MAINT: 1.9.2 backports

.github/workflows/wheels.yml

@@ -0,0 +1,220 @@
+# Workflow to build and test wheels.
+# To work on the wheel building infrastructure on a fork, comment out:
+#
+# if: github.repository == 'scipy/scipy'
+#
+# in the get_commit_message job include [wheel build] in your commit
+# message to trigger the build. All files related to wheel building are located
+# at tools/wheels/
+name: Wheel builder
+
+on:
+  schedule:
+  #        ┌───────────── minute (0 - 59)
+  #        │  ┌───────────── hour (0 - 23)
+  #        │  │ ┌───────────── day of the month (1 - 31)
+  #        │  │ │ ┌───────────── month (1 - 12 or JAN-DEC)
+  #        │  │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
+  #        │  │ │ │ │
+  - cron: "9  9 * * 6"
+  # push:
+  pull_request:
+    branches:
+      - main
+      - maintenance/**
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  get_commit_message:
+    name: Get commit message
+    runs-on: ubuntu-latest
+    if: github.repository == 'scipy/scipy'
+    outputs:
+      message: ${{ steps.commit_message.outputs.message }}
+    steps:
+      - name: Checkout scipy
+        uses: actions/checkout@v3
+        # Gets the correct commit message for pull request
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+      - name: Get commit message
+        id: commit_message
+        run: |
+          set -xe
+          COMMIT_MSG=$(git log --no-merges -1)
+          RUN="0"
+          if [[ "$COMMIT_MSG" == *"[wheel build]"* ]]; then
+              RUN="1" 
+          fi
+          echo "::set-output name=message::$RUN"
+          echo github.ref ${{ github.ref }}
+
+  build_wheels:
+    name: Build wheel for ${{ matrix.python[0] }}-${{ matrix.buildplat[1] }} ${{ matrix.buildplat[2] }}
+    needs: get_commit_message
+    if: >-
+      contains(needs.get_commit_message.outputs.message, '1') ||
+      github.event_name == 'schedule' ||
+      github.event_name == 'workflow_dispatch' ||
+      (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v') && ( ! endsWith(github.ref, 'dev0')))
+    runs-on: ${{ matrix.buildplat[0] }}
+
+    strategy:
+      # Ensure that a wheel builder finishes even if another fails
+      fail-fast: false
+      matrix:
+        # Github Actions doesn't support pairing matrix values together, let's improvise
+        # https://github.com/github/feedback/discussions/7835#discussioncomment-1769026
+        buildplat:
+        # should also be able to do multi-archs on a single entry, e.g.
+        # [windows-2019, win*, "AMD64 x86"]. However, those two require a different compiler setup
+        # so easier to separate out here.
+        - [ubuntu-20.04, manylinux, x86_64]
+        - [ubuntu-20.04, manylinux, aarch64]
+
+        # When the macos-10.15 image is retired the gfortran/openblas chain
+        # may have to be reworked because the gfortran-4.9.0 compiler currently
+        # used in CI doesn't work in the macos-11.0 image. This will require a more
+        # recent gfortran (gfortran-9 is present on the macOS-11.0 image), and
+        # will probably require that the prebuilt openBLAS is updated.
+        # xref https://github.com/andyfaff/scipy/pull/28#issuecomment-1203496836
+        - [macos-10.15, macosx, x86_64]
+        - [macos-12, macosx, arm64]
+        - [windows-2019, win, AMD64]
+
+        python: [["cp38", "3.8"], ["cp39", "3.9"], ["cp310", "3.10"], ["cp311", "3.11.0-alpha - 3.11.0"]]
+        # python[0] is used to specify the python versions made by cibuildwheel
+        # python[1] is installed by actions/setup-python for the separate
+        # macosx_arm64 build. Once cibuildwheel can do the macosx_arm64 cross build
+        # we can get rid of this duplication and just have ["cp38", "cp39"].
+        # The actions/setup-python can only use the form ["3.8'].
+    env:
+      IS_32_BIT: ${{ matrix.buildplat[2] == 'x86' }}
+      IS_PUSH: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v') }}
+      IS_SCHEDULE_DISPATCH: ${{ github.event_name == 'schedule' || github.event_name == 'workflow_dispatch' }}
+
+    steps:
+      - name: Checkout scipy
+        uses: actions/checkout@v3
+        with:
+          submodules: true
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v4.2.0
+        with:
+          python-version: ${{ matrix.python[1]}}
+
+      - name: win_amd64 - install rtools
+        run: |
+          # mingw-w64
+          choco install rtools --no-progress
+          echo "c:\rtools40\ucrt64\bin;" >> $env:GITHUB_PATH
+        if: ${{ runner.os == 'Windows' && env.IS_32_BIT == 'false' }}
+
+#      - name: win32 - configure mingw for 32-bit builds
+#        run: |
+#          # taken from numpy wheels.yml script
+#          # Force 32-bit mingw. v 8.1.0 is the current version used to build
