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[pkgsrc/trunk]: pkgsrc/math/py-scipy py-scipy: updated to 1.1.0



details:   https://anonhg.NetBSD.org/pkgsrc/rev/1b3bea6eb7ac
branches:  trunk
changeset: 307812:1b3bea6eb7ac
user:      adam <adam%pkgsrc.org@localhost>
date:      Mon May 14 06:39:32 2018 +0000
description:
py-scipy: updated to 1.1.0

SciPy 1.1.0 is the culmination of 7 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
1.1.x branch, and on adding new features on the master branch.

diffstat:

 math/py-scipy/Makefile     |  11 +-----
 math/py-scipy/PLIST        |  82 +++++++++++++++++++++++++++++++++++++++++++--
 math/py-scipy/PLIST.Darwin |  65 ------------------------------------
 math/py-scipy/distinfo     |  10 ++--
 4 files changed, 85 insertions(+), 83 deletions(-)

diffs (truncated from 348 to 300 lines):

diff -r d31ea9aa1f90 -r 1b3bea6eb7ac math/py-scipy/Makefile
--- a/math/py-scipy/Makefile    Mon May 14 06:36:17 2018 +0000
+++ b/math/py-scipy/Makefile    Mon May 14 06:39:32 2018 +0000
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.32 2018/05/12 21:21:46 jperkin Exp $
+# $NetBSD: Makefile,v 1.33 2018/05/14 06:39:32 adam Exp $
 
-DISTNAME=      scipy-1.0.1
+DISTNAME=      scipy-1.1.0
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
 CATEGORIES=    math python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=s/scipy/}
@@ -13,8 +13,6 @@
 USE_LANGUAGES+=        c c++ fortran
 MAKE_ENV+=     ATLAS=None
 
-PLIST_VARS+=   dsym
-
 # XXX Avoid picking up other compilers when installed
 .include "../../mk/compiler.mk"
 
@@ -22,9 +20,6 @@
 PYSETUPBUILDARGS+=     --fcompiler=g95
 .elif defined(PKGSRC_FORTRAN) && !empty(PKGSRC_FORTRAN:Mgfortran)
 PYSETUPBUILDARGS+=     --fcompiler=gnu95
-.  if defined(GFORTRAN_VERSION) && ${GFORTRAN_VERSION} == "7"
-PLIST.dsym=    yes
-.  endif
 LDFLAGS.Darwin+=       -undefined dynamic_lookup
 .else
 BROKEN=                Requires fortran 95
@@ -93,7 +88,6 @@
 post-install: fix-darwin-install-name
 fix-darwin-install-name:
        ${FIND} ${DESTDIR}${PREFIX} -name "*.so" |                      \
-               ${GREP} -v "dSYM/Contents/Resources/DWARF/" |           \
                while read lib; do                                      \
                libname=`basename $${lib}`;                             \
                libdir=`dirname $${lib} | sed -e 's,${DESTDIR},,'`;     \
@@ -110,7 +104,6 @@
 # https://github.com/scipy/scipy/issues/6499
 do-test:
        ${PYTHONBIN} -c "import scipy; scipy.test('full')"
-#      cd ${WRKSRC} && ${PYTHONBIN} runtests.py -v
 
