Merge pull request #19279 from tylerjereddy/treddy_1_11_3_prep

MAINT: SciPy 1.11.3 backports/prep
scipy · Sep 27, 2023 · 329b980 · 329b980
2 parents b56f4c9 + 8208cf6
commit 329b980
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diff --git a/.github/workflows/linux_meson.yml b/.github/workflows/linux_meson.yml
@@ -230,9 +230,9 @@ jobs:
         run: |
           pip install "numpy==1.21.6" &&
           # build deps
-          pip install build meson-python ninja pythran "pybind11<2.11.0" "cython<3.0.0" "wheel<0.41.0"
+          pip install build "meson-python<0.14.0" ninja "pythran<0.14.0" "pybind11<2.11.0" "cython<3.0.0" "wheel<0.41.0"
           # test deps
-          pip install gmpy2 threadpoolctl mpmath pooch pythran "pybind11<2.11.0" pytest pytest-xdist==2.5.0 pytest-timeout
+          pip install gmpy2 threadpoolctl mpmath pooch "pythran<0.14.0" "pybind11<2.11.0" pytest pytest-xdist==2.5.0 pytest-timeout
 
       - name: Build wheel and install
         run: |

diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -131,14 +131,15 @@ jobs:
           CIBW_PRERELEASE_PYTHONS: True
 
           # required so that cp312 can grab a nightly wheel
-          # can remove when cp312 is release and we don't need to search
+          # can remove when cp312 is released and we don't need to search
           # other wheel locations.
-          CIBW_ENVIRONMENT: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple PIP_PRE=1
+          # PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+          CIBW_ENVIRONMENT: PIP_PRE=1
 
           CIBW_ENVIRONMENT_WINDOWS: >
             PKG_CONFIG_PATH=c:/opt/64/lib/pkgconfig
             PIP_PRE=1
-            PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+            # PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
 
           # setting SDKROOT necessary when using the gfortran compiler
           # installed in cibw_before_build_macos.sh
@@ -153,7 +154,7 @@ jobs:
             MACOS_DEPLOYMENT_TARGET=10.9
             _PYTHON_HOST_PLATFORM=macosx-10.9-x86_64
             PIP_PRE=1
-            PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+            # PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
 
           CIBW_REPAIR_WHEEL_COMMAND_MACOS: >
             DYLD_LIBRARY_PATH=/usr/local/lib delocate-listdeps {wheel} &&

diff --git a/.mailmap b/.mailmap
@@ -167,6 +167,7 @@ Ed Schofield <edschofield@localhost> edschofield <edschofield@localhost>
 Egor Zemlyanoy <egorz734@mail.ru> egorz734 <egorz734@mail.ru>
 Egor Zemlyanoy <egorz734@mail.ru> Egorz734 <egorz734@mail.ru>
 Egor Zemlyanoy <egorz734@mail.ru> Egor <egorz734@mail.ru>
+Ellie Litwack <ellie@PF2WXP6T.ad.bac.work> ellieLitwack <ellie@PF2WXP6T.ad.bac.work>
 Eric Larson <larson.eric.d@gmail.com> Eric89GXL <larson.eric.d@gmail.com>
 Eric Quintero <eric.antonio.quintero@gmail.com> e-q <eric.antonio.quintero@gmail.com>
 Eric Quintero <eric.antonio.quintero@gmail.com> Eric Quintero <e-q@users.noreply.github.com>

diff --git a/benchmarks/benchmarks/signal_filtering.py b/benchmarks/benchmarks/signal_filtering.py
@@ -6,7 +6,7 @@
 
 with safe_import():
     from scipy.signal import (lfilter, firwin, decimate, butter, sosfilt,
-                              medfilt2d)
+                              medfilt2d, freqz)
 
 
 class Decimate(Benchmark):
@@ -102,3 +102,19 @@ def time_medfilt2d(self, threads):
 
