Merge branch 'main' into remove-npyrandom-staticlib

numpy · lysnikolaou · Dec 13, 2023 · Dec 14, 2023 · Dec 14, 2023 · Dec 18, 2023
commit e90dcc7a0a7e20ef83eedbe7352f171a74ba729c
diff --git a/.editorconfig b/.editorconfig
@@ -0,0 +1,8 @@
+root = true
+
+[*.{c,cxx,h,hpp}]
+# https://numpy.org/neps/nep-0045-c_style_guide.html
+indent_size = 4
+indent_style = space
+max_line_length = 80
+trim_trailing_whitespace = true
diff --git a/.gitattributes b/.gitattributes
@@ -54,7 +54,6 @@ numpy/version.py linguist-generated
 # F2py
 ./doc/source/f2py/*.pyf text
 ./doc/source/f2py/*.dat text
-./numpy/f2py/tests/src/module_data/mod.mod binary
 
 # Documents
 *.md    text diff=markdown

diff --git a/.github/workflows/dependency-review.yml b/.github/workflows/dependency-review.yml
@@ -17,4 +17,4 @@ jobs:
       - name: 'Checkout Repository'
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
       - name: 'Dependency Review'
-        uses: actions/dependency-review-action@4901385134134e04cec5fbe5ddfe3b2c5bd5d976 # v4.0.0
+        uses: actions/dependency-review-action@9129d7d40b8c12c1ed0f60400d00c92d437adcce # v4.1.3
diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
@@ -129,8 +129,10 @@ jobs:
         set -xe
         sudo apt update
         sudo apt install gfortran libgfortran5
-        python -m pip install -r requirements/ci_requirements.txt
-        spin config-openblas --with-scipy-openblas=32
+        python -m pip install -r requirements/ci32_requirements.txt
+        mkdir -p ./.openblas
+        python -c"import scipy_openblas32 as ob32; print(ob32.get_pkg_config())" > ./.openblas/scipy-openblas.pc
+
     - name: Build a wheel
       env:
         PKG_CONFIG_PATH: ${{ github.workspace }}/.openblas
@@ -186,15 +188,15 @@ jobs:
     - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
       with:
         python-version: '3.11'
-    - name: Install gfortran and setup OpenBLAS (MacPython build)
+    - name: Install gfortran and setup OpenBLAS (sdist build)
       run: |
         set -xe
-        sudo apt update
-        sudo apt install gfortran libgfortran5
-        target=$(python tools/openblas_support.py)
-        sudo cp -r $target/lib/* /usr/lib
-        sudo cp $target/include/* /usr/include
+        python -m pip install -r requirements/ci_requirements.txt
+        mkdir -p ./.openblas
+        python -c"import scipy_openblas64 as ob64; print(ob64.get_pkg_config())" > ./.openblas/scipy-openblas.pc
     - name: Build a wheel via an sdist
+      env:
+        PKG_CONFIG_PATH: ${{ github.workspace }}/.openblas
       run: |
         pip install build
         python -m build

diff --git a/.github/workflows/linux_blas.yml b/.github/workflows/linux_blas.yml
@@ -75,14 +75,16 @@ jobs:
       run: |
         pip install -r requirements/build_requirements.txt
         # Install OpenBLAS
-        set -xe
         if [[ $USE_NIGHTLY_OPENBLAS == "true" ]]; then
-          target=$(python tools/openblas_support.py --nightly)
+            python -m pip install -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple scipy-openblas32
         else
-          target=$(python tools/openblas_support.py)
+            python -m pip install -r requirements/ci32_requirements.txt
         fi
-        sudo cp -r $target/lib/* /usr/lib
-        sudo cp $target/include/* /usr/include
+        mkdir -p ./.openblas
+        python -c"import scipy_openblas32 as ob32; print(ob32.get_pkg_config())" > ./.openblas/scipy-openblas.pc
+        echo "PKG_CONFIG_PATH=${{ github.workspace }}/.openblas" >> $GITHUB_ENV
+        ld_library_path=$(python -c"import scipy_openblas32 as ob32; print(ob32.get_lib_dir())")
+        echo "LD_LIBRARY_PATH=$ld_library_path" >> $GITHUB_ENV
 
