!55 upgrade to 1.12.0
From: @SuperSix173 Reviewed-by: @wangbin224 Signed-off-by: @wangbin224
This commit is contained in:
openeuler-ci-bot
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commit
33377d95d2
@ -1,66 +0,0 @@
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From 3c89445b6439f3ce7bffc4cf11c6407c39faedc5 Mon Sep 17 00:00:00 2001
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From: Matus Valo <matusvalo@users.noreply.github.com>
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Date: Thu, 6 Jul 2023 16:55:25 +0200
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Subject: [PATCH] BLD: copy `cython_optimize.pxd` to build dir (#18810)
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Closes gh-18792
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[skip cirrus] [skip circle]
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---------
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Co-authored-by: Ralf Gommers <ralf.gommers@gmail.com>
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---
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scipy/optimize/cython_optimize.pxd | 2 +-
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scipy/optimize/cython_optimize/meson.build | 1 +
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scipy/optimize/meson.build | 8 +++++++-
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3 files changed, 9 insertions(+), 2 deletions(-)
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diff --git a/scipy/optimize/cython_optimize.pxd b/scipy/optimize/cython_optimize.pxd
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index d5a0bdd75..d35f8da68 100644
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--- a/scipy/optimize/cython_optimize.pxd
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+++ b/scipy/optimize/cython_optimize.pxd
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@@ -7,5 +7,5 @@
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# support. Changing it causes an ABI forward-compatibility break
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# (gh-11793), so we currently leave it as is (no further cimport
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# statements should be used in this file).
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-from .cython_optimize._zeros cimport (
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+from scipy.optimize.cython_optimize._zeros cimport (
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brentq, brenth, ridder, bisect, zeros_full_output)
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diff --git a/scipy/optimize/cython_optimize/meson.build b/scipy/optimize/cython_optimize/meson.build
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index 359ea8418..ee8def39b 100644
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--- a/scipy/optimize/cython_optimize/meson.build
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+++ b/scipy/optimize/cython_optimize/meson.build
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@@ -17,6 +17,7 @@ cy_opt_gen = generator(cython,
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arguments : cython_args,
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output : '@BASENAME@.c',
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depends : [_cython_tree,
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+ cython_optimize_pxd,
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_dummy_init_optimize,
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_dummy_init_cyoptimize])
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diff --git a/scipy/optimize/meson.build b/scipy/optimize/meson.build
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index 26458b05c..4c5ab7983 100644
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--- a/scipy/optimize/meson.build
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+++ b/scipy/optimize/meson.build
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@@ -206,10 +206,16 @@ endif
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_dummy_init_optimize = fs.copyfile('__init__.py')
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+# Copying this .pxd file is only needed because of a Cython bug, see
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+# discussion on SciPy PR gh-18810.
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+cython_optimize_pxd = [
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+ fs.copyfile('cython_optimize.pxd'),
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+]
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+
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opt_gen = generator(cython,
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arguments : cython_args,
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output : '@BASENAME@.c',
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- depends : [_cython_tree, cython_linalg, _dummy_init_optimize])
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+ depends : [_cython_tree, cython_linalg, cython_optimize_pxd, _dummy_init_optimize])
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_bglu_dense_c = opt_gen.process('_bglu_dense.pyx')
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--
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2.23.0
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@ -1,47 +0,0 @@
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From a181fd5b75f2e05d1b7beafbb48157feaa468941 Mon Sep 17 00:00:00 2001
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From: Matus Valo <matusvalo@users.noreply.github.com>
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Date: Wed, 3 May 2023 22:22:36 +0200
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Subject: [PATCH] MAINT: Allow scipy to be compiled in cython3 (#18242)
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- Unpin Cython and use Cython master in the pre-release CI job
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- Use absolute instead of relative imports in a few places
