alvistack/v1.5.4

    git clean -xdf
    tar zcvf ../python-scipy_1.5.4.orig.tar.gz --exclude=.git .
    debuild -uc -us
    cp python-scipy.spec ../python-scipy_1.5.4-1.spec
    cp ../python*-scipy*1.5.4*.{gz,xz,spec,dsc} /osc/home\:alvistack/scipy-scipy-1.5.4/
    rm -rf ../python*-scipy*1.5.4*.*

See scipy#16719

Signed-off-by: Wong Hoi Sing Edison <hswong3i@pantarei-design.com>

.gitignore

@@ -271,3 +271,5 @@ scipy/optimize/_group_columns.c
 scipy/optimize/cython_optimize/_zeros.c
 scipy/optimize/cython_optimize/_zeros.pyx
 scipy/optimize/lbfgsb/_lbfgsbmodule.c
+
+.pybuild/

debian/.gitignore

@@ -0,0 +1,6 @@
+*.substvars
+*debhelper*
+.debhelper
+files
+python3-scipy
+tmp

debian/changelog

@@ -0,0 +1,5 @@
+python-scipy (100:1.5.4-1) UNRELEASED; urgency=medium
+
+  * https://github.com/scipy/scipy/releases/tag/v1.5.4
+
+ -- Wong Hoi Sing Edison <hswong3i@pantarei-design.com>  Sun, 24 Dec 2023 12:34:50 +0800

debian/control

@@ -0,0 +1,47 @@
+Source: python-scipy
+Section: python
+Priority: optional
+Standards-Version: 4.5.0
+Maintainer: Wong Hoi Sing Edison <hswong3i@gmail.com>
+Homepage: https://github.com/scipy/scipy/tags
+Vcs-Browser: https://github.com/alvistack/scipy-scipy
+Vcs-Git: https://github.com/alvistack/scipy-scipy.git
+Build-Depends:
+ debhelper,
+ debhelper-compat (= 10),
+ dh-python,
+ cython3 (>= 0.29.18),
+ cython3 (<< 3.0.0),
+ fdupes,
+ gfortran,
+ liblapack-dev,
+ liblbfgsb-dev,
+ libopenblas-dev,
+ libsuitesparse-dev,
+ python3-decorator,
+ python3-dev,
+ python3-numpy (>= 1.14.5),
+ python3-pybind11 (>= 2.4.3),
+ python3-setuptools,
+
+Package: python3-scipy
+Architecture: amd64
+Description: Scientific Library for Python
+ SciPy (pronounced "Sigh Pie") is open-source software for mathematics,
+ science, and engineering. The SciPy library depends on NumPy, which
+ provides convenient and fast N-dimensional array manipulation. The SciPy
+ library is built to work with NumPy arrays, and provides many
+ user-friendly and efficient numerical routines such as routines for
+ numerical integration and optimization. Together, they run on all
+ popular operating systems, are quick to install, and are free of charge.
+ NumPy and SciPy are easy to use, but powerful enough to be depended upon
+ by some of the world’s leading scientists and engineers. If you need to
+ manipulate numbers on a computer and display or publish the results,
+ give SciPy a try!
+Depends:
+ ${misc:Depends},
+ ${python3:Depends},
+ ${shlibs:Depends},
+ python3,
+ python3-decorator,
+ python3-numpy (>= 1.14.5),

debian/copyright

@@ -0,0 +1,21 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+
+Files: debian/*
+Copyright: 2023 Wong Hoi Sing Edison <hswong3i@pantarei-design.com>
+License: Apache-2.0
+
+License: Apache-2.0
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+ .
+ http://www.apache.org/licenses/LICENSE-2.0
+ .
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+ .
+ The complete text of the Apache version 2.0 license
+ can be found in "/usr/share/common-licenses/Apache-2.0".