     def peakmem_medfilt2d(self, threads):
         self._medfilt2d(threads)
+
+
+class FreqzRfft(Benchmark):
+    param_names = ['whole', 'nyquist', 'worN']
+    params = [
+        [False, True],
+        [False, True],
+        [64, 65, 128, 129, 256, 257, 258, 512, 513, 65536, 65537, 65538],
+    ]
+
+    def setup(self, whole, nyquist, worN):
+        self.y = np.zeros(worN)
+        self.y[worN//2] = 1.0
+
+    def time_freqz(self, whole, nyquist, worN):
+        freqz(self.y, whole=whole, include_nyquist=nyquist, worN=worN)
diff --git a/ci/cirrus_wheels.yml b/ci/cirrus_wheels.yml
@@ -30,8 +30,8 @@ cirrus_wheels_linux_aarch64_task:
   env:
     CIBW_PRERELEASE_PYTHONS: True
     CIBW_ENVIRONMENT: >
-      PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
       PIP_PRE=1
+    #      PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
 
   build_script: |
     apt install -y python3-venv python-is-python3
@@ -59,8 +59,8 @@ cirrus_wheels_macos_arm64_task:
     CIBW_ENVIRONMENT: >
       MACOSX_DEPLOYMENT_TARGET=12.0
       _PYTHON_HOST_PLATFORM="macosx-12.0-arm64"             
-      PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
       PIP_PRE=1
+      # PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
     PKG_CONFIG_PATH: /opt/arm64-builds/lib/pkgconfig
     # assumes that the cmake config is in /usr/local/lib/cmake
     CMAKE_PREFIX_PATH: /opt/arm64-builds/

diff --git a/dev.py b/dev.py
@@ -111,14 +111,6 @@ def task_meta(cls, **kwargs):
 import traceback
 from concurrent.futures.process import _MAX_WINDOWS_WORKERS
 
-# distutils is required to infer meson install path
-# if this needs to be replaced for Python 3.12 support and there's no
-# stdlib alternative, use CmdAction and the hack discussed in gh-16058
-with warnings.catch_warnings():
-    warnings.filterwarnings("ignore", category=DeprecationWarning)
-    from distutils import dist
-    from distutils.command.install import INSTALL_SCHEMES
-
 from pathlib import Path
 from collections import namedtuple
 from types import ModuleType as new_module
@@ -337,14 +329,23 @@ def get_site_packages(self):
         Depending on whether we have debian python or not,
         return dist_packages path or site_packages path.
         """
-        if 'deb_system' in INSTALL_SCHEMES:
-            # debian patched python in use
-            install_cmd = dist.Distribution().get_command_obj('install')
-            install_cmd.select_scheme('deb_system')
-            install_cmd.finalize_options()
-            plat_path = Path(install_cmd.install_platlib)
-        else:
+        if sys.version_info >= (3, 12):
             plat_path = Path(get_path('platlib'))
+        else:
+            # distutils is required to infer meson install path
+            # for python < 3.12 in debian patched python
+            with warnings.catch_warnings():
+                warnings.filterwarnings("ignore", category=DeprecationWarning)
+                from distutils import dist
+                from distutils.command.install import INSTALL_SCHEMES
+            if 'deb_system' in INSTALL_SCHEMES:
+                # debian patched python in use
+                install_cmd = dist.Distribution().get_command_obj('install')
+                install_cmd.select_scheme('deb_system')
+                install_cmd.finalize_options()
+                plat_path = Path(install_cmd.install_platlib)
+            else:
+                plat_path = Path(get_path('platlib'))
         return self.installed / plat_path.relative_to(sys.exec_prefix)
 
