Merge pull request #19797 from tylerjereddy/treddy_1_12_0rc2_prep

WIP, MAINT:  1.12.0rc2 prep

.github/workflows/linux_meson.yml

@@ -268,81 +268,6 @@ jobs:
           python -m pytest --pyargs scipy -n2 --durations=10
           popd
 
-  #################################################################################
-  prerelease_deps_coverage_64bit_blas:
-    # TODO: re-enable ILP64 build.
-    name: Prerelease deps, coverage, and 64-bit BLAS
-    needs: get_commit_message
-    if: >
-      needs.get_commit_message.outputs.message == 1
-      && (github.repository == 'scipy/scipy' || github.repository == '')
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.9]
-
-    steps:
-    - uses: actions/checkout@v3
-      with:
-        submodules: recursive
-
-    - name: Setup Python
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install Ubuntu dependencies
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y libgmp-dev libmpfr-dev libmpc-dev ccache gfortran
-
-    - name: Caching Python dependencies
-      uses: actions/cache@v3
-      id: cache
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-prerelease
-
-    - name: Install Python packages
-      run: |
-        python -m pip install cython pythran ninja meson-python pybind11 click rich_click pydevtool
-        python -m pip install --pre --upgrade --timeout=60 -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy
-        python -m pip install --pre --upgrade pytest pytest-cov pytest-xdist mpmath gmpy2 threadpoolctl pooch matplotlib hypothesis
-        # TODO: once the scipy_ symbol prefix issue is fixed, install
-        # scipy-openblas32 from the pre-releases bucket again (see gh-19640)
-        python -m pip install "scipy-openblas32<=0.3.23.293.2"
-
-    - name:  Prepare compiler cache
-      id:    prep-ccache
-      shell: bash
-      run: |
-        mkdir -p "${CCACHE_DIR}"
-        echo "dir=$CCACHE_DIR" >> $GITHUB_OUTPUT
-        NOW=$(date -u +"%F-%T")
-        echo "timestamp=${NOW}" >> $GITHUB_OUTPUT
-
-    - name: Setup compiler cache
-      uses:  actions/cache@v3
-      id:    cache-ccache
-      with:
-        path: ${{ steps.prep-ccache.outputs.dir }}
-        # Restores ccache from either a previous build on this branch or on main
-        key:  ${{ github.workflow }}-${{ matrix.python-version }}-ccache-linux-prerelease-${{ steps.prep-ccache.outputs.timestamp }}
-        restore-keys: |
-          ${{ github.workflow }}-${{ matrix.python-version }}-ccache-linux-prerelease-
-
-    - name: Build and install SciPy
-      run: |
-        python dev.py build --gcov --with-scipy-openblas
-
-    - name: Ccache performance
-      shell: bash -l {0}
-      run: ccache -s
-
-    - name: Test SciPy
-      run: |
-        export OPENBLAS_NUM_THREADS=1
-        python dev.py test -j2 --mode full -- --cov --cov-report term-missing 
 
   #################################################################################
   linux_32bit:

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2001-2002 Enthought, Inc. 2003-2023, SciPy Developers.
+Copyright (c) 2001-2002 Enthought, Inc. 2003-2024, SciPy Developers.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

doc/source/release/1.12.0-notes.rst

@@ -274,6 +274,14 @@ Deprecated features
 - All wavelet functions have been deprecated, as PyWavelets provides suitable
   implementations; affected functions are: ``signal.{daub, qmf, cascade,
   morlet, morlet2, ricker, cwt}``
+- ``scipy.integrate.trapz``, ``scipy.integrate.cumtrapz``, and ``scipy.integrate.simps`` have
+  been deprecated in favour of `scipy.integrate.trapezoid`, `scipy.integrate.cumulative_trapezoid`,
+  and `scipy.integrate.simpson` respectively and will be removed in SciPy 1.14.
+- The ``tol`` argument of ``scipy.sparse.linalg.{bcg,bicstab,cg,cgs,gcrotmk,gmres,lgmres,minres,qmr,tfqmr}``
+  is now deprecated in favour of ``rtol`` and will be removed in SciPy 1.14.
+  Furthermore, the default value of ``atol`` for these functions is due
+  to change to ``0.0`` in SciPy 1.14.
+
 
 
 *********************
@@ -282,8 +290,11 @@ Expired Deprecations
 There is an ongoing effort to follow through on long-standing deprecations.
 The following previously deprecated features are affected:
 
-- The ``centered`` keyword of `stats.qmc.LatinHypercube` has been removed.
+- The ``centered`` keyword of `scipy.stats.qmc.LatinHypercube` has been removed.
   Use ``scrambled=False`` instead of ``centered=True``.
+- ``scipy.stats.binom_test`` has been removed in favour of `scipy.stats.binomtest`.
+- In `scipy.stats.iqr`, the use of ``scale='raw'`` has been removed in favour 
+  of ``scale=1``.
 