 .include "../../lang/python/application.mk"
 .include "../../lang/python/distutils.mk"
diff -r d31ea9aa1f90 -r 1b3bea6eb7ac math/py-scipy/PLIST
--- a/math/py-scipy/PLIST       Mon May 14 06:36:17 2018 +0000
+++ b/math/py-scipy/PLIST       Mon May 14 06:39:32 2018 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.13 2017/11/02 09:40:29 adam Exp $
+@comment $NetBSD: PLIST,v 1.14 2018/05/14 06:39:32 adam Exp $
 ${PYSITELIB}/${EGG_FILE}/PKG-INFO
 ${PYSITELIB}/${EGG_FILE}/SOURCES.txt
 ${PYSITELIB}/${EGG_FILE}/dependency_links.txt
@@ -70,6 +70,7 @@
 ${PYSITELIB}/scipy/_lib/tests/test__util.py
 ${PYSITELIB}/scipy/_lib/tests/test__version.py
 ${PYSITELIB}/scipy/_lib/tests/test_ccallback.py
+${PYSITELIB}/scipy/_lib/tests/test_import_cycles.py
 ${PYSITELIB}/scipy/_lib/tests/test_tmpdirs.py
 ${PYSITELIB}/scipy/_lib/tests/test_warnings.py
 ${PYSITELIB}/scipy/cluster/__init__.py
@@ -561,6 +562,9 @@
 ${PYSITELIB}/scipy/linalg/_cython_signature_generator.py
 ${PYSITELIB}/scipy/linalg/_cython_signature_generator.pyc
 ${PYSITELIB}/scipy/linalg/_cython_signature_generator.pyo
+${PYSITELIB}/scipy/linalg/_decomp_ldl.py
+${PYSITELIB}/scipy/linalg/_decomp_ldl.pyc
+${PYSITELIB}/scipy/linalg/_decomp_ldl.pyo
 ${PYSITELIB}/scipy/linalg/_decomp_polar.py
 ${PYSITELIB}/scipy/linalg/_decomp_polar.pyc
 ${PYSITELIB}/scipy/linalg/_decomp_polar.pyo
@@ -668,6 +672,7 @@
 ${PYSITELIB}/scipy/linalg/tests/test_cython_lapack.py
 ${PYSITELIB}/scipy/linalg/tests/test_decomp.py
 ${PYSITELIB}/scipy/linalg/tests/test_decomp_cholesky.py
+${PYSITELIB}/scipy/linalg/tests/test_decomp_ldl.py
 ${PYSITELIB}/scipy/linalg/tests/test_decomp_polar.py
 ${PYSITELIB}/scipy/linalg/tests/test_decomp_update.py
 ${PYSITELIB}/scipy/linalg/tests/test_fblas.py
@@ -689,6 +694,7 @@
 ${PYSITELIB}/scipy/misc/doccer.py
 ${PYSITELIB}/scipy/misc/doccer.pyc
 ${PYSITELIB}/scipy/misc/doccer.pyo
+${PYSITELIB}/scipy/misc/ecg.dat
 ${PYSITELIB}/scipy/misc/face.dat
 ${PYSITELIB}/scipy/misc/pilutil.py
 ${PYSITELIB}/scipy/misc/pilutil.pyc
@@ -732,6 +738,9 @@
 ${PYSITELIB}/scipy/ndimage/_ctest_oldapi.so
 ${PYSITELIB}/scipy/ndimage/_cytest.so
 ${PYSITELIB}/scipy/ndimage/_nd_image.so
+${PYSITELIB}/scipy/ndimage/_ni_docstrings.py
+${PYSITELIB}/scipy/ndimage/_ni_docstrings.pyc
+${PYSITELIB}/scipy/ndimage/_ni_docstrings.pyo
 ${PYSITELIB}/scipy/ndimage/_ni_label.so
 ${PYSITELIB}/scipy/ndimage/_ni_support.py
 ${PYSITELIB}/scipy/ndimage/_ni_support.pyc
@@ -770,6 +779,7 @@
 ${PYSITELIB}/scipy/ndimage/tests/test_measurements.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
 ${PYSITELIB}/scipy/odr/__init__.pyo
@@ -795,10 +805,19 @@
 ${PYSITELIB}/scipy/optimize/_basinhopping.pyc
 ${PYSITELIB}/scipy/optimize/_basinhopping.pyo
 ${PYSITELIB}/scipy/optimize/_cobyla.so