+#          # the 32 bit openBLAS library (not sure if that matters)
+#          choco uninstall mingw
+#          choco install -y mingw --forcex86 --force --version=8.1.0
+#          echo "C:\ProgramData\chocolatey\lib\mingw\tools\install\mingw32\bin;" >> $env:GITHUB_PATH
+#          echo $(gfortran --version)
+#          echo $(gcc --version)
+#        if: ${{ runner.os == 'Windows' && env.IS_32_BIT == 'true' }}
+
+      - name: Set up QEMU
+        if: ${{ runner.os == 'Linux' && matrix.buildplat[2] == 'aarch64' }}
+        uses: docker/setup-qemu-action@v1
+        with:
+          platforms: all
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.10.1
+        # Build all wheels here, but the macosx_arm64 job in its own entry.
+        # cibuildwheel is currently unable to pass configuration flags to
+        # CIBW_BUILD_FRONTEND https://github.com/pypa/cibuildwheel/issues/1227
+        # (pip/build). Cross compilation with meson requires an initial
+        # configuration step to create a build directory. The subsequent wheel
+        # build then needs to use that directory. This can be done with pip
+        # using a command like:
+        # python -m pip wheel --config-settings builddir=build .
+        if: >-
+          ( ! contains(matrix.buildplat[2], 'arm64' ) )
+        env:
+          CIBW_BUILD: ${{ matrix.python[0] }}-${{ matrix.buildplat[1] }}*
+          CIBW_ARCHS: ${{ matrix.buildplat[2] }}
+          CIBW_ENVIRONMENT_PASS_LINUX: RUNNER_OS
+
+      - name: Build macosx_arm64
+        if: ${{ matrix.buildplat[1] == 'macosx' && matrix.buildplat[2] == 'arm64' }}
+        run: |
+          export PLAT="arm64"
+          export _PYTHON_HOST_PLATFORM="macosx-12.0-arm64"
+          export CROSS_COMPILE=1
+
+          # Need macOS >= 11 for arm compilation.
+          export MACOSX_DEPLOYMENT_TARGET=11.0
+
+          # SDK root needs to be set early, installation of gfortran/openblas
+          # needs to go in the correct location.
+          export SDKROOT=/Applications/Xcode_13.2.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk
+          export ARCHFLAGS=" -arch arm64 "
+
+          # install dependencies for the build machine
+          pip install meson cython pybind11 pythran ninja oldest-supported-numpy build delocate meson-python
+
+          # sets up gfortran compiler/openblas, sets compiler flags.
+          bash tools/wheels/cibw_before_build_macos.sh $(pwd)
+          export PKG_CONFIG_PATH=/opt/arm64-builds/lib/pkgconfig
+          export PKG_CONFIG=/usr/local/bin/pkg-config
+          export CFLAGS=" -arch arm64 $CFLAGS"
+          export CXXFLAGS=" -arch arm64 $CXXFLAGS"
+          export LD_LIBRARY_PATH="/opt/arm64-builds/lib:$FC_LIBDIR:$LD_LIBRARY_PATH"
+          meson setup --cross-file $(pwd)/tools/wheels/cross_arm64.txt build
+
+          # use the pip frontend because the build front end does not end up
+          # obeying the configuration flags it's passed.
+          # For example: `python -m build -Cbuilddir=dir` does not end up using
+          # dir as the meson build directory. This is an issue because
+          # the cross-compile specification is contained in that directory.
+
+          python -m pip wheel -w dist -vvv --config-settings builddir=build .
+          rm dist/numpy*.whl
+
+          # The `.so` are all converted to `-rpath/libgfortran` by
+          # gfortran/meson, with all absolute paths removed.
+          # Enables delocate to find the libopenblas/libgfortran libraries.
+          export DYLD_LIBRARY_PATH=/opt/gfortran-darwin-arm64/lib/gcc/arm64-apple-darwin20.0.0/10.2.1:/opt/arm64-builds/lib
+
+          delocate-listdeps dist/scipy*.whl
+          delocate-wheel --require-archs=arm64 -k -w wheelhouse dist/scipy*.whl
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./wheelhouse/*.whl
+          name: ${{ matrix.python[0] }}-${{ matrix.buildplat[1] }}
+
+        # TODO uncomment when those responsible for uploading
+        # nightly/release wheels want to make this script live.
+
+      # - name: Upload wheels
+      #  if: success()
+      #  shell: bash
+      #  env:
+      #    SCIPY_STAGING_UPLOAD_TOKEN: ${{ secrets.SCIPY_STAGING_UPLOAD_TOKEN }}
+      #    SCIPY_NIGHTLY_UPLOAD_TOKEN: ${{ secrets.SCIPY_NIGHTLY_UPLOAD_TOKEN }}
+      #  run: |
+      #    source tools/wheels/upload_wheels.sh
+      #    set_upload_vars
+      #    # trigger an upload to
+      #    # https://anaconda.org/scipy-wheels-nightly/scipy
+      #    # for cron jobs or "Run workflow" (restricted to main branch).
+      #    # Tags will upload to
+      #    # https://anaconda.org/multibuild-wheels-staging/scipy
+      #    # The tokens were originally generated at anaconda.org
+      #    upload_wheels