     - name: Build
       shell: 'script -q -e -c "bash --noprofile --norc -eo pipefail {0}"'
@@ -98,12 +100,15 @@ jobs:
     - name: Check installed test and stub files
       run:
         python tools/check_installed_files.py $(find ./build-install -path '*/site-packages/numpy')
+    - name: Ensure scipy-openblas
+      run: |
+        set -ex
+        spin python tools/check_openblas_version.py 0.3.26
 
     - name: Test
       shell: 'script -q -e -c "bash --noprofile --norc -eo pipefail {0}"'
       env:
         TERM: xterm-256color
-        LD_LIBRARY_PATH: "/usr/local/lib/"  # to find libopenblas.so.0
 
       run: |
         pip install pytest pytest-xdist hypothesis typing_extensions
@@ -197,6 +202,7 @@ jobs:
       run: |
         pip install -r requirements/build_requirements.txt
         pip install pytest pytest-xdist hypothesis typing_extensions
+        sudo apt-get update
         sudo apt-get install libopenblas-dev cmake
         sudo apt-get remove pkg-config
 
@@ -223,6 +229,7 @@ jobs:
     - name: Install dependencies
       run: |
         pip install -r requirements/build_requirements.txt
+        sudo apt-get update
         sudo apt-get install liblapack-dev pkg-config
 
     - name: Build
@@ -346,6 +353,7 @@ jobs:
       run: |
         pip install -r requirements/build_requirements.txt
         pip install pytest pytest-xdist hypothesis typing_extensions
+        sudo apt-get update
         sudo apt-get install libblis-dev libopenblas-dev pkg-config
 
     - name: Add BLIS pkg-config file
@@ -381,6 +389,7 @@ jobs:
       run: |
         pip install -r requirements/build_requirements.txt
         pip install pytest pytest-xdist hypothesis typing_extensions
+        sudo apt-get update
         sudo apt-get install libatlas-base-dev pkg-config
 
     - name: Build

diff --git a/.github/workflows/linux_compiler_sanitizers.yml b/.github/workflows/linux_compiler_sanitizers.yml
@@ -50,7 +50,6 @@ jobs:
       run: |
         pip install pytest pytest-xdist hypothesis typing_extensions
         ASAN_OPTIONS=detect_leaks=0:symbolize=1:strict_init_order=true:allocator_may_return_null=1:halt_on_error=1 \
+        UBSAN_OPTIONS=halt_on_error=0 \
         LD_PRELOAD=$(gcc --print-file-name=libasan.so) \
         python -m spin test -- -v -s
-
-
diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
@@ -51,7 +51,7 @@ jobs:
           ${{ github.workflow }}-${{ matrix.python-version }}-ccache-macos-
 
     - name: Setup Mambaforge
-      uses: conda-incubator/setup-miniconda@11b562958363ec5770fef326fe8ef0366f8cbf8a # v3.0.1
+      uses: conda-incubator/setup-miniconda@392cf345b1784333caa1a1185081c71e6ffd61bc # v3.0.2
       with:
         python-version: ${{ matrix.python-version }}
         channels: conda-forge
@@ -99,10 +99,17 @@ jobs:
         conda activate numpy-dev
         ccache -s
 
+
   accelerate:
-    name: Accelerate (LP64, ILP64)
+    name: Accelerate (LP64, ILP64) - ${{ matrix.build_runner[1] }}
     if: "github.repository == 'numpy/numpy'"
-    runs-on: macos-13
+    runs-on: ${{ matrix.build_runner[0] }}
+    strategy:
+      matrix:
+        build_runner:
+          - [ macos-13, "macos_x86_64" ]
+          - [ macos-14, "macos_arm64" ]
+
     steps:
     - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
       with:
@@ -114,6 +121,7 @@ jobs:
         python-version: '3.10'
 
     - uses: maxim-lobanov/setup-xcode@60606e260d2fc5762a71e64e74b2174e8ea3c8bd # v1.6.0
+      if: ${{ matrix.build_runner[0] == 'macos-13' }}
       with:
         xcode-version: '14.3'
 

diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -107,7 +107,14 @@ jobs:
 
       - name: pkg-config-for-win
         run: |
-          choco install -y --checksum 6004DF17818F5A6DBF19CB335CC92702 pkgconfiglite
+          choco install -y --no-progress --stoponfirstfailure --checksum 6004DF17818F5A6DBF19CB335CC92702 pkgconfiglite
+          $CIBW = "${{ github.workspace }}/.openblas"
+          # pkgconfig needs a complete path, and not just "./openblas since the
+          # build is run in a tmp dir (?)
+          # It seems somewhere in the env passing, `\` is not
+          # passed through, so convert it to '/'
+          $CIBW = $CIBW.replace("\","/")
+          echo "CIBW_ENVIRONMENT_WINDOWS=PKG_CONFIG_PATH=$CIBW" >> $env:GITHUB_ENV
         if: runner.os == 'windows'
 
