MAINT: backports/prep for 1.13.1

.github/workflows/linux_meson.yml

@@ -244,7 +244,7 @@ jobs:
 
       - name: Setup Python build deps
         run: |
-          pip install build meson-python ninja pythran pybind11 cython "numpy>=2.0.0b1"
+          pip install build meson-python ninja "pythran<0.16.0" pybind11 cython "numpy>=2.0.0b1"
 
       - name: Build wheel and install
         run: |

.github/workflows/macos_meson.yml

@@ -110,6 +110,7 @@ jobs:
       shell: bash -l {0}
       run: |
         conda activate scipy-dev
+        mamba install python=${{ matrix.python-version}}
 
         # optional test dependencies
         mamba install scikit-umfpack scikit-sparse
@@ -166,13 +167,14 @@ jobs:
 
         git submodule update --init
         # for some reason gfortran is not on the path
-        GFORTRAN_LOC=$(brew --prefix gfortran)/bin/gfortran 
+        GFORTRAN_LOC=$(which gfortran-13)
         ln -s $GFORTRAN_LOC gfortran
         export PATH=$PWD:$PATH
 
         # make sure we have openblas
         bash tools/wheels/cibw_before_build_macos.sh $PWD
-        export DYLD_LIBRARY_PATH=/usr/local/gfortran/lib:/opt/arm64-builds/lib
+        GFORTRAN_LIB=$(dirname `gfortran --print-file-name libgfortran.dylib`)
+        export DYLD_LIBRARY_PATH=$GFORTRAN_LIB
         export PKG_CONFIG_PATH=/opt/arm64-builds/lib/pkgconfig
 
         pip install click doit pydevtool rich_click meson cython pythran pybind11 ninja numpy

.github/workflows/wheels.yml

@@ -128,21 +128,16 @@ jobs:
         run: |
           if [[ ${{ matrix.buildplat[2] }} == 'arm64' ]]; then
             # macosx_arm64
-
-            # use homebrew gfortran
+            LIB_PATH=$LIB_PATH:/opt/arm64-builds/lib
             sudo xcode-select -s /Applications/Xcode_15.2.app            
-            # for some reason gfortran is not on the path
-            GFORTRAN_LOC=$(brew --prefix gfortran)/bin/gfortran 
-            ln -s $GFORTRAN_LOC gfortran
-            export PATH=$PWD:$PATH
-            echo "PATH=$PATH" >> "$GITHUB_ENV"
 
             # location of the gfortran's libraries
-            GFORTRAN_LIB=$(dirname `gfortran --print-file-name libgfortran.dylib`)
+            GFORTRAN_LIB="\$(dirname \$(gfortran --print-file-name libgfortran.dylib))"
 
             CIBW="MACOSX_DEPLOYMENT_TARGET=12.0\
               MACOS_DEPLOYMENT_TARGET=12.0\
-              LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH\
+              LD_LIBRARY_PATH=$LIB_PATH:$LD_LIBRARY_PATH\
+              SDKROOT=$(xcrun --sdk macosx --show-sdk-path)\
               _PYTHON_HOST_PLATFORM=macosx-12.0-arm64\
               PKG_CONFIG_PATH=/opt/arm64-builds/lib/pkgconfig"
             echo "CIBW_ENVIRONMENT_MACOS=$CIBW" >> "$GITHUB_ENV"
@@ -152,8 +147,8 @@ jobs:
 
             echo "REPAIR_PATH=/opt/arm64-builds/lib" >> "$GITHUB_ENV"
 
-            CIBW="DYLD_LIBRARY_PATH=$GFORTRAN_LIB:/opt/arm64-builds/lib delocate-listdeps {wheel} &&\
-              DYLD_LIBRARY_PATH=$GFORTRAN_LIB:/opt/arm64-builds/lib delocate-wheel --require-archs {delocate_archs} -w {dest_dir} {wheel}"
+            CIBW="DYLD_LIBRARY_PATH=$GFORTRAN_LIB:$LIB_PATH delocate-listdeps {wheel} &&\
+              DYLD_LIBRARY_PATH=$GFORTRAN_LIB:$LIB_PATH delocate-wheel --require-archs {delocate_archs} -w {dest_dir} {wheel}"
             echo "CIBW_REPAIR_WHEEL_COMMAND_MACOS=$CIBW" >> "$GITHUB_ENV"
 
           else

.gitignore

@@ -94,6 +94,7 @@ build-install/
 .doit.db.dir
 .doit.db.db
 .doit.db
+doc/source/.jupyterlite.doit.db
 