doc/release/1.9.2-notes.rst

@@ -5,15 +5,60 @@ SciPy 1.9.2 Release Notes
 .. contents::
 
 SciPy 1.9.2 is a bug-fix release with no new features
-compared to 1.9.1.
+compared to 1.9.1. It also provides wheel for Python 3.11
+on several platforms.
 
 Authors
 =======
 
+* Hood Chatham (1)
+* Thomas J. Fan (1)
+* Ralf Gommers (7)
+* Matt Haberland (3)
+* Julien Jerphanion (1)
+* Loïc Estève (1)
+* Nicholas McKibben (1)
+* Naoto Mizuno (1)
+* Andrew Nelson (3)
+* Tyler Reddy (21)
+* Pamphile Roy (1)
+* Ewout ter Hoeven (2)
+* Meekail Zain (1) +
+
+A total of 13 people contributed to this release.
+People with a "+" by their names contributed a patch for the first time.
+This list of names is automatically generated, and may not be fully complete.
 
 Issues closed for 1.9.2
 -----------------------
 
+* `#16569 <https://github.com/scipy/scipy/issues/16569>`__: BUG: \`sparse.hstack\` returns incorrect result when the stack...
+* `#16898 <https://github.com/scipy/scipy/issues/16898>`__: BUG: optimize.minimize backwards compatability in scipy 1.9
+* `#16935 <https://github.com/scipy/scipy/issues/16935>`__: BUG: using msvc + meson to build scipy --> cl cannot be used...
+* `#16952 <https://github.com/scipy/scipy/issues/16952>`__: BUG: error from \`scipy.stats.mode\` with \`NaN\`s, \`axis !=...
+* `#16964 <https://github.com/scipy/scipy/issues/16964>`__: BUG: scipy 1.7.3 wheels on PyPI require numpy<1.23 in contradiction...
+* `#17026 <https://github.com/scipy/scipy/issues/17026>`__: BUG: ncf_gen::ppf(..) causes segfault
+* `#17124 <https://github.com/scipy/scipy/issues/17124>`__: BUG: OSX-64 Test failure test_ppf_against_tables getting NaN
 