       # Used to push the built wheels
@@ -126,7 +133,7 @@ jobs:
           name: ${{ matrix.python }}-${{ startsWith(matrix.buildplat[1], 'macosx') && 'macosx' || matrix.buildplat[1] }}
           path: ./wheelhouse/*.whl
 
-      - uses: conda-incubator/setup-miniconda@11b562958363ec5770fef326fe8ef0366f8cbf8a # v3.0.1
+      - uses: conda-incubator/setup-miniconda@392cf345b1784333caa1a1185081c71e6ffd61bc # v3.0.2
         with:
           # for installation of anaconda-client, required for upload to
           # anaconda.org
@@ -210,7 +217,7 @@ jobs:
           name: sdist
           path: ./dist/*
 
-      - uses: conda-incubator/setup-miniconda@11b562958363ec5770fef326fe8ef0366f8cbf8a # v3.0.1
+      - uses: conda-incubator/setup-miniconda@392cf345b1784333caa1a1185081c71e6ffd61bc # v3.0.2
         with:
           # for installation of anaconda-client, required for upload to
           # anaconda.org

diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
@@ -39,7 +39,9 @@ jobs:
 
     - name: Install pkg-config
       run: |
-        choco install -y --checksum 6004DF17818F5A6DBF19CB335CC92702 pkgconfiglite
+        choco install -y --stoponfirstfailure --checksum 6004DF17818F5A6DBF19CB335CC92702 pkgconfiglite
+        echo "PKG_CONFIG_PATH=${{ github.workspace }}/.openblas" >> $env:GITHUB_ENV
+
 
     - name: Install Clang-cl
       if: matrix.compiler == 'Clang-cl'
@@ -48,16 +50,12 @@ jobs:
 
     - name: Install NumPy (MSVC)
       if: matrix.compiler == 'MSVC'
-      env:
-        PKG_CONFIG_PATH: ${{ github.workspace }}/.openblas
       run: |
         pip install -r requirements/ci_requirements.txt
         spin build --with-scipy-openblas=32 -j2 -- --vsenv
 
     - name: Install NumPy (Clang-cl)
       if: matrix.compiler == 'Clang-cl'
-      env:
-        PKG_CONFIG_PATH: ${{ github.workspace }}/.openblas
       run: |
         "[binaries]","c = 'clang-cl'","cpp = 'clang-cl'","ar = 'llvm-lib'","c_ld = 'lld-link'","cpp_ld = 'lld-link'" | Out-File $PWD/clang-cl-build.ini -Encoding ascii
         pip install -r requirements/ci_requirements.txt

diff --git a/.gitignore b/.gitignore
@@ -41,6 +41,7 @@ GTAGS
 *.o.d
 *.py[ocd]
 *.so
+*.mod
 
 # Packages #
 ############

diff --git a/.gitmodules b/.gitmodules
@@ -13,6 +13,9 @@
 [submodule "numpy/_core/src/highway"]
 	path = numpy/_core/src/highway
 	url = https://github.com/google/highway.git
+[submodule "numpy/fft/pocketfft"]
+	path = numpy/fft/pocketfft
+	url = https://github.com/mreineck/pocketfft
 [submodule "subprojects/libnpymath"]
 	path = subprojects/libnpymath
 	url = https://github.com/numpy/libnpymath.git
diff --git a/.spin/cmds.py b/.spin/cmds.py
@@ -566,7 +566,7 @@ def _config_openblas(blas_variant):
         os.makedirs(openblas_dir, exist_ok=True)
         with open(pkg_config_fname, "wt", encoding="utf8") as fid:
             fid.write(
-                openblas.get_pkg_config(use_preloading=True).replace("\\", "/")
+                openblas.get_pkg_config(use_preloading=True)
             )
 