 # Logs and databases #
 ######################

ci/cirrus_wheels.yml

@@ -19,6 +19,7 @@ cirrus_wheels_linux_aarch64_task:
     platform: linux
     cpu: 2
     memory: 4G
+    timeout_in: 72m
   matrix:
     # build in a matrix because building and testing all four wheels in a
     # single task takes longer than 60 mins (the default time limit for a

doc/source/release/1.13.0-notes.rst

@@ -140,13 +140,39 @@ Deprecated features
 - Complex dtypes in ``PchipInterpolator`` and ``Akima1DInterpolator`` have
   been deprecated and will raise an error in SciPy 1.15.0. If you are trying
   to use the real components of the passed array, use ``np.real`` on ``y``.
-
+- Non-integer values of ``n`` together with ``exact=True`` are deprecated for
+  `scipy.special.factorial`.
+
+
+*********************
+Expired Deprecations
+*********************
+There is an ongoing effort to follow through on long-standing deprecations.
+The following previously deprecated features are affected:
+
+- ``scipy.signal.{lsim2,impulse2,step2}`` have been removed in favour of
+  ``scipy.signal.{lsim,impulse,step}``.
+- Window functions can no longer be imported from the `scipy.signal` namespace and
+  instead should be accessed through either `scipy.signal.windows` or
+  `scipy.signal.get_window`.
+- `scipy.sparse` no longer supports multi-Ellipsis indexing
+- ``scipy.signal.{bspline,quadratic,cubic}`` have been removed in favour of alternatives
+  in `scipy.interpolate`.
+- ``scipy.linalg.tri{,u,l}`` have been removed in favour of ``numpy.tri{,u,l}``.
+- Non-integer arrays in `scipy.special.factorial` with ``exact=True`` now raise an
+  error.
+- Functions from NumPy's main namespace which were exposed in SciPy's main
+  namespace, such as ``numpy.histogram`` exposed by ``scipy.histogram``, have
+  been removed from SciPy's main namespace. Please use the functions directly
+  from ``numpy``. This was originally performed for SciPy 1.12.0 however was missed from
+  the release notes so is included here for completeness.
 
 
 ******************************
 Backwards incompatible changes
 ******************************
 
+
 *************
 Other changes
 *************

doc/source/release/1.13.1-notes.rst

@@ -5,19 +5,98 @@ SciPy 1.13.1 Release Notes
 .. contents::
 
 SciPy 1.13.1 is a bug-fix release with no new features
-compared to 1.13.0.
+compared to 1.13.0. The version of OpenBLAS shipped with
+the PyPI binaries has been increased to 0.3.27.
 
 
 
 Authors
 =======
 * Name (commits)
+* h-vetinari (1)
+* Jake Bowhay (2)
+* Evgeni Burovski (6)
+* Sean Cheah (2)
+* Lucas Colley (2)
+* DWesl (2)
+* Ralf Gommers (7)
+* Ben Greiner (1) +
+* Matt Haberland (2)
+* Gregory R. Lee (1)
+* Philip Loche (1) +
+* Sijo Valayakkad Manikandan (1) +
+* Matti Picus (1)
+* Tyler Reddy (62)
+* Atsushi Sakai (1)
+* Daniel Schmitz (2)
+* Dan Schult (3)
+* Scott Shambaugh (2)
+* Edgar Andrés Margffoy Tuay (1)
+
+A total of 19 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 1.13.1
 ------------------------
 