 

diff --git a/doc/source/release/1.11.3-notes.rst b/doc/source/release/1.11.3-notes.rst
@@ -12,13 +12,65 @@ compared to 1.11.2.
 Authors
 =======
 * Name (commits)
+* Jake Bowhay (2)
+* CJ Carey (1)
+* Colin Carroll (1) +
+* Anirudh Dagar (2)
+* drestebon (1) +
+* Ralf Gommers (5)
+* Matt Haberland (2)
+* Julien Jerphanion (1)
+* Uwe L. Korn (1) +
+* Ellie Litwack (2)
+* Andrew Nelson (5)
+* Bharat Raghunathan (1)
+* Tyler Reddy (37)
+* Søren Fuglede Jørgensen (2)
+* Hielke Walinga (1) +
+* Warren Weckesser (1)
+* Bernhard M. Wiedemann (1)
+
+A total of 17 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 1.11.3
 ------------------------
 
+* `#15093 <https://github.com/scipy/scipy/issues/15093>`__: BUG: scipy.optimize's trust-constr algorithm hangs when keep-feasible...
+* `#15273 <https://github.com/scipy/scipy/issues/15273>`__: freqz: suboptimal performance for worN=2\*\*n+1, include_nyquist=True...
+* `#17269 <https://github.com/scipy/scipy/issues/17269>`__: Bug in scipy.sparse.csgraph.min_weight_full_bipartite_matching
+* `#17289 <https://github.com/scipy/scipy/issues/17289>`__: BUG: Different results between numpy.fft.rfft and scipy.signal.freqz
+* `#18716 <https://github.com/scipy/scipy/issues/18716>`__: Buffer dtype mismatch, expected 'ITYPE_t' but got 'long'
+* `#18782 <https://github.com/scipy/scipy/issues/18782>`__: BUG: johnsonsu distribution no longer accepts integer \`b\` parameter
+* `#18922 <https://github.com/scipy/scipy/issues/18922>`__: BUG: dev.py has \`distutils\` usage
+* `#19101 <https://github.com/scipy/scipy/issues/19101>`__: BUG: mesonpy embeds random path in .pyx files
+* `#19103 <https://github.com/scipy/scipy/issues/19103>`__: BUG: Regression in 1.11.2: optimize.least_squares with method='trf'...
+* `#19132 <https://github.com/scipy/scipy/issues/19132>`__: BUG: Build fails on latest commit
+* `#19149 <https://github.com/scipy/scipy/issues/19149>`__: BUG: scipy.sparse.csgraph.laplacian raises AttributeError on...
+* `#19197 <https://github.com/scipy/scipy/issues/19197>`__: BUG: Incorrect sampling from zero rank covariance
 