 
 ******************************
@@ -304,7 +315,7 @@ Authors
 
 * Name (commits)
 * endolith (1)
-* h-vetinari (29)
+* h-vetinari (32)
 * Tom Adamczewski (3) +
 * Anudeep Adiraju (1) +
 * akeemlh (1)
@@ -321,16 +332,17 @@ Authors
 * Sebastian Berg (1)
 * Ben Boeckel (1) +
 * David Boetius (1) +
-* Jake Bowhay (102)
+* Matt Borland (1)
+* Jake Bowhay (103)
 * Larry Bradley (1) +
 * Dietrich Brunn (5)
-* Evgeni Burovski (101)
+* Evgeni Burovski (102)
 * Matthias Bussonnier (18)
 * CJ Carey (6)
 * Colin Carroll (1) +
 * Aadya Chinubhai (1) +
 * Luca Citi (1)
-* Lucas Colley (140) +
+* Lucas Colley (141) +
 * com3dian (1) +
 * Anirudh Dagar (4)
 * Danni (1) +
@@ -349,7 +361,7 @@ Authors
 * Lukas Geiger (9) +
 * Artem Glebov (22) +
 * Caden Gobat (1)
-* Ralf Gommers (125)
+* Ralf Gommers (126)
 * Alexander Goscinski (2) +
 * Rohit Goswami (2) +
 * Olivier Grisel (1)
@@ -386,7 +398,7 @@ Authors
 * Thomas Loke (4) +
 * Malte Londschien (1) +
 * Christian Lorentzen (6)
-* Adam Lugowski (9) +
+* Adam Lugowski (10) +
 * lutefiskhotdish (1)
 * mainak33 (1) +
 * Ben Mares (11) +
@@ -395,6 +407,7 @@ Authors
 * Nikolay Mayorov (4)
 * Nicholas McKibben (1)
 * Melissa Weber Mendonça (7)
+* Michał Górny (1)
 * Kat Mistberg (2) +
 * mkiffer (1) +
 * mocquin (1) +
@@ -403,7 +416,7 @@ Authors
 * Roberto Pastor Muela (3) +
 * Bijay Nayak (1) +
 * Andrew Nelson (105)
-* Praveer Nidamaluri (2) +
+* Praveer Nidamaluri (3) +
 * Lysandros Nikolaou (2)
 * Dimitri Papadopoulos Orfanos (7)
 * Pablo Rodríguez Pérez (1) +
@@ -418,7 +431,7 @@ Authors
 * Bharat Raghunathan (1)
 * Chris Rapson (1) +
 * Matteo Raso (4)
-* Tyler Reddy (165)
+* Tyler Reddy (201)
 * Martin Reinecke (1)
 * Tilo Reneau-Cardoso (1) +
 * resting-dove (2) +
@@ -430,7 +443,7 @@ Authors
 * Masahiro Sakai (2) +
 * Omar Salman (14)
 * Andrej Savikin (1) +
-* Daniel Schmitz (52)
+* Daniel Schmitz (54)
 * Dan Schult (19)
 * Scott Shambaugh (9)
 * Sheila-nk (2) +
@@ -465,7 +478,7 @@ Authors
 * Jinzhe Zeng (1) +
 * JIMMY ZHAO (1) +
 
-A total of 161 people contributed to this release.
+A total of 163 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.
 