+* `#19423 <https://github.com/scipy/scipy/issues/19423>`__: BUG: \`scipy.ndimage.value_indices\` returns empty dict for \`intc\`/\`uintc\` dtype on Windows
+* `#20264 <https://github.com/scipy/scipy/issues/20264>`__: DOC, MAINT: .jupyterlite.doit.db shows up untracked
+* `#20392 <https://github.com/scipy/scipy/issues/20392>`__: DOC: optimize.root(method='lm') option
+* `#20415 <https://github.com/scipy/scipy/issues/20415>`__: BUG: csr_array can no longer be initialized with 1D array
+* `#20471 <https://github.com/scipy/scipy/issues/20471>`__: BUG: \`TestEig.test_falker\` fails on windows + MKL as well as...
+* `#20491 <https://github.com/scipy/scipy/issues/20491>`__: BUG: Cannot find \`OpenBLAS\` on Cygwin
+* `#20506 <https://github.com/scipy/scipy/issues/20506>`__: BUG: special.spherical_in: derivative at \`z=0, n=1\` incorrect
+* `#20512 <https://github.com/scipy/scipy/issues/20512>`__: BUG: \`eigh\` fails for size 1 array with driver=evd
+* `#20531 <https://github.com/scipy/scipy/issues/20531>`__: BUG: warning from \`optimize.least_squares\` for astropy with...
+* `#20555 <https://github.com/scipy/scipy/issues/20555>`__: BUG: spatial: error in \`Rotation.align_vectors()\` with an infinite...
+* `#20576 <https://github.com/scipy/scipy/issues/20576>`__: MAINT, TST: two types of failures observed on maintenance/1.13.x...
+* `#20580 <https://github.com/scipy/scipy/issues/20580>`__: BUG: scipy.special.factorial2 doesn't handle \`uint32\` dtypes
+* `#20591 <https://github.com/scipy/scipy/issues/20591>`__: BUG: scipy.stats.wilcoxon in 1.13 fails on 2D array with nan...
+* `#20623 <https://github.com/scipy/scipy/issues/20623>`__: BUG: scipy.spatial.Delaunay, scipy.interpolate.LinearNDInterpolator...
+* `#20648 <https://github.com/scipy/scipy/issues/20648>`__: BUG: stats.yulesimon: incorrect kurtosis values
+* `#20652 <https://github.com/scipy/scipy/issues/20652>`__: BUG: incorrect origin tuple handling in ndimage \`minimum_filter\`...
+* `#20660 <https://github.com/scipy/scipy/issues/20660>`__: BUG: spatial: \`Rotation.align_vectors()\` incorrect for anti-parallel...
+* `#20670 <https://github.com/scipy/scipy/issues/20670>`__: BUG: sparse matrix creation in 1.13 with indices not summing...
+* `#20692 <https://github.com/scipy/scipy/issues/20692>`__: BUG: stats.zipf: incorrect pmf values
+* `#20714 <https://github.com/scipy/scipy/issues/20714>`__: CI: scipy installation failing in umfpack tests
 
 
 Pull requests for 1.13.1
 ------------------------
+
+* `#20280 <https://github.com/scipy/scipy/pull/20280>`__: MAINT: added doc/source/.jupyterlite.doit.db to .gitignore See...
+* `#20322 <https://github.com/scipy/scipy/pull/20322>`__: BUG: sparse: align dok_array.pop() to dict.pop() for case with...
+* `#20333 <https://github.com/scipy/scipy/pull/20333>`__: BUG: sync pocketfft again
+* `#20381 <https://github.com/scipy/scipy/pull/20381>`__: REL, MAINT: prep for 1.13.1
+* `#20401 <https://github.com/scipy/scipy/pull/20401>`__: DOC: optimize: fix wrong optional argument name in \`root(method="lm")\`.
+* `#20435 <https://github.com/scipy/scipy/pull/20435>`__: DOC: add missing deprecations from 1.13.0 release notes
+* `#20437 <https://github.com/scipy/scipy/pull/20437>`__: MAINT/DOC: fix syntax in 1.13.0 release notes
+* `#20444 <https://github.com/scipy/scipy/pull/20444>`__: BUG: sparse: Clean up 1D input handling to sparse array/matrix...
+* `#20449 <https://github.com/scipy/scipy/pull/20449>`__: DOC: remove spurious backtick from release notes
+* `#20473 <https://github.com/scipy/scipy/pull/20473>`__: BUG: linalg: fix ordering of complex conj gen eigenvalues
+* `#20474 <https://github.com/scipy/scipy/pull/20474>`__: TST: tolerance bumps for the conda-forge builds
+* `#20484 <https://github.com/scipy/scipy/pull/20484>`__: TST: compare absolute values of U and VT in pydata-sparse SVD...
+* `#20505 <https://github.com/scipy/scipy/pull/20505>`__: BUG: Include Python.h before system headers.
+* `#20516 <https://github.com/scipy/scipy/pull/20516>`__: BUG: linalg: fix eigh(1x1 array, driver='evd') f2py check
+* `#20527 <https://github.com/scipy/scipy/pull/20527>`__: BUG: \`spherical_in\` for \`n=0\` and \`z=0\`
+* `#20530 <https://github.com/scipy/scipy/pull/20530>`__: BLD: Fix error message for f2py generation fail
+* `#20533 <https://github.com/scipy/scipy/pull/20533>`__: TST: Adapt to \`__array__(copy=True)\`
+* `#20537 <https://github.com/scipy/scipy/pull/20537>`__: BLD: Move Python-including files to start of source.
+* `#20567 <https://github.com/scipy/scipy/pull/20567>`__: REV: 1.13.x: revert changes to f2py and tempita handling in meson.build...
+* `#20569 <https://github.com/scipy/scipy/pull/20569>`__: update openblas to 0.3.27
+* `#20573 <https://github.com/scipy/scipy/pull/20573>`__: BUG: Fix error with 180 degree rotation in Rotation.align_vectors()...
+* `#20586 <https://github.com/scipy/scipy/pull/20586>`__: MAINT: optimize.linprog: fix bug when integrality is a list of...
+* `#20592 <https://github.com/scipy/scipy/pull/20592>`__: MAINT: stats.wilcoxon: fix failure with multidimensional \`x\`...
+* `#20601 <https://github.com/scipy/scipy/pull/20601>`__: MAINT: lint: temporarily disable UP031
+* `#20607 <https://github.com/scipy/scipy/pull/20607>`__: BUG: handle uint arrays in factorial{,2,k}
+* `#20611 <https://github.com/scipy/scipy/pull/20611>`__: BUG: prevent QHull message stream being closed twice
+* `#20629 <https://github.com/scipy/scipy/pull/20629>`__: MAINT/DEV: lint: disable UP032
+* `#20633 <https://github.com/scipy/scipy/pull/20633>`__: BUG: fix Vor/Delaunay segfaults
+* `#20644 <https://github.com/scipy/scipy/pull/20644>`__: BUG: ndimage.value_indices: deal with unfixed types
+* `#20653 <https://github.com/scipy/scipy/pull/20653>`__: BUG: ndimage: fix origin handling for \`{minimum, maximum}_filter\`
+* `#20654 <https://github.com/scipy/scipy/pull/20654>`__: MAINT: stats.yulesimon: fix kurtosis
+* `#20687 <https://github.com/scipy/scipy/pull/20687>`__: BUG: sparse: Fix summing duplicates for CSR/CSC creation from...
+* `#20702 <https://github.com/scipy/scipy/pull/20702>`__: BUG: stats: Fix \`zipf.pmf\` and \`zipfian.pmf\` for int32 \`k\`
+* `#20727 <https://github.com/scipy/scipy/pull/20727>`__: CI: pin Python for MacOS conda

