py
${PYSITELIB}/scipy/stats/_morestats.pyc
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${PYSITELIB}/scipy/stats/_mstats_basic.py
${PYSITELIB}/scipy/stats/_mstats_basic.pyc
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${PYSITELIB}/scipy/stats/_mstats_extras.py
${PYSITELIB}/scipy/stats/_mstats_extras.pyc
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${PYSITELIB}/scipy/stats/_multicomp.py
${PYSITELIB}/scipy/stats/_multicomp.pyc
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${PYSITELIB}/scipy/stats/_multivariate.py
${PYSITELIB}/scipy/stats/_multivariate.pyc
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${PYSITELIB}/scipy/stats/_mvn.so
${PYSITELIB}/scipy/stats/_odds_ratio.py
${PYSITELIB}/scipy/stats/_odds_ratio.pyc
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${PYSITELIB}/scipy/stats/_page_trend_test.py
${PYSITELIB}/scipy/stats/_page_trend_test.pyc
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${PYSITELIB}/scipy/stats/_qmc.py
${PYSITELIB}/scipy/stats/_qmc.pyc
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${PYSITELIB}/scipy/stats/_qmc_cy.pyi
${PYSITELIB}/scipy/stats/_qmc_cy.so
${PYSITELIB}/scipy/stats/_qmvnt.py
${PYSITELIB}/scipy/stats/_qmvnt.pyc
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${PYSITELIB}/scipy/stats/_rcont/__init__.py
${PYSITELIB}/scipy/stats/_rcont/__init__.pyc
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${PYSITELIB}/scipy/stats/_rcont/rcont.so
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${PYSITELIB}/scipy/stats/_relative_risk.py
${PYSITELIB}/scipy/stats/_relative_risk.pyc
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${PYSITELIB}/scipy/stats/_resampling.py
${PYSITELIB}/scipy/stats/_resampling.pyc
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${PYSITELIB}/scipy/stats/_result_classes.py
${PYSITELIB}/scipy/stats/_result_classes.pyc
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${PYSITELIB}/scipy/stats/_rvs_sampling.py
${PYSITELIB}/scipy/stats/_rvs_sampling.pyc
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${PYSITELIB}/scipy/stats/_sensitivity_analysis.py
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${PYSITELIB}/scipy/stats/_sobol.pyi
${PYSITELIB}/scipy/stats/_sobol.so
${PYSITELIB}/scipy/stats/_sobol_direction_numbers.npz
${PYSITELIB}/scipy/stats/_statlib.so
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${PYSITELIB}/scipy/stats/_stats.so
${PYSITELIB}/scipy/stats/_stats_mstats_common.py
${PYSITELIB}/scipy/stats/_stats_mstats_common.pyc
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${PYSITELIB}/scipy/stats/_stats_py.py
${PYSITELIB}/scipy/stats/_stats_py.pyc
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${PYSITELIB}/scipy/stats/_survival.py
${PYSITELIB}/scipy/stats/_survival.pyc
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${PYSITELIB}/scipy/stats/_tukeylambda_stats.py
${PYSITELIB}/scipy/stats/_tukeylambda_stats.pyc
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${PYSITELIB}/scipy/stats/_unuran/__init__.py
${PYSITELIB}/scipy/stats/_unuran/__init__.pyc
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${PYSITELIB}/scipy/stats/_warnings_errors.py
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${PYSITELIB}/scipy/stats/kde.py
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${PYSITELIB}/scipy/stats/mstats.py
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${PYSITELIB}/scipy/stats/mstats_basic.py
${PYSITELIB}/scipy/stats/mstats_basic.pyc
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${PYSITELIB}/scipy/stats/mstats_extras.pyc
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${PYSITELIB}/scipy/stats/mvn.py
${PYSITELIB}/scipy/stats/mvn.pyc
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${PYSITELIB}/scipy/stats/qmc.py
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${PYSITELIB}/scipy/stats/sampling.py
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${PYSITELIB}/scipy/stats/statlib.py
${PYSITELIB}/scipy/stats/statlib.pyc
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${PYSITELIB}/scipy/stats/stats.py
${PYSITELIB}/scipy/stats/stats.pyc
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${PYSITELIB}/scipy/stats/tests/__init__.py
+${PYSITELIB}/scipy/stats/tests/__init__.pyc
${PYSITELIB}/scipy/stats/tests/common_tests.py
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${PYSITELIB}/scipy/stats/tests/data/_mvt.py
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${PYSITELIB}/scipy/stats/tests/data/fisher_exact_results_from_r.py
-${PYSITELIB}/scipy/stats/tests/data/levy_stable/meson.build