+${PYSITELIB}/scipy/optimize/_constraints.py
+${PYSITELIB}/scipy/optimize/_constraints.pyc
+${PYSITELIB}/scipy/optimize/_constraints.pyo
+${PYSITELIB}/scipy/optimize/_differentiable_functions.py
+${PYSITELIB}/scipy/optimize/_differentiable_functions.pyc
+${PYSITELIB}/scipy/optimize/_differentiable_functions.pyo
 ${PYSITELIB}/scipy/optimize/_differentialevolution.py
 ${PYSITELIB}/scipy/optimize/_differentialevolution.pyc
 ${PYSITELIB}/scipy/optimize/_differentialevolution.pyo
 ${PYSITELIB}/scipy/optimize/_group_columns.so
+${PYSITELIB}/scipy/optimize/_hessian_update_strategy.py
+${PYSITELIB}/scipy/optimize/_hessian_update_strategy.pyc
+${PYSITELIB}/scipy/optimize/_hessian_update_strategy.pyo
 ${PYSITELIB}/scipy/optimize/_hungarian.py
 ${PYSITELIB}/scipy/optimize/_hungarian.pyc
 ${PYSITELIB}/scipy/optimize/_hungarian.pyo
@@ -865,6 +884,37 @@
 ${PYSITELIB}/scipy/optimize/_trustregion.py
 ${PYSITELIB}/scipy/optimize/_trustregion.pyc
 ${PYSITELIB}/scipy/optimize/_trustregion.pyo
+${PYSITELIB}/scipy/optimize/_trustregion_constr/__init__.py
+${PYSITELIB}/scipy/optimize/_trustregion_constr/__init__.pyc
+${PYSITELIB}/scipy/optimize/_trustregion_constr/__init__.pyo
+${PYSITELIB}/scipy/optimize/_trustregion_constr/canonical_constraint.py
+${PYSITELIB}/scipy/optimize/_trustregion_constr/canonical_constraint.pyc
+${PYSITELIB}/scipy/optimize/_trustregion_constr/canonical_constraint.pyo
+${PYSITELIB}/scipy/optimize/_trustregion_constr/equality_constrained_sqp.py
+${PYSITELIB}/scipy/optimize/_trustregion_constr/equality_constrained_sqp.pyc
+${PYSITELIB}/scipy/optimize/_trustregion_constr/equality_constrained_sqp.pyo
+${PYSITELIB}/scipy/optimize/_trustregion_constr/minimize_trustregion_constr.py
+${PYSITELIB}/scipy/optimize/_trustregion_constr/minimize_trustregion_constr.pyc
+${PYSITELIB}/scipy/optimize/_trustregion_constr/minimize_trustregion_constr.pyo
+${PYSITELIB}/scipy/optimize/_trustregion_constr/projections.py
+${PYSITELIB}/scipy/optimize/_trustregion_constr/projections.pyc
+${PYSITELIB}/scipy/optimize/_trustregion_constr/projections.pyo
+${PYSITELIB}/scipy/optimize/_trustregion_constr/qp_subproblem.py
+${PYSITELIB}/scipy/optimize/_trustregion_constr/qp_subproblem.pyc
+${PYSITELIB}/scipy/optimize/_trustregion_constr/qp_subproblem.pyo
+${PYSITELIB}/scipy/optimize/_trustregion_constr/report.py
+${PYSITELIB}/scipy/optimize/_trustregion_constr/report.pyc
+${PYSITELIB}/scipy/optimize/_trustregion_constr/report.pyo
+${PYSITELIB}/scipy/optimize/_trustregion_constr/setup.py
+${PYSITELIB}/scipy/optimize/_trustregion_constr/setup.pyc
+${PYSITELIB}/scipy/optimize/_trustregion_constr/setup.pyo
+${PYSITELIB}/scipy/optimize/_trustregion_constr/tests/__init__.py