 
 Pull requests for 1.11.3
 ------------------------
 
+* `#17633 <https://github.com/scipy/scipy/pull/17633>`__: BUG: add infeasibility checks to min_weight_full_bipartite_matching
+* `#18784 <https://github.com/scipy/scipy/pull/18784>`__: BUG: Allow johnsonsu parameters to be floats
+* `#18913 <https://github.com/scipy/scipy/pull/18913>`__: BUG: sparse.csgraph: Support int64 indices in traversal.pyx
+* `#18924 <https://github.com/scipy/scipy/pull/18924>`__: BUG: Fix python3.12 distutils dev.py build
+* `#18956 <https://github.com/scipy/scipy/pull/18956>`__: BUG: trust-constr Bounds exclusive
+* `#19076 <https://github.com/scipy/scipy/pull/19076>`__: MAINT: should not be using np.float64() on arrays
+* `#19084 <https://github.com/scipy/scipy/pull/19084>`__: REL, MAINT: prep for 1.11.3
+* `#19111 <https://github.com/scipy/scipy/pull/19111>`__: BUG: Fixes #19103 by adding back make_strictly_feasible to lsq...
+* `#19123 <https://github.com/scipy/scipy/pull/19123>`__: BLD: Avoid absolute pathnames in .pyx files
+* `#19135 <https://github.com/scipy/scipy/pull/19135>`__: MAINT: signal: Remove the cval parameter from the private function...
+* `#19139 <https://github.com/scipy/scipy/pull/19139>`__: BLD: revert to using published wheels [wheel build]
+* `#19156 <https://github.com/scipy/scipy/pull/19156>`__: BUG: Support sparse arrays in scipy.sparse.csgraph.laplacian
+* `#19199 <https://github.com/scipy/scipy/pull/19199>`__: MAINT: stats.CovViaEigendecomposition: fix \`_LA\` attribute...
+* `#19200 <https://github.com/scipy/scipy/pull/19200>`__: TST: fix \`TestODR.test_implicit\` test failure with tolerance...
+* `#19208 <https://github.com/scipy/scipy/pull/19208>`__: BUG: freqz rfft grid fix
+* `#19280 <https://github.com/scipy/scipy/pull/19280>`__: MAINT: newton, make sure x0 is an inexact type
+* `#19286 <https://github.com/scipy/scipy/pull/19286>`__: BUG: stats: fix build failure due to incorrect Boost policies...
+* `#19290 <https://github.com/scipy/scipy/pull/19290>`__: BLD: add float.h include to \`_fpumode.c\`, fixes Clang on Windows...
+* `#19299 <https://github.com/scipy/scipy/pull/19299>`__: MAINT: fix libquadmath licence
diff --git a/pyproject.toml b/pyproject.toml
@@ -10,13 +10,15 @@
 [build-system]
 build-backend = 'mesonpy'
 requires = [
-    "meson-python>=0.12.1,<0.14.0", # already working with 0.13.x series at branch time
-    "Cython>=0.29.35,<3.0",  # when updating version, also update check in meson.build
-    "pybind11>=2.10.4,<2.11.0",
-    "pythran>=0.12.0,<0.14.0", # already working with 0.13.x series at branch time
-    # `wheel` is needed for non-isolated builds, given that `meson-python`
-    # doesn't list it as a runtime requirement (at least in 0.5.0)
-    "wheel<0.41.0",
+    # Reason for `<`: future-proofing (0.14.0 released and known to work)
+    "meson-python>=0.12.1,<0.15.0",
+    # Reason for `<`: we want to build the 1.11.x releases with Cython 0.29.x
+    # (too many changes in 3.0)
+    "Cython>=0.29.35,<3.0",   # when updating version, also update check in meson.build
+    # Reason for `<`: future-proofing (2.11.1 is the most recent version)
+    "pybind11>=2.10.4,<2.11.1",
+    # Reason for `<`: future-proofing (0.14.0 released and known to work)
+    "pythran>=0.12.0,<0.15.0",
 
     # NumPy dependencies - to update these, sync from
     # https://github.com/scipy/oldest-supported-numpy/, and then
@@ -41,13 +43,14 @@ requires = [
     # (see oldest-supported-numpy issues gh-28 and gh-45)
     "numpy==1.21.6; python_version=='3.10' and (platform_system!='Windows' and platform_machine!='loongarch64') and platform_python_implementation != 'PyPy'",
     "numpy==1.23.2; python_version=='3.11' and platform_python_implementation != 'PyPy'",
+    "numpy>=1.26.0,<1.27.0; python_version=='3.12'",  # no `==` because we expect relevant bug fixes in 1.26.1/2
 
     # For Python versions which aren't yet officially supported,
     # we specify an unpinned NumPy which allows source distributions
     # to be used and allows wheels to be used as soon as they
     # become available.
     "numpy; python_version>='3.9' and platform_python_implementation=='PyPy'",
-    "numpy==1.26.0b1; python_version>='3.12.0.rc1'",
+    "numpy>=1.26.0; python_version>='3.13'",
 ]
 
 [project]
@@ -64,8 +67,6 @@ maintainers = [
 #     https://scipy.github.io/devdocs/dev/core-dev/index.html#version-ranges-for-numpy-and-other-dependencies
 requires-python = ">=3.9,<3.13"
 dependencies = [
-    # TODO: update to "pin-compatible" once possible, see
-    # https://github.com/FFY00/meson-python/issues/29
     "numpy>=1.21.6,<1.28.0",
 ]
 readme = "README.rst"
@@ -80,6 +81,7 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Topic :: Software Development :: Libraries",
     "Topic :: Scientific/Engineering",
     "Operating System :: Microsoft :: Windows",