@@ -482,6 +495,7 @@ Issues closed for 1.12.0
 * `#5022 <https://github.com/scipy/scipy/issues/5022>`__: bicg returns last iterate, not the smallest-residue vector
 * `#6198 <https://github.com/scipy/scipy/issues/6198>`__: callback for Krylov methods
 * `#7241 <https://github.com/scipy/scipy/issues/7241>`__: ENH: Implement Chandrupatla's algorithm for root finding (simpler/faster...
+* `#8792 <https://github.com/scipy/scipy/issues/8792>`__: Newton-CG throws error when Hessian is a \`scipy.sparse\` class
 * `#9527 <https://github.com/scipy/scipy/issues/9527>`__: Anderson-Darling ksamples can not estimate p-values beyond given...
 * `#11516 <https://github.com/scipy/scipy/issues/11516>`__: Recommend ccache for benchmarks in contributor documentation
 * `#12017 <https://github.com/scipy/scipy/issues/12017>`__: Expose FACTOR parameter instead of using magic number in scipy.optimize.nnls
@@ -491,7 +505,6 @@ Issues closed for 1.12.0
 * `#13437 <https://github.com/scipy/scipy/issues/13437>`__: DOC: Add example as to how to use solve_ivp to solve complex...
 * `#14037 <https://github.com/scipy/scipy/issues/14037>`__: ENH: other quality metrics for random sampling
 * `#14480 <https://github.com/scipy/scipy/issues/14480>`__: LSODA implementation of dense output yields incorrect result
-* `#15533 <https://github.com/scipy/scipy/issues/15533>`__: BUG: test failure with MKL in presence of AVX512-capable processor
 * `#15676 <https://github.com/scipy/scipy/issues/15676>`__: ENH: Implement \`multivariate_normal.fit\`
 * `#15738 <https://github.com/scipy/scipy/issues/15738>`__: DEP: change default of atol in \`scipy.sparse.linalg.\*\`
 * `#16729 <https://github.com/scipy/scipy/issues/16729>`__: _fitpack / dfitpack duplication
@@ -594,6 +607,7 @@ Issues closed for 1.12.0
 * `#19448 <https://github.com/scipy/scipy/issues/19448>`__: DOC:fft: next_fast_len signature is empty in docs
 * `#19490 <https://github.com/scipy/scipy/issues/19490>`__: MAINT: lint: fail inventory
 * `#19544 <https://github.com/scipy/scipy/issues/19544>`__: DOC/MAINT: refguide-check errors
+* `#19553 <https://github.com/scipy/scipy/issues/19553>`__: BUG: Test suite leaks file descriptors (\`OSError: [Errno 24]...
 * `#19565 <https://github.com/scipy/scipy/issues/19565>`__: DOC/DX: \`meson-python\` missing from 'required build dependencies'
 * `#19568 <https://github.com/scipy/scipy/issues/19568>`__: DOC/DX: \`cd scipy\` missing from 'Building from source'
 * `#19575 <https://github.com/scipy/scipy/issues/19575>`__: BUG: scipy.ndimage.watershed_ift cost data type is too small...
@@ -604,6 +618,11 @@ Issues closed for 1.12.0
 * `#19620 <https://github.com/scipy/scipy/issues/19620>`__: _lib: Test error in test_warning_calls_filters because of a Python...
 * `#19636 <https://github.com/scipy/scipy/issues/19636>`__: DOC: issue in documentation for the callback argument in scipy.optimize.minimize
 * `#19640 <https://github.com/scipy/scipy/issues/19640>`__: CI, MAINT: pre-release job failures with scipy-openblas32
+* `#19726 <https://github.com/scipy/scipy/issues/19726>`__: BUG: 1.12.0rc1: build failure on windows due to macro collision...
+* `#19747 <https://github.com/scipy/scipy/issues/19747>`__: BUG: Invalid \`IndexError\` from \`scipy.stats.nbinom.logcdf\`
+* `#19795 <https://github.com/scipy/scipy/issues/19795>`__: MAINT: need stable Pythran release for SciPy 1.12.0 RC2
+* `#19804 <https://github.com/scipy/scipy/issues/19804>`__: MAINT/TST: Warnings failing test suite with \`pytest 8\`
+* `#19852 <https://github.com/scipy/scipy/issues/19852>`__: CI, MAINT: Windows 3.11 CI failure with file access issue
 