 

diff --git a/README.md b/README.md
@@ -13,7 +13,7 @@ https://anaconda.org/conda-forge/numpy)
 https://stackoverflow.com/questions/tagged/numpy)
 [![Nature Paper](https://img.shields.io/badge/DOI-10.1038%2Fs41586--020--2649--2-blue)](
 https://doi.org/10.1038/s41586-020-2649-2)
-[![OpenSSF Scorecard](https://api.securityscorecards.dev/projects/github.com/numpy/numpy/badge)](https://api.securityscorecards.dev/projects/github.com/numpy/numpy)
+[![OpenSSF Scorecard](https://api.securityscorecards.dev/projects/github.com/numpy/numpy/badge)](https://securityscorecards.dev/viewer/?uri=github.com/numpy/numpy)
 
 
 NumPy is the fundamental package for scientific computing with Python.

diff --git a/azure-steps-windows.yml b/azure-steps-windows.yml
@@ -14,9 +14,9 @@ steps:
   displayName: 'Install dependencies; some are optional to avoid test skips'
 
 - powershell: |
-    choco install unzip -y
-    choco install -y --checksum 6004DF17818F5A6DBF19CB335CC92702 pkgconfiglite
-    choco install ninja
+    choco install -y --stoponfirstfailure unzip
+    choco install -y --stoponfirstfailure --checksum 6004DF17818F5A6DBF19CB335CC92702 pkgconfiglite
+    choco install --stoponfirstfailure ninja
     echo "##vso[task.setvariable variable=RTOOLS43_HOME]c:\rtools43"
   displayName: 'Install utilities'
 

diff --git a/doc/DISTUTILS.rst b/doc/DISTUTILS.rst
@@ -37,9 +37,9 @@ SciPy packages should be kept minimal or zero.
 A SciPy package contains, in addition to its sources, the following
 files and directories:
 
-  + ``setup.py`` --- building script
-  + ``__init__.py`` --- package initializer
-  + ``tests/`` --- directory of unittests
++ ``setup.py`` --- building script
++ ``__init__.py`` --- package initializer
++ ``tests/`` --- directory of unittests
 
 Their contents are described below.
 
@@ -594,7 +594,7 @@ Specifying config_fc options for libraries in setup.py script
 -------------------------------------------------------------
 
 It is possible to specify config_fc options in setup.py scripts.
-For example, using
+For example, using::
 