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${PYSITELIB}/scipy/stats/tests/data/levy_stable/stable-Z1-cdf-sample-data.npy
${PYSITELIB}/scipy/stats/tests/data/levy_stable/stable-Z1-pdf-sample-data.npy
${PYSITELIB}/scipy/stats/tests/data/levy_stable/stable-loc-scale-sample-data.npy
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${PYSITELIB}/scipy/stats/tests/data/nist_anova/AtmWtAg.dat
${PYSITELIB}/scipy/stats/tests/data/nist_anova/SiRstv.dat
${PYSITELIB}/scipy/stats/tests/data/nist_anova/SmLs01.dat
@@ -2390,48 +1997,70 @@ ${PYSITELIB}/scipy/stats/tests/data/nist
${PYSITELIB}/scipy/stats/tests/data/nist_anova/SmLs07.dat
${PYSITELIB}/scipy/stats/tests/data/nist_anova/SmLs08.dat
${PYSITELIB}/scipy/stats/tests/data/nist_anova/SmLs09.dat
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${PYSITELIB}/scipy/stats/tests/data/nist_linregress/Norris.dat
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${PYSITELIB}/scipy/stats/tests/data/rel_breitwigner_pdf_sample_data_ROOT.npy
${PYSITELIB}/scipy/stats/tests/data/studentized_range_mpmath_ref.json
-${PYSITELIB}/scipy/stats/tests/meson.build
${PYSITELIB}/scipy/stats/tests/test_axis_nan_policy.py
+${PYSITELIB}/scipy/stats/tests/test_axis_nan_policy.pyc
${PYSITELIB}/scipy/stats/tests/test_binned_statistic.py
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${PYSITELIB}/scipy/stats/tests/test_boost_ufuncs.py
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${PYSITELIB}/scipy/stats/tests/test_censored_data.py
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${PYSITELIB}/scipy/stats/tests/test_continuous_basic.py
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${PYSITELIB}/scipy/stats/tests/test_continuous_fit_censored.py
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${PYSITELIB}/scipy/stats/tests/test_crosstab.py
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${PYSITELIB}/scipy/stats/tests/test_discrete_basic.py
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${PYSITELIB}/scipy/stats/tests/test_discrete_distns.py
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${PYSITELIB}/scipy/stats/tests/test_fit.py
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${PYSITELIB}/scipy/stats/tests/test_hypotests.py
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${PYSITELIB}/scipy/stats/tests/test_kdeoth.py
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${PYSITELIB}/scipy/stats/tests/test_multivariate.py
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${PYSITELIB}/scipy/stats/tests/test_relative_risk.py
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${PYSITELIB}/scipy/stats/tests/test_sensitivity_analysis.py
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${PYSITELIB}/scipy/stats/tests/test_stats.py
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${PYSITELIB}/scipy/stats/tests/test_survival.py
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${PYSITELIB}/scipy/stats/tests/test_tukeylambda_stats.py
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${PYSITELIB}/scipy/stats/tests/test_variation.py
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${PYSITELIB}/scipy/version.py
${PYSITELIB}/scipy/version.pyc
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Index: pkgsrc/math/py-scipy/distinfo
diff -u pkgsrc/math/py-scipy/distinfo:1.46 pkgsrc/math/py-scipy/distinfo:1.47
--- pkgsrc/math/py-scipy/distinfo:1.46 Mon Jul 17 19:39:56 2023
+++ pkgsrc/math/py-scipy/distinfo Fri Aug 25 15:19:19 2023
@@ -1,8 +1,8 @@
-$NetBSD: distinfo,v 1.46 2023/07/17 19:39:56 tnn Exp $
+$NetBSD: distinfo,v 1.47 2023/08/25 15:19:19 adam Exp $
-BLAKE2s (scipy-1.11.1.tar.gz) = 1fe93584ad30db4c1e2686cb74ad291e3f62ffe49c4d8afcc6d1d5bccfd26268
-SHA512 (scipy-1.11.1.tar.gz) = 2859fc73c4fef713497f450b76a57d274bb46477a08ac909714823225f065a13c1e42a61ce67575cfc475e1e4612090cc4ca0920411fe32370c5b5c476352f97
-Size (scipy-1.11.1.tar.gz) = 56031509 bytes
+BLAKE2s (scipy-1.11.2.tar.gz) = b1b604d63b97d0cf5fb551d227761214b88881f9e3be2195c0f69f5902eb96be
+SHA512 (scipy-1.11.2.tar.gz) = f6902d48617827d01f69c057f3c4790c7388bc58df0791ade96e073740253bc0529475f9fc22d00c23c0b649acaeb820792528d3805d0ac68588c329aa87b3f2
+Size (scipy-1.11.2.tar.gz) = 56045065 bytes
SHA1 (patch-scipy_spatial___ckdtree.pyx) = 09f79827790edb78204cca7bbe25b5f373834dd4
SHA1 (patch-scipy_spatial_ckdtree_src_ckdtree__decl.h) = c5684427731eef00c012b1ebc7fba00da560f493
SHA1 (patch-scipy_special_Faddeeva.hh) = 9f6c0bb808fc9be0a1c1b7e65395d29f13821233
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