scipy/interpolate/tests/test_rbfinterp.py

@@ -2,7 +2,7 @@
 import pytest
 import numpy as np
 from numpy.linalg import LinAlgError
-from numpy.testing import assert_allclose, assert_array_equal
+from numpy.testing import assert_allclose
 from scipy.stats.qmc import Halton
 from scipy.spatial import cKDTree
 from scipy.interpolate._rbfinterp import (
@@ -415,7 +415,7 @@ def test_pickleable(self):
         yitp1 = interp(xitp)
         yitp2 = pickle.loads(pickle.dumps(interp))(xitp)
 
-        assert_array_equal(yitp1, yitp2)
+        assert_allclose(yitp1, yitp2, atol=1e-16)
 
 
 class TestRBFInterpolatorNeighborsNone(_TestRBFInterpolator):

scipy/interpolate/tests/test_rgi.py

@@ -137,7 +137,7 @@ def test_derivatives(self):
 
         # 2nd derivatives of a linear function are zero
         assert_allclose(interp(sample, nu=(0, 1, 1, 0)),
-                        [0, 0, 0], atol=1e-12)
+                        [0, 0, 0], atol=2e-12)
 
     @parametrize_rgi_interp_methods
     def test_complex(self, method):
@@ -983,7 +983,11 @@ def test_matrix_input(self, method):
 
         v1 = interpn((x, y), values, sample, method=method)
         v2 = interpn((x, y), np.asarray(values), sample, method=method)
-        assert_allclose(v1, v2)
+        if method == "quintic":
+            # https://github.com/scipy/scipy/issues/20472
+            assert_allclose(v1, v2, atol=5e-5, rtol=2e-6)
+        else:
+            assert_allclose(v1, v2)
 
     def test_length_one_axis(self):
         # gh-5890, gh-9524 : length-1 axis is legal for method='linear'.

scipy/linalg/_testutils.py

@@ -12,6 +12,8 @@ def __init__(self, data):
         self._data = data
 
     def __array__(self, dtype=None, copy=None):
+        if copy:
+            return self._data.copy()
         return self._data
 