 ************************
 Pull requests for 1.12.0
@@ -1052,9 +1071,22 @@ Pull requests for 1.12.0
 * `#19658 <https://github.com/scipy/scipy/pull/19658>`__: MAINT: git blame ignores for lint clean-ups
 * `#19660 <https://github.com/scipy/scipy/pull/19660>`__: STY: special: use indent width of 4 in clang-format
 * `#19661 <https://github.com/scipy/scipy/pull/19661>`__: CI: fix pre-release job by correct version pin for scipy-openblas32
+* `#19670 <https://github.com/scipy/scipy/pull/19670>`__: MAINT: version bounds for 1.12.0rc1
 * `#19677 <https://github.com/scipy/scipy/pull/19677>`__: DOC: array types: mention partial support in \`special\`
 * `#19686 <https://github.com/scipy/scipy/pull/19686>`__: TST: fix incorrect signal.sosfilt tests
 * `#19690 <https://github.com/scipy/scipy/pull/19690>`__: BLD: avoid fast-math for oneAPI compilers, fix up handling of...
 * `#19691 <https://github.com/scipy/scipy/pull/19691>`__: BUG: fix negative overflow in stats.boxcox_normmax
 * `#19693 <https://github.com/scipy/scipy/pull/19693>`__: BUG: Prevent mutation of \`w\` parameter in \`spatial.distance.\*\`
 * `#19702 <https://github.com/scipy/scipy/pull/19702>`__: DEP: Adopt \`\*tol\` deprecations also for \`gcrotmk/lgmres/minres/tfqmr\`
+* `#19709 <https://github.com/scipy/scipy/pull/19709>`__: MAINT: Cumulative simpson follow-up comments
+* `#19735 <https://github.com/scipy/scipy/pull/19735>`__: DOC: update release notes with all deprecations for 1.12 release
+* `#19748 <https://github.com/scipy/scipy/pull/19748>`__: TST: skip RGI(..., method="pchip" for complex values)
+* `#19751 <https://github.com/scipy/scipy/pull/19751>`__: BUG: Make FMM classes \`py::module_local\` (fix for 1.12RC)
+* `#19761 <https://github.com/scipy/scipy/pull/19761>`__: MAINT: Avoid use of aligned_alloc in pocketfft on windows
+* `#19779 <https://github.com/scipy/scipy/pull/19779>`__: BUG: Fix \`nbinom.logcdf\` for invalid input
+* `#19785 <https://github.com/scipy/scipy/pull/19785>`__: BUG: support sparse Hessian in \`Newton-CG\`
+* `#19800 <https://github.com/scipy/scipy/pull/19800>`__: TST: loosen tolerances for tests that fail otherwise on windows+MKL
+* `#19806 <https://github.com/scipy/scipy/pull/19806>`__: TST: fix compatibility with pytest 8
+* `#19830 <https://github.com/scipy/scipy/pull/19830>`__: REL: bump copyright to 2024
+* `#19842 <https://github.com/scipy/scipy/pull/19842>`__: TST: move reference data for test_real_transforms to a fixture
+* `#19859 <https://github.com/scipy/scipy/pull/19859>`__: BLD: improve scipy-openblas dependency check

pyproject.toml

@@ -13,7 +13,7 @@ requires = [
     "meson-python>=0.15.0,<0.16.0", # working with 0.15.x series at branch time
     "Cython>=0.29.35,!=3.0.3,<3.1.0",  # when updating version, also update check in meson.build
     "pybind11>=2.10.4,<2.12.0", # working with 2.11.x series at branch time
-    "pythran@git+https://github.com/serge-sans-paille/pythran", # TODO: pin back to stable release when ready
+    "pythran>=0.15.0,<0.16.0", # working with 0.15.x series at branch time
 
     # When numpy 2.0.0rc1 comes out, we should update this to build against 2.0,
     # and then runtime depend on the range 1.22.X to <2.3. No need to switch to

scipy/fft/_pocketfft/pocketfft_hdronly.h

@@ -43,7 +43,7 @@ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #error This file is C++ and requires a C++ compiler.
 #endif
 
-#if !(__cplusplus >= 201103L || _MSVC_LANG+0L >= 201103L)
+#if !(__cplusplus >= 201103L || (defined(_MSVC_LANG) && _MSVC_LANG >= 201103L))
 #error This file requires at least C++11 support.
 #endif
 
@@ -149,7 +149,11 @@ template<> struct VLEN<double> { static constexpr size_t val=2; };
 #endif
 #endif
 
-#if __cplusplus >= 201703L
+// MSVC does not provide the standard aligned allocation functions,
+// yet _still_ sets the feature test macro (__cpp_aligned_new)...
+// While there are replacement functions (_aligned_malloc & _aligned_free),
+// those produce crashes when used here, see GH-19726
+#if __cplusplus >= 201703L && !defined(_MSC_VER)
 inline void *aligned_alloc(size_t align, size_t size)
   {
   void *ptr = ::aligned_alloc(align,size);