+${PYSITELIB}/scipy/optimize/_trustregion_constr/tests/test_canonical_constraint.py
+${PYSITELIB}/scipy/optimize/_trustregion_constr/tests/test_projections.py
+${PYSITELIB}/scipy/optimize/_trustregion_constr/tests/test_qp_subproblem.py
+${PYSITELIB}/scipy/optimize/_trustregion_constr/tr_interior_point.py
+${PYSITELIB}/scipy/optimize/_trustregion_constr/tr_interior_point.pyc
+${PYSITELIB}/scipy/optimize/_trustregion_constr/tr_interior_point.pyo
 ${PYSITELIB}/scipy/optimize/_trustregion_dogleg.py
 ${PYSITELIB}/scipy/optimize/_trustregion_dogleg.pyc
 ${PYSITELIB}/scipy/optimize/_trustregion_dogleg.pyo
@@ -920,6 +970,9 @@
 ${PYSITELIB}/scipy/optimize/tests/test__root.py
 ${PYSITELIB}/scipy/optimize/tests/test__spectral.py
 ${PYSITELIB}/scipy/optimize/tests/test_cobyla.py
+${PYSITELIB}/scipy/optimize/tests/test_constraints.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
@@ -927,6 +980,7 @@
 ${PYSITELIB}/scipy/optimize/tests/test_linprog.py
 ${PYSITELIB}/scipy/optimize/tests/test_lsq_common.py
 ${PYSITELIB}/scipy/optimize/tests/test_lsq_linear.py
+${PYSITELIB}/scipy/optimize/tests/test_minimize_constrained.py
 ${PYSITELIB}/scipy/optimize/tests/test_minpack.py
 ${PYSITELIB}/scipy/optimize/tests/test_nnls.py
 ${PYSITELIB}/scipy/optimize/tests/test_nonlin.py
@@ -960,6 +1014,7 @@
 ${PYSITELIB}/scipy/signal/_peak_finding.py
 ${PYSITELIB}/scipy/signal/_peak_finding.pyc
 ${PYSITELIB}/scipy/signal/_peak_finding.pyo
+${PYSITELIB}/scipy/signal/_peak_finding_utils.so
 ${PYSITELIB}/scipy/signal/_savitzky_golay.py
 ${PYSITELIB}/scipy/signal/_savitzky_golay.pyc
 ${PYSITELIB}/scipy/signal/_savitzky_golay.pyo
@@ -1017,9 +1072,15 @@
 ${PYSITELIB}/scipy/signal/wavelets.py
 ${PYSITELIB}/scipy/signal/wavelets.pyc
 ${PYSITELIB}/scipy/signal/wavelets.pyo
-${PYSITELIB}/scipy/signal/windows.py
-${PYSITELIB}/scipy/signal/windows.pyc
-${PYSITELIB}/scipy/signal/windows.pyo
+${PYSITELIB}/scipy/signal/windows/__init__.py
+${PYSITELIB}/scipy/signal/windows/__init__.pyc
+${PYSITELIB}/scipy/signal/windows/__init__.pyo
+${PYSITELIB}/scipy/signal/windows/setup.py
+${PYSITELIB}/scipy/signal/windows/setup.pyc
+${PYSITELIB}/scipy/signal/windows/setup.pyo
+${PYSITELIB}/scipy/signal/windows/windows.py
+${PYSITELIB}/scipy/signal/windows/windows.pyc
+${PYSITELIB}/scipy/signal/windows/windows.pyo
 ${PYSITELIB}/scipy/sparse/__init__.py
 ${PYSITELIB}/scipy/sparse/__init__.pyc
 ${PYSITELIB}/scipy/sparse/__init__.pyo
@@ -1185,6 +1246,7 @@
 ${PYSITELIB}/scipy/sparse/linalg/isolve/tests/test_lgmres.py
 ${PYSITELIB}/scipy/sparse/linalg/isolve/tests/test_lsmr.py
 ${PYSITELIB}/scipy/sparse/linalg/isolve/tests/test_lsqr.py
+${PYSITELIB}/scipy/sparse/linalg/isolve/tests/test_minres.py
 ${PYSITELIB}/scipy/sparse/linalg/isolve/tests/test_utils.py