 

scipy/linalg/flapack_sym_herm.pyf.src

@@ -124,7 +124,7 @@ subroutine <prefix2>syevd(compute_v,lower,n,w,a,lda,work,lwork,iwork,liwork,info
     <ftype2> dimension(n),intent(out),depend(n) :: w
 
     integer optional,intent(in),depend(n,compute_v) :: lwork=max((compute_v?1+6*n+2*n*n:2*n+1),1)
-    check(lwork>=(compute_v?1+6*n+2*n*n:2*n+1)) :: lwork
+    check( (lwork>=((compute_v?1+6*n+2*n*n:2*n+1))) || ((n==1)&&(lwork>=1)) ) :: lwork
     <ftype2> dimension(lwork),intent(hide,cache),depend(lwork) :: work
 
     integer optional,intent(in),depend(n,compute_v) :: liwork = (compute_v?3+5*n:1)
@@ -180,7 +180,7 @@ subroutine <prefix2c>heevd(compute_v,lower,n,w,a,lda,work,lwork,iwork,liwork,rwo
     <ftype2> dimension(n),intent(out),depend(n) :: w
 
     integer optional,intent(in),depend(n,compute_v) :: lwork=max((compute_v?2*n+n*n:n+1),1)
-    check(lwork>=(compute_v?2*n+n*n:n+1)) :: lwork
+    check( (lwork>=(compute_v?2*n+n*n:n+1)) || ((n==1)&&(lwork>=1)) ) :: lwork
     <ftype2c> dimension(lwork),intent(hide,cache),depend(lwork) :: work
 
     integer optional,intent(in),depend(n,compute_v) :: liwork = (compute_v?3+5*n:1)

scipy/linalg/tests/test_decomp.py

@@ -230,8 +230,8 @@ def _check_gen_eig(self, A, B, atol_homog=1e-13, rtol_homog=1e-13):
         w_fin = -1j * np.real_if_close(1j*w_fin, tol=1e-10)
         wt_fin = -1j * np.real_if_close(1j*wt_fin, tol=1e-10)
 
-        perm = argsort(w_fin)
-        permt = argsort(wt_fin)
+        perm = argsort(abs(w_fin) + w_fin.imag)
+        permt = argsort(abs(wt_fin) + wt_fin.imag)
 
         assert_allclose(w_fin[perm], wt_fin[permt],
                         atol=1e-7, rtol=1e-7, err_msg=msg)
@@ -877,6 +877,17 @@ def test_various_drivers_standard(self, driver, dtype_):
                         atol=1000*np.finfo(dtype_).eps,
                         rtol=0.)
 
+    @pytest.mark.parametrize('driver', ("ev", "evd", "evr", "evx"))
+    def test_1x1_lwork(self, driver):
+        w, v = eigh([[1]], driver=driver)
+        assert_allclose(w, array([1.]), atol=1e-15)
+        assert_allclose(v, array([[1.]]), atol=1e-15)
+
+        # complex case now
+        w, v = eigh([[1j]], driver=driver)
+        assert_allclose(w, array([0]), atol=1e-15)
+        assert_allclose(v, array([[1.]]), atol=1e-15)
+
     @pytest.mark.parametrize('type', (1, 2, 3))
     @pytest.mark.parametrize('driver', ("gv", "gvd", "gvx"))
     def test_various_drivers_generalized(self, driver, type):

scipy/ndimage/_filters.py

@@ -1266,25 +1266,31 @@ def _min_or_max_filter(input, size, footprint, structure, output, mode,
         else:
             output[...] = input[...]
     else:
-        origins = _ni_support._normalize_sequence(origin, input.ndim)
+        origins = _ni_support._normalize_sequence(origin, num_axes)
         if num_axes < input.ndim:
             if footprint.ndim != num_axes:
                 raise RuntimeError("footprint array has incorrect shape")
             footprint = numpy.expand_dims(
                 footprint,
                 tuple(ax for ax in range(input.ndim) if ax not in axes)
             )
+            # set origin = 0 for any axes not being filtered
+            origins_temp = [0,] * input.ndim
+            for o, ax in zip(origins, axes):
+                origins_temp[ax] = o
+            origins = origins_temp
+
         fshape = [ii for ii in footprint.shape if ii > 0]
         if len(fshape) != input.ndim:
             raise RuntimeError('footprint array has incorrect shape.')
         for origin, lenf in zip(origins, fshape):
             if (lenf // 2 + origin < 0) or (lenf // 2 + origin >= lenf):
-                raise ValueError('invalid origin')
+                raise ValueError("invalid origin")
         if not footprint.flags.contiguous:
             footprint = footprint.copy()
         if structure is not None:
             if len(structure.shape) != input.ndim:
-                raise RuntimeError('structure array has incorrect shape')
+                raise RuntimeError("structure array has incorrect shape")
             if num_axes != structure.ndim:
                 structure = numpy.expand_dims(
                     structure,