debian/python3-scipy.install

@@ -0,0 +1 @@
+usr/lib/python*/*-packages/*

debian/python3-scipy.lintian-overrides

@@ -0,0 +1,4 @@
+python3-scipy: copyright-without-copyright-notice
+python3-scipy: initial-upload-closes-no-bugs
+python3-scipy: no-manual-page
+python3-scipy: zero-byte-file-in-doc-directory

debian/rules

@@ -0,0 +1,15 @@
+#!/usr/bin/make -f
+
+SHELL := /bin/bash
+
+override_dh_auto_install:
+	dh_auto_install --destdir=debian/tmp
+	find debian/tmp/usr/lib/python*/*-packages -type f -name '*.pyc' -exec rm -rf {} \;
+	fdupes -qnrps debian/tmp/usr/lib/python*/*-packages
+
+override_dh_auto_test:
+
+override_dh_auto_clean:
+
+%:
+	dh $@ --buildsystem=pybuild --with python3

debian/source/format

@@ -0,0 +1 @@
+3.0 (quilt)

debian/source/lintian-overrides

@@ -0,0 +1,5 @@
+python-scipy source: file-without-copyright-information
+python-scipy source: no-debian-changes
+python-scipy source: source-contains-prebuilt-windows-binary
+python-scipy source: source-is-missing
+python-scipy source: source-package-encodes-python-version

python-scipy.spec

@@ -0,0 +1,130 @@
+# Copyright 2023 Wong Hoi Sing Edison <hswong3i@pantarei-design.com>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+%global debug_package %{nil}
+
+Name: python-scipy
+Epoch: 100
+Version: 1.5.4
+Release: 1%{?dist}
+Summary: Scientific Library for Python
+License: BSD-3-Clause
+URL: https://github.com/scipy/scipy/tags
+Source0: %{name}_%{version}.orig.tar.gz
+BuildRequires: fdupes
+BuildRequires: gcc-gfortran
+BuildRequires: lapack-devel
+BuildRequires: openblas-devel
+BuildRequires: pybind11-devel >= 2.4.3
+BuildRequires: python-rpm-macros
+BuildRequires: python3-cython >= 0.29.18
+BuildRequires: python3-cython < 3.0.0
+BuildRequires: python3-decorator
+BuildRequires: python3-devel
+BuildRequires: python3-numpy >= 1.14.5
+BuildRequires: python3-numpy-f2py >= 1.14.5
+BuildRequires: python3-pybind11 >= 2.4.3
+BuildRequires: python3-setuptools
+BuildRequires: suitesparse-devel
+
+%description
+SciPy (pronounced "Sigh Pie") is open-source software for mathematics,
+science, and engineering. The SciPy library depends on NumPy, which
+provides convenient and fast N-dimensional array manipulation. The SciPy
+library is built to work with NumPy arrays, and provides many
+user-friendly and efficient numerical routines such as routines for
+numerical integration and optimization. Together, they run on all
+popular operating systems, are quick to install, and are free of charge.
+NumPy and SciPy are easy to use, but powerful enough to be depended upon
+by some of the world’s leading scientists and engineers. If you need to
+manipulate numbers on a computer and display or publish the results,
+give SciPy a try!
+
+%prep
+%autosetup -T -c -n %{name}_%{version}-%{release}
+tar -zx -f %{S:0} --strip-components=1 -C .
+
+%build
+%py3_build
+
+%install
+%py3_install
+find %{buildroot}%{python3_sitearch} -type f -name '*.pyc' -exec rm -rf {} \;
+fdupes -qnrps %{buildroot}%{python3_sitearch}
+
+%check
+
+%if 0%{?suse_version} > 1500
+%package -n python%{python3_version_nodots}-scipy
+Summary: Scientific Library for Python
+Requires: python3
+Requires: python3-decorator
+Requires: python3-numpy >= 1.14.5
+Provides: python3-scipy = %{epoch}:%{version}-%{release}
+Provides: python3dist(scipy) = %{epoch}:%{version}-%{release}
+Provides: python%{python3_version}-scipy = %{epoch}:%{version}-%{release}
+Provides: python%{python3_version}dist(scipy) = %{epoch}:%{version}-%{release}
+Provides: python%{python3_version_nodots}-scipy = %{epoch}:%{version}-%{release}
+Provides: python%{python3_version_nodots}dist(scipy) = %{epoch}:%{version}-%{release}
+
+%description -n python%{python3_version_nodots}-scipy
+SciPy (pronounced "Sigh Pie") is open-source software for mathematics,
+science, and engineering. The SciPy library depends on NumPy, which
+provides convenient and fast N-dimensional array manipulation. The SciPy
+library is built to work with NumPy arrays, and provides many
+user-friendly and efficient numerical routines such as routines for
+numerical integration and optimization. Together, they run on all
+popular operating systems, are quick to install, and are free of charge.
+NumPy and SciPy are easy to use, but powerful enough to be depended upon
+by some of the world’s leading scientists and engineers. If you need to
+manipulate numbers on a computer and display or publish the results,
+give SciPy a try!
+
+%files -n python%{python3_version_nodots}-scipy
+%license LICENSE.txt
+%{python3_sitearch}/*
+%endif
+
+%if !(0%{?suse_version} > 1500)
+%package -n python3-scipy
+Summary: Scientific Library for Python
+Requires: python3
+Requires: python3-decorator
+Requires: python3-numpy >= 1.14.5
+Provides: python3-scipy = %{epoch}:%{version}-%{release}
+Provides: python3dist(scipy) = %{epoch}:%{version}-%{release}
+Provides: python%{python3_version}-scipy = %{epoch}:%{version}-%{release}
+Provides: python%{python3_version}dist(scipy) = %{epoch}:%{version}-%{release}
+Provides: python%{python3_version_nodots}-scipy = %{epoch}:%{version}-%{release}
+Provides: python%{python3_version_nodots}dist(scipy) = %{epoch}:%{version}-%{release}
+
+%description -n python3-scipy
+SciPy (pronounced "Sigh Pie") is open-source software for mathematics,
+science, and engineering. The SciPy library depends on NumPy, which
+provides convenient and fast N-dimensional array manipulation. The SciPy
+library is built to work with NumPy arrays, and provides many
+user-friendly and efficient numerical routines such as routines for
+numerical integration and optimization. Together, they run on all
+popular operating systems, are quick to install, and are free of charge.
+NumPy and SciPy are easy to use, but powerful enough to be depended upon
+by some of the world’s leading scientists and engineers. If you need to
+manipulate numbers on a computer and display or publish the results,
+give SciPy a try!
+
+%files -n python3-scipy
+%license LICENSE.txt
+%{python3_sitearch}/*
+%endif
+
+%changelog