   config.add_library('library',
                      sources=[...],

diff --git a/doc/changelog/1.20.0-changelog.rst b/doc/changelog/1.20.0-changelog.rst
@@ -320,7 +320,7 @@ A total of 716 pull requests were merged for this release.
 * `#16472 <https://github.com/numpy/numpy/pull/16472>`__: DOC: Fixes for 18 broken links
 * `#16474 <https://github.com/numpy/numpy/pull/16474>`__: MAINT: use zip instead of range in piecewise
 * `#16476 <https://github.com/numpy/numpy/pull/16476>`__: ENH: add ``norm=forward,backward`` to numpy.fft functions
-* `#16482 <https://github.com/numpy/numpy/pull/16482>`__: SIMD: Optimize the performace of np.packbits in ARM-based machine.
+* `#16482 <https://github.com/numpy/numpy/pull/16482>`__: SIMD: Optimize the performance of np.packbits in ARM-based machine.
 * `#16485 <https://github.com/numpy/numpy/pull/16485>`__: BUG: Fix result when a gufunc output broadcasts the inputs.
 * `#16500 <https://github.com/numpy/numpy/pull/16500>`__: DOC: Point Contributing page to new NEP 45
 * `#16501 <https://github.com/numpy/numpy/pull/16501>`__: MAINT: make Py_SET_SIZE and Py_SET_TYPE macros a bit safer
@@ -487,7 +487,7 @@ A total of 716 pull requests were merged for this release.
 * `#16890 <https://github.com/numpy/numpy/pull/16890>`__: TST, BUG: Re-raise MemoryError exception in test_large_zip's...
 * `#16894 <https://github.com/numpy/numpy/pull/16894>`__: DOC: Fix wrong markups in ``arrays.dtypes``
 * `#16896 <https://github.com/numpy/numpy/pull/16896>`__: DOC: Remove links for C codes
-* `#16897 <https://github.com/numpy/numpy/pull/16897>`__: DOC: Fix the declarations of C fuctions
+* `#16897 <https://github.com/numpy/numpy/pull/16897>`__: DOC: Fix the declarations of C functions
 * `#16899 <https://github.com/numpy/numpy/pull/16899>`__: MNT: also use Py_SET_REFCNT instead of Py_REFCNT
 * `#16900 <https://github.com/numpy/numpy/pull/16900>`__: MAINT: Chaining exceptions in numpy/__init__.py
 * `#16907 <https://github.com/numpy/numpy/pull/16907>`__: DOC: update val to be scalar or array like optional closes #16901
@@ -737,7 +737,7 @@ A total of 716 pull requests were merged for this release.
 * `#17493 <https://github.com/numpy/numpy/pull/17493>`__: DOC: New round of NEP 42 edits
 * `#17497 <https://github.com/numpy/numpy/pull/17497>`__: DOC: Use consistent lowercase on docs landing page
 * `#17498 <https://github.com/numpy/numpy/pull/17498>`__: MAINT: fix incompatible type comparison in numpy.lib.utils.info
-* `#17501 <https://github.com/numpy/numpy/pull/17501>`__: BUG: Fix failures in master related to userdtype registeration
+* `#17501 <https://github.com/numpy/numpy/pull/17501>`__: BUG: Fix failures in master related to userdtype registration
 * `#17502 <https://github.com/numpy/numpy/pull/17502>`__: BUG: remove ``sys`` from the type stubs
 * `#17503 <https://github.com/numpy/numpy/pull/17503>`__: DOC: Fix empty 'C style guide' page
 * `#17504 <https://github.com/numpy/numpy/pull/17504>`__: DOC: Rename 'Quickstart tutorial'
@@ -902,7 +902,7 @@ A total of 716 pull requests were merged for this release.
 * `#18127 <https://github.com/numpy/numpy/pull/18127>`__: REL: Update 1.20.x after 1.19.5 release.
 * `#18130 <https://github.com/numpy/numpy/pull/18130>`__: BUG: Fix promotion of half and string
 * `#18146 <https://github.com/numpy/numpy/pull/18146>`__: BUG, MAINT: improve avx512 mask logical operations
-* `#18154 <https://github.com/numpy/numpy/pull/18154>`__: BUG: Promotion between strings and objects was assymetric
+* `#18154 <https://github.com/numpy/numpy/pull/18154>`__: BUG: Promotion between strings and objects was asymmetric
 * `#18192 <https://github.com/numpy/numpy/pull/18192>`__: MAINT: Use explicit reexports for numpy.typing objects
 * `#18201 <https://github.com/numpy/numpy/pull/18201>`__: BUG: Keep ignoring most errors during array-protocol lookup
 * `#18219 <https://github.com/numpy/numpy/pull/18219>`__: MAINT: random shuffle: warn on unrecognized objects, fix empty...

diff --git a/doc/neps/conf.py b/doc/neps/conf.py
@@ -66,7 +66,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

diff --git a/doc/neps/nep-0050-scalar-promotion.rst b/doc/neps/nep-0050-scalar-promotion.rst
@@ -162,8 +162,6 @@ following hold::
     np.bool_(True) + 1 == np.int64(2)
     True + np.uint8(2) == np.uint8(3)
 
-.. _nep50_comparison_table::
-
 Note that while this NEP uses simple operators as example, the rules described
 generally apply to all of NumPy operations.
 

diff --git a/doc/neps/nep-0052-python-api-cleanup.rst b/doc/neps/nep-0052-python-api-cleanup.rst
@@ -39,7 +39,7 @@ NumPy has a large API surface that evolved organically over many years:
    >>> len(modules)
    14
 
-The above doesn't even include items that are public but have been
+The above doesn't even include items that are public but have
 been hidden from ``__dir__``.
 A particularly problematic example of that is ``np.core``,
 which is technically private but heavily used in practice.

diff --git a/doc/neps/nep-0054-simd-cpp-highway.rst b/doc/neps/nep-0054-simd-cpp-highway.rst
@@ -101,7 +101,7 @@ merged clang-cl support a while back (see `gh-20866`_), and SciPy builds with
 Mingw-w64. It may however impact other redistributors or end users who build
 from source on Windows.
 
-In response to the earlier dicussions around this NEP, Highway is now
+In response to the earlier discussions around this NEP, Highway is now
 dual-licensed as Apache 2 / BSD-3.
 
 

diff --git a/doc/release/upcoming_changes/19355.new_feature.rst b/doc/release/upcoming_changes/19355.new_feature.rst
-Original file line number
+Diff line change
@@ Expand Up / @@ -41,6 +41,7 @@ GTAGS @@
     *.o.d
     *.py[ocd]
     *.so
+    *.mod
     # Packages #
     ############
@@ Expand Down @@