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- Use `CYTHON_EXTERN_C` for C++ code exposing a C API
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[skip ci]
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---
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.github/workflows/linux_meson.yml | 5 ++---
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scipy/linalg.pxd | 2 +-
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scipy/special.pxd | 2 +-
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scipy/special/meson.build | 2 +-
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4 files changed, 5 insertions(+), 6 deletions(-)
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diff --git a/scipy/linalg.pxd b/scipy/linalg.pxd
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index 1f656b870..c7c49f9ad 100644
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--- a/scipy/linalg.pxd
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+++ b/scipy/linalg.pxd
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@@ -1 +1 @@
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-from .linalg cimport cython_blas, cython_lapack
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+from scipy.linalg cimport cython_blas, cython_lapack
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diff --git a/scipy/special.pxd b/scipy/special.pxd
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index 62cb82807..1daa9fb37 100644
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--- a/scipy/special.pxd
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+++ b/scipy/special.pxd
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@@ -1 +1 @@
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-from .special cimport cython_special
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+from scipy.special cimport cython_special
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diff --git a/scipy/special/meson.build b/scipy/special/meson.build
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index 334f87943..e7e25aa54 100644
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--- a/scipy/special/meson.build
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+++ b/scipy/special/meson.build
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@@ -371,7 +371,7 @@ py3.extension_module('_ufuncs_cxx',
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[ufuncs_cxx_sources,
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uf_cython_gen_cpp.process(cython_special[2]), # _ufuncs_cxx.pyx
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],
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- cpp_args: cython_cpp_args,
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+ cpp_args: [cython_cpp_args, '-DCYTHON_EXTERN_C=extern "C"'],
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include_directories: [inc_np, '../_lib/boost', '../_lib',
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'../_build_utils/src'],
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link_args: version_link_args,
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--
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2.23.0
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File diff suppressed because it is too large
Load Diff
@ -1,67 +0,0 @@
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From 50d0825256ddb76c5567e6cc8eb50e7d36908e21 Mon Sep 17 00:00:00 2001
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From: Matus Valo <matusvalo@gmail.com>
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Date: Mon, 17 Apr 2023 23:00:04 +0200
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Subject: [PATCH] Mark function pointer ctypedefs as noexcept
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---
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scipy/cluster/_hierarchy_distance_update.pxi | 2 +-
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scipy/optimize/cython_optimize/_zeros.pxd | 2 +-
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scipy/stats/_qmc_cy.pyx | 2 +-
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scipy/stats/_unuran/unuran_wrapper.pyx.templ | 2 +-
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4 files changed, 4 insertions(+), 4 deletions(-)
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diff --git a/scipy/cluster/_hierarchy_distance_update.pxi b/scipy/cluster/_hierarchy_distance_update.pxi
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index 17dedb305..bc57a3fa1 100644
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--- a/scipy/cluster/_hierarchy_distance_update.pxi
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+++ b/scipy/cluster/_hierarchy_distance_update.pxi
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@@ -24,7 +24,7 @@ d_xyi : double
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"""
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ctypedef double (*linkage_distance_update)(double d_xi, double d_yi,
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double d_xy, int size_x,
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- int size_y, int size_i)
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+ int size_y, int size_i) noexcept
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cdef double _single(double d_xi, double d_yi, double d_xy,
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diff --git a/scipy/optimize/cython_optimize/_zeros.pxd b/scipy/optimize/cython_optimize/_zeros.pxd
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index c6241d022..d3c9e98f0 100644
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--- a/scipy/optimize/cython_optimize/_zeros.pxd
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+++ b/scipy/optimize/cython_optimize/_zeros.pxd
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@@ -4,7 +4,7 @@
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# should be made to this file** --- any API additions/changes should be
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# done in `cython_optimize.pxd` (see gh-11793).