scipy/stats/_stats.pyx

@@ -171,6 +171,11 @@ def _toint64(x):
 @cython.wraparound(False)
 @cython.boundscheck(False)
 def _weightedrankedtau(ordered[:] x, ordered[:] y, intp_t[:] rank, weigher, bool additive):
+    # y_local and rank_local (declared below) are a work-around for a Cython
+    # bug; see gh-16718.  When we can require Cython 3.0, y_local and
+    # rank_local can be removed, and the closure weigh() can refer directly
+    # to y and rank.
+    cdef ordered[:] y_local = y
     cdef intp_t i, first
     cdef float64_t t, u, v, w, s, sq
     cdef int64_t n = np.int64(len(x))
@@ -189,6 +194,8 @@ def _weightedrankedtau(ordered[:] x, ordered[:] y, intp_t[:] rank, weigher, bool
         rank[...] = perm[::-1]
         _invert_in_place(rank)
 
+    cdef intp_t[:] rank_local = rank
+
     # weigh joint ties
     first = 0
     t = 0
@@ -237,28 +244,28 @@ def _weightedrankedtau(ordered[:] x, ordered[:] y, intp_t[:] rank, weigher, bool
         cdef float64_t weight, residual
 
         if length == 1:
-            return weigher(rank[perm[offset]])
+            return weigher(rank_local[perm[offset]])
         length0 = length // 2
         length1 = length - length0
         middle = offset + length0
         residual = weigh(offset, length0)
         weight = weigh(middle, length1) + residual
-        if y[perm[middle - 1]] < y[perm[middle]]:
+        if y_local[perm[middle - 1]] < y_local[perm[middle]]:
             return weight
 
         # merging
         i = j = k = 0
 
         while j < length0 and k < length1:
-            if y[perm[offset + j]] <= y[perm[middle + k]]:
+            if y_local[perm[offset + j]] <= y_local[perm[middle + k]]:
                 temp[i] = perm[offset + j]
-                residual -= weigher(rank[temp[i]])
+                residual -= weigher(rank_local[temp[i]])
                 j += 1
             else:
                 temp[i] = perm[middle + k]
-                exchanges_weight[0] += weigher(rank[temp[i]]) * (
+                exchanges_weight[0] += weigher(rank_local[temp[i]]) * (
                     length0 - j) + residual if additive else weigher(
-                    rank[temp[i]]) * residual
+                    rank_local[temp[i]]) * residual
                 k += 1
             i += 1