diff --git a/scipy/_lib/_fpumode.c b/scipy/_lib/_fpumode.c
@@ -4,6 +4,7 @@
 
 
 #ifdef _MSC_VER
+#include <float.h>
 #pragma float_control(precise, on)
 #pragma fenv_access (on)
 #endif

diff --git a/scipy/integrate/_quadrature.py b/scipy/integrate/_quadrature.py
@@ -502,8 +502,8 @@ def _basic_simpson(y, start, stop, x, dx, axis):
         h = np.diff(x, axis=axis)
         sl0 = tupleset(slice_all, axis, slice(start, stop, step))
         sl1 = tupleset(slice_all, axis, slice(start+1, stop+1, step))
-        h0 = np.float64(h[sl0])
-        h1 = np.float64(h[sl1])
+        h0 = h[sl0].astype(float, copy=False)
+        h1 = h[sl1].astype(float, copy=False)
         hsum = h0 + h1
         hprod = h0 * h1
         h0divh1 = np.true_divide(h0, h1, out=np.zeros_like(h0), where=h1 != 0)

diff --git a/scipy/odr/tests/test_odr.py b/scipy/odr/tests/test_odr.py
@@ -5,7 +5,8 @@
 import numpy as np
 from numpy import pi
 from numpy.testing import (assert_array_almost_equal,
-                           assert_equal, assert_warns)
+                           assert_equal, assert_warns,
+                           assert_allclose)
 import pytest
 from pytest import raises as assert_raises
 
@@ -127,7 +128,7 @@ def test_implicit(self):
             np.array([0.1113840353364371, 0.1097673310686467, 0.0041060738314314,
                 0.0027500347539902, 0.0034962501532468]),
         )
-        assert_array_almost_equal(
+        assert_allclose(
             out.cov_beta,
             np.array([[2.1089274602333052e+00, -1.9437686411979040e+00,
                   7.0263550868344446e-02, -4.7175267373474862e-02,
@@ -144,6 +145,7 @@ def test_implicit(self):
                [5.2515575927380355e-02, -5.8822307501391467e-02,
                   1.4528860663055824e-03, -1.2692942951415293e-03,
                   2.0778813389755596e-03]]),
+            rtol=1e-6, atol=2e-6,
         )
 
     # Multi-variable Example

diff --git a/scipy/optimize/_lsq/least_squares.py b/scipy/optimize/_lsq/least_squares.py
@@ -12,7 +12,7 @@
 
 from .trf import trf
 from .dogbox import dogbox
-from .common import EPS, in_bounds
+from .common import EPS, in_bounds, make_strictly_feasible
 
 
 TERMINATION_MESSAGES = {
@@ -821,6 +821,9 @@ def least_squares(
 
     ftol, xtol, gtol = check_tolerance(ftol, xtol, gtol, method)
 
+    if method == 'trf':
+        x0 = make_strictly_feasible(x0, lb, ub, rstep=0)
+
     def fun_wrapped(x):
         return np.atleast_1d(fun(x, *args, **kwargs))
 

diff --git a/scipy/optimize/_trustregion_constr/minimize_trustregion_constr.py b/scipy/optimize/_trustregion_constr/minimize_trustregion_constr.py
@@ -3,7 +3,7 @@
 from scipy.sparse.linalg import LinearOperator
 from .._differentiable_functions import VectorFunction
 from .._constraints import (
-    NonlinearConstraint, LinearConstraint, PreparedConstraint, strict_bounds)
+    NonlinearConstraint, LinearConstraint, PreparedConstraint, Bounds, strict_bounds)
 from .._hessian_update_strategy import BFGS
 from .._optimize import OptimizeResult
 from .._differentiable_functions import ScalarFunction
@@ -323,6 +323,11 @@ def _minimize_trustregion_constr(fun, x0, args, grad,
         verbose = 1
 
     if bounds is not None:
+        modified_lb = np.nextafter(bounds.lb