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-ctypedef double (*callback_type)(double, void*)
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+ctypedef double (*callback_type)(double, void*) noexcept
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ctypedef struct zeros_parameters:
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callback_type function
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diff --git a/scipy/stats/_qmc_cy.pyx b/scipy/stats/_qmc_cy.pyx
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index f165cb0d1..a9e94354f 100644
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--- a/scipy/stats/_qmc_cy.pyx
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+++ b/scipy/stats/_qmc_cy.pyx
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@@ -290,7 +290,7 @@ cdef double c_update_discrepancy(double[::1] x_new_view,
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ctypedef double (*func_type)(double[:, ::1], Py_ssize_t,
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- Py_ssize_t) nogil
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+ Py_ssize_t) noexcept nogil
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cdef double threaded_loops(func_type loop_func,
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diff --git a/scipy/stats/_unuran/unuran_wrapper.pyx.templ b/scipy/stats/_unuran/unuran_wrapper.pyx.templ
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index 2279dfc34..9eb63fb1c 100644
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--- a/scipy/stats/_unuran/unuran_wrapper.pyx.templ
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+++ b/scipy/stats/_unuran/unuran_wrapper.pyx.templ
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@@ -58,7 +58,7 @@ class UNURANError(RuntimeError):
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pass
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-ctypedef double (*URNG_FUNCT)(void *) nogil
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+ctypedef double (*URNG_FUNCT)(void *) noexcept nogil
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IF not NPY_OLD:
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cdef object get_numpy_rng(object seed = None):
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--
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2.23.0
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BIN
PROPACK.zip
Normal file
BIN
PROPACK.zip
Normal file
Binary file not shown.
BIN
array_api_compat.zip
Normal file
BIN
array_api_compat.zip
Normal file
Binary file not shown.
Binary file not shown.
BIN
scipy-1.12.0.tar.gz
Normal file
BIN
scipy-1.12.0.tar.gz
Normal file
Binary file not shown.
72
scipy.spec
72
scipy.spec
@ -1,21 +1,26 @@
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%global py_setup_args config_fc --fcompiler=gnu95 --noarch
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%global debug_package %{nil}
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Name: scipy
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Version: 1.10.1
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Release: 3
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Version: 1.12.0
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Release: 1
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Summary: A Python-based ecosystem of open-source software for mathematics, science, and engineering
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License: Qhull and Apache-2.0
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URL: https://www.scipy.org
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Source0: https://github.com/scipy/scipy/releases/download/v%{version}/scipy-%{version}.tar.gz
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# https://github.com/data-apis/array-api-compat/archive/affd3a56927d3d1c178023121f43c9fa624eced0.zip
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Source1: array_api_compat.zip
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# https://github.com/boostorg/math/archive/6bfe5818acdf86432f3e1a78ec5e1d3cdb8c6480.zip
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Source2: boost_math.zip
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# https://github.com/scipy/HiGHS/archive/4a122958a82e67e725d08153e099efe4dad099a2.zip
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Source3: highs.zip
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# https://github.com/scipy/unuran/archive/1d315c690787b14781a12e0beca6d25cc75562d6.zip
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Source4: unuran.zip
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# https://github.com/scipy/PROPACK/archive/96f6800451372dd003e627bbfd732937ac0c685e.zip
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Source5: PROPACK.zip
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Patch6001: 0001-MAINT-Explicitly-mark-cdef-functions-not-raising-exc.patch
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Patch6002: 0001-Mark-function-pointer-ctypedefs-as-noexcept.patch
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Patch6003: 0001-MAINT-Allow-scipy-to-be-compiled-in-cython3-18242.patch
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Patch6004: 0001-BLD-copy-cython_optimize.pxd-to-build-dir-18810.patch
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BuildRequires: python3-devel python3-numpy >= 1.8.2 python3-numpy-f2py
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BuildRequires: python3-devel python3-numpy-f2py
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BuildRequires: gcc-c++ openblas-devel gcc-gfortran chrpath
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BuildRequires: pybind11-devel python3-pybind11 python3-Cython
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BuildRequires: python3-meson-python python3-pip
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%description
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SciPy (pronounced "Sigh Pie") is open-source software for mathematics, science, and engineering.