 Pull requests for 1.9.2
 -----------------------
+
+* `#16628 <https://github.com/scipy/scipy/pull/16628>`__: FIX: Updated dtype resolution in \`_stack_along_minor_axis\`
+* `#16842 <https://github.com/scipy/scipy/pull/16842>`__: ENH: cibuildwheel infrastructure
+* `#16909 <https://github.com/scipy/scipy/pull/16909>`__: MAINT: minimize, restore squeezed ((1.0)) addresses #16898
+* `#16911 <https://github.com/scipy/scipy/pull/16911>`__: REL: prep for SciPy 1.9.2
+* `#16922 <https://github.com/scipy/scipy/pull/16922>`__: DOC: update version switcher for 1.9.1 and pin theme to 0.9
+* `#16934 <https://github.com/scipy/scipy/pull/16934>`__: MAINT: cast \`linear_sum_assignment\` to PyCFunction
+* `#16943 <https://github.com/scipy/scipy/pull/16943>`__: BLD: use compiler flags in a more portable way
+* `#16954 <https://github.com/scipy/scipy/pull/16954>`__: MAINT: stats.mode: fix bug with \`axis!=1\`, \`nan_policy='omit'\`,...
+* `#16966 <https://github.com/scipy/scipy/pull/16966>`__: MAINT: fix NumPy upper bound
+* `#16969 <https://github.com/scipy/scipy/pull/16969>`__: BLD: fix usage of \`get_install_data\`, which defaults to purelib
+* `#16975 <https://github.com/scipy/scipy/pull/16975>`__: DOC: Update numpy supported versions for 1.9.2
+* `#16991 <https://github.com/scipy/scipy/pull/16991>`__: BLD: fixes for building with MSVC and Intel Fortran
+* `#17011 <https://github.com/scipy/scipy/pull/17011>`__: Rudimentary test for manylinux_aarch64 with cibuildwheel
+* `#17013 <https://github.com/scipy/scipy/pull/17013>`__: BLD: make MKL detection a little more robust, add notes on TODOs
+* `#17046 <https://github.com/scipy/scipy/pull/17046>`__: CI: Update cibuildwheel to 2.10.1
+* `#17064 <https://github.com/scipy/scipy/pull/17064>`__: BUG: Fix numerical precision error of \`truncnorm.logcdf\` when...
+* `#17096 <https://github.com/scipy/scipy/pull/17096>`__: FIX: ensure a hold on GIL before raising warnings/errors
+* `#17127 <https://github.com/scipy/scipy/pull/17127>`__: TST: stats.studentized_range: fix incorrect test
+* `#17131 <https://github.com/scipy/scipy/pull/17131>`__: MAINT: pyproject.toml: Update build system requirements

doc/source/dev/contributor/building_faq.rst

@@ -93,7 +93,7 @@ library is MKL and if so, use the CBLAS API instead of the BLAS API.
 If autodetection fails or if the user wants to override this
 autodetection mechanism, use the following:
 
-_For ``meson`` based builds (new in 1.9.0):_
+*For ``meson`` based builds (new in 1.9.0):*
 
 Use the ``-Duse-g77-abi=true`` build option. E.g.,::
 
@@ -106,7 +106,7 @@ example)::
     $ meson setup builddir -Duse-g77-abi=true -Dblas=blas -Dlapack=lapack -Dpython.install_env=auto
     $ meson install -C builddir
 
-_For ``distutils`` based builds:_
+*For ``distutils`` based builds:*
 
 Set the environment variable ``SCIPY_USE_G77_ABI_WRAPPER`` to 0 or 1 to disable
 or enable using CBLAS API.