 ${PYSITELIB}/scipy/sparse/linalg/isolve/utils.py
 ${PYSITELIB}/scipy/sparse/linalg/isolve/utils.pyc
@@ -1319,15 +1381,24 @@
 ${PYSITELIB}/scipy/special/_precompute/gammainc_data.py
 ${PYSITELIB}/scipy/special/_precompute/gammainc_data.pyc
 ${PYSITELIB}/scipy/special/_precompute/gammainc_data.pyo
+${PYSITELIB}/scipy/special/_precompute/lambertw.py
+${PYSITELIB}/scipy/special/_precompute/lambertw.pyc
+${PYSITELIB}/scipy/special/_precompute/lambertw.pyo
 ${PYSITELIB}/scipy/special/_precompute/loggamma.py
 ${PYSITELIB}/scipy/special/_precompute/loggamma.pyc
 ${PYSITELIB}/scipy/special/_precompute/loggamma.pyo
 ${PYSITELIB}/scipy/special/_precompute/setup.py
 ${PYSITELIB}/scipy/special/_precompute/setup.pyc
 ${PYSITELIB}/scipy/special/_precompute/setup.pyo
+${PYSITELIB}/scipy/special/_precompute/struve_convergence.py
+${PYSITELIB}/scipy/special/_precompute/struve_convergence.pyc
+${PYSITELIB}/scipy/special/_precompute/struve_convergence.pyo
 ${PYSITELIB}/scipy/special/_precompute/utils.py
 ${PYSITELIB}/scipy/special/_precompute/utils.pyc
 ${PYSITELIB}/scipy/special/_precompute/utils.pyo
+${PYSITELIB}/scipy/special/_precompute/zetac.py
+${PYSITELIB}/scipy/special/_precompute/zetac.pyc
+${PYSITELIB}/scipy/special/_precompute/zetac.pyo
 ${PYSITELIB}/scipy/special/_spherical_bessel.py
 ${PYSITELIB}/scipy/special/_spherical_bessel.pyc
 ${PYSITELIB}/scipy/special/_spherical_bessel.pyo
@@ -1380,8 +1451,10 @@
 ${PYSITELIB}/scipy/special/tests/test_logit.py
 ${PYSITELIB}/scipy/special/tests/test_logsumexp.py
 ${PYSITELIB}/scipy/special/tests/test_mpmath.py
+${PYSITELIB}/scipy/special/tests/test_nan_inputs.py
 ${PYSITELIB}/scipy/special/tests/test_orthogonal.py
 ${PYSITELIB}/scipy/special/tests/test_orthogonal_eval.py
+${PYSITELIB}/scipy/special/tests/test_owens_t.py
 ${PYSITELIB}/scipy/special/tests/test_pcf.py
 ${PYSITELIB}/scipy/special/tests/test_precompute_expn_asy.py
 ${PYSITELIB}/scipy/special/tests/test_precompute_gammainc.py
@@ -1395,6 +1468,7 @@
 ${PYSITELIB}/scipy/special/tests/test_spherical_bessel.py
 ${PYSITELIB}/scipy/special/tests/test_trig.py
 ${PYSITELIB}/scipy/special/tests/test_wrightomega.py
+${PYSITELIB}/scipy/special/tests/test_zeta.py
 ${PYSITELIB}/scipy/stats/__init__.py
 ${PYSITELIB}/scipy/stats/__init__.pyc
 ${PYSITELIB}/scipy/stats/__init__.pyo
diff -r d31ea9aa1f90 -r 1b3bea6eb7ac math/py-scipy/PLIST.Darwin
--- a/math/py-scipy/PLIST.Darwin        Mon May 14 06:36:17 2018 +0000
+++ /dev/null   Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-@comment $NetBSD: PLIST.Darwin,v 1.1 2018/05/11 14:18:47 minskim Exp $
-${PLIST.dsym}${PYSITELIB}/scipy/fftpack/_fftpack.so.dSYM/Contents/Info.plist
-${PLIST.dsym}${PYSITELIB}/scipy/fftpack/_fftpack.so.dSYM/Contents/Resources/DWARF/_fftpack.so