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@ -39,46 +44,48 @@ python3 package for scipy
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%prep
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%autosetup -n %{name}-%{version} -p1
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cat > site.cfg << EOF
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[amd]
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library_dirs = %{_libdir}
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include_dirs = /usr/include/suitesparse
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amd_libs = amd
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sed -i '/pythran/d' pyproject.toml
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[umfpack]
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library_dirs = %{_libdir}
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include_dirs = /usr/include/suitesparse
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umfpack_libs = umfpack
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cat >> pyproject.toml << EOF
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[openblas]
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library_dirs = %{_libdir}
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openblas_libs = openblasp
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[tool.meson-python.args]
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setup = ['-Duse-pythran=false']
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EOF
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unzip %{SOURCE1}
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unzip %{SOURCE2}
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unzip %{SOURCE3}
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unzip %{SOURCE4}
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unzip %{SOURCE5}
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mv array-api-compat-affd3a56927d3d1c178023121f43c9fa624eced0/* scipy/_lib/array_api_compat/
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mv math-6bfe5818acdf86432f3e1a78ec5e1d3cdb8c6480/* scipy/_lib/boost_math/
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mv HiGHS-4a122958a82e67e725d08153e099efe4dad099a2/* scipy/_lib/highs/
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mv unuran-1d315c690787b14781a12e0beca6d25cc75562d6/* scipy/_lib/unuran/
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mv PROPACK-96f6800451372dd003e627bbfd732937ac0c685e/* scipy/sparse/linalg/_propack/PROPACK/
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rm -rf array-api-compat-affd3a56927d3d1c178023121f43c9fa624eced0
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rm -rf math-6bfe5818acdf86432f3e1a78ec5e1d3cdb8c6480
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rm -rf HiGHS-4a122958a82e67e725d08153e099efe4dad099a2
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rm -rf unuran-1d315c690787b14781a12e0beca6d25cc75562d6
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rm -rf PROPACK-96f6800451372dd003e627bbfd732937ac0c685e
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rm -rf %{py3dir}
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cp -a . %{py3dir}
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%build
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export SCIPY_USE_PYTHRAN=0
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export CFLAGS="$RPM_OPT_FLAGS -lm"
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export LDFLAGS="$RPM_LD_FLAGS -Wall -shared"
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export PKG_CONFIG_PATH=/use/lib64/pkgconfig
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pushd %{py3dir}
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%global _hardening_clang_cflags %{nil}
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env FFLAGS="$RPM_OPT_FLAGS -fPIC -w -fallow-argument-mismatch -O2"\
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OPENBLAS=%{_libdir} FFTW=%{_libdir} BLAS=%{_libdir} LAPACK=%{_libdir} \
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%py3_build
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%pyproject_build
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popd
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%install
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export SCIPY_USE_PYTHRAN=0
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export CFLAGS="$RPM_OPT_FLAGS -lm"
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export LDFLAGS="$RPM_LD_FLAGS -Wall -shared"
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pushd %{py3dir}
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env FFLAGS="$RPM_OPT_FLAGS -fPIC" \
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OPENBLAS=%{_libdir} FFTW=%{_libdir} BLAS=%{_libdir} LAPACK=%{_libdir} \
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%py3_install
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%pyproject_install scipy
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popd
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find %{buildroot} -type f -name '*.so' -exec strip '{}' ';'
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@ -102,10 +109,13 @@ echo "%{_libdir}/%{name}" >> $RPM_BUILD_ROOT/etc/ld.so.conf.d/%{name}-%{_arch}.c
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%files -n python3-scipy
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%license LICENSE.txt
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%{python3_sitearch}/scipy
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%{python3_sitearch}/*.egg-info
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%{python3_sitearch}/*.dist-info
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%config(noreplace) /etc/ld.so.conf.d/*
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%changelog
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* Thu Feb 22 2024 Liu Chao <liuchao173@huawei.com> - 1.12.0-1
|
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- Upgrade to 1.12.0
|
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* Thu Feb 1 2024 Liu Chao <liuchao173@huawei.com> - 1.10.1-3
|
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- Fix scipy compile error in cython3
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BIN
unuran.zip
Normal file
BIN
unuran.zip
Normal file
Binary file not shown.
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