doc/source/dev/toolchain.rst

@@ -78,6 +78,8 @@ The table shows the NumPy versions suitable for each major Python version.
  1.7.0/1            >=3.7, <3.10                >=1.16.5, <1.23.0
  1.7.2-x            >=3.7, <3.11                >=1.16.5, <1.24.0
  1.8                >=3.8, <3.11                >=1.17.3, <1.24.0
+ 1.9.0/1            >=3.8, <3.12                >=1.18.5, <1.25.0
+ 1.9.2              >=3.8, <3.12                >=1.18.5, <1.26.0
 =================  ========================    =======================
 
 In specific cases, such as a particular architecture, these requirements

meson.build

@@ -4,17 +4,13 @@ project(
   # Note that the git commit hash cannot be added dynamically here (it is added
   # in the dynamically generated and installed `scipy/version.py` though - see
   # tools/version_utils.py
-  version: '1.9.2',
+  version: '1.9.2.dev0',
   license: 'BSD-3',
   meson_version: '>= 0.62.2',
   default_options: [
     'buildtype=debugoptimized',
     'c_std=c99',
     'cpp_std=c++14',
-    # TODO: the below -Wno flags are all needed to silence warnings in
-    # f2py-generated code. This should be fixed in f2py itself.
-    'c_args=-Wno-unused-function -Wno-conversion -Wno-misleading-indentation -Wno-incompatible-pointer-types',
-    'fortran_args=-Wno-conversion',
     'fortran_std=legacy',
     'blas=openblas',
     'lapack=openblas'
@@ -23,12 +19,24 @@ project(
 
 cc = meson.get_compiler('c')
 cpp = meson.get_compiler('cpp')
+
 # This argument is called -Wno-unused-but-set-variable by GCC, however Clang
 # doesn't recognize that.
 if cc.has_argument('-Wno-unused-but-set-variable')
   add_global_arguments('-Wno-unused-but-set-variable', language : 'c')
 endif
 
+# TODO: the below -Wno flags are all needed to silence warnings in
+# f2py-generated code. This should be fixed in f2py itself.
+_global_c_args = cc.get_supported_arguments(
+  '-Wno-unused-but-set-variable',
+  '-Wno-unused-function',
+  '-Wno-conversion',
+  '-Wno-misleading-indentation',
+  '-Wno-incompatible-pointer-types',
+)
+add_project_arguments(_global_c_args, language : 'c')
+
 # We need -lm for all C code (assuming it uses math functions, which is safe to
 # assume for SciPy). For C++ it isn't needed, because libstdc++/libc++ is
 # guaranteed to depend on it. For Fortran code, Meson already adds `-lm`.
@@ -39,6 +47,18 @@ endif
 
 # Adding at project level causes many spurious -lgfortran flags.
 add_languages('fortran', native: false)
+ff = meson.get_compiler('fortran')
+if ff.has_argument('-Wno-conversion')
+  add_project_arguments('-Wno-conversion', language: 'fortran')
+endif
+
+is_windows = host_machine.system() == 'windows'
+
+# Intel Fortran on Windows does things differently, so deal with that
+if is_windows and ff.get_id() == 'intel-cl'
+  _ifort_flags = ff.get_supported_arguments('/MD', '/names:lowercase', '/assume:underscore')
+  add_project_arguments(_ifort_flags, language: 'fortran')
+endif
 
 cython = find_program('cython')
 pythran = find_program('pythran')
@@ -48,6 +68,8 @@ copier = find_program(['cp', 'scipy/_build_utils/copyfiles.py'])
 
 # https://mesonbuild.com/Python-module.html
 py_mod = import('python')
+# NOTE: with Meson >=0.64.0 we can add `pure: false` here and remove that line
+# everywhere else, see https://github.com/mesonbuild/meson/pull/10783.
 py3 = py_mod.find_installation()
 # SciPy 1.9.0-specific error message, see the same message in
 # `scipy/__init__.py` and gh-14986