-${PLIST.dsym}${PYSITELIB}/scipy/fftpack/convolve.so.dSYM/Contents/Info.plist
-${PLIST.dsym}${PYSITELIB}/scipy/fftpack/convolve.so.dSYM/Contents/Resources/DWARF/convolve.so
-${PLIST.dsym}${PYSITELIB}/scipy/integrate/_dop.so.dSYM/Contents/Info.plist
-${PLIST.dsym}${PYSITELIB}/scipy/integrate/_dop.so.dSYM/Contents/Resources/DWARF/_dop.so
-${PLIST.dsym}${PYSITELIB}/scipy/integrate/_odepack.so.dSYM/Contents/Info.plist
-${PLIST.dsym}${PYSITELIB}/scipy/integrate/_odepack.so.dSYM/Contents/Resources/DWARF/_odepack.so
-${PLIST.dsym}${PYSITELIB}/scipy/integrate/_quadpack.so.dSYM/Contents/Info.plist
-${PLIST.dsym}${PYSITELIB}/scipy/integrate/_quadpack.so.dSYM/Contents/Resources/DWARF/_quadpack.so
-${PLIST.dsym}${PYSITELIB}/scipy/integrate/_test_odeint_banded.so.dSYM/Contents/Info.plist
-${PLIST.dsym}${PYSITELIB}/scipy/integrate/_test_odeint_banded.so.dSYM/Contents/Resources/DWARF/_test_odeint_banded.so
-${PLIST.dsym}${PYSITELIB}/scipy/integrate/lsoda.so.dSYM/Contents/Info.plist
-${PLIST.dsym}${PYSITELIB}/scipy/integrate/lsoda.so.dSYM/Contents/Resources/DWARF/lsoda.so
-${PLIST.dsym}${PYSITELIB}/scipy/integrate/vode.so.dSYM/Contents/Info.plist
-${PLIST.dsym}${PYSITELIB}/scipy/integrate/vode.so.dSYM/Contents/Resources/DWARF/vode.so
-${PLIST.dsym}${PYSITELIB}/scipy/interpolate/_bspl.so.dSYM/Contents/Info.plist
-${PLIST.dsym}${PYSITELIB}/scipy/interpolate/_bspl.so.dSYM/Contents/Resources/DWARF/_bspl.so
-${PLIST.dsym}${PYSITELIB}/scipy/interpolate/_fitpack.so.dSYM/Contents/Info.plist
-${PLIST.dsym}${PYSITELIB}/scipy/interpolate/_fitpack.so.dSYM/Contents/Resources/DWARF/_fitpack.so
-${PLIST.dsym}${PYSITELIB}/scipy/interpolate/dfitpack.so.dSYM/Contents/Info.plist
-${PLIST.dsym}${PYSITELIB}/scipy/interpolate/dfitpack.so.dSYM/Contents/Resources/DWARF/dfitpack.so
-${PLIST.dsym}${PYSITELIB}/scipy/io/_test_fortran.so.dSYM/Contents/Info.plist
-${PLIST.dsym}${PYSITELIB}/scipy/io/_test_fortran.so.dSYM/Contents/Resources/DWARF/_test_fortran.so
-${PLIST.dsym}${PYSITELIB}/scipy/linalg/_fblas.so.dSYM/Contents/Info.plist
-${PLIST.dsym}${PYSITELIB}/scipy/linalg/_fblas.so.dSYM/Contents/Resources/DWARF/_fblas.so
-${PLIST.dsym}${PYSITELIB}/scipy/linalg/_flapack.so.dSYM/Contents/Info.plist
-${PLIST.dsym}${PYSITELIB}/scipy/linalg/_flapack.so.dSYM/Contents/Resources/DWARF/_flapack.so
-${PLIST.dsym}${PYSITELIB}/scipy/linalg/_flinalg.so.dSYM/Contents/Info.plist
-${PLIST.dsym}${PYSITELIB}/scipy/linalg/_flinalg.so.dSYM/Contents/Resources/DWARF/_flinalg.so
-${PLIST.dsym}${PYSITELIB}/scipy/linalg/_interpolative.so.dSYM/Contents/Info.plist
-${PLIST.dsym}${PYSITELIB}/scipy/linalg/_interpolative.so.dSYM/Contents/Resources/DWARF/_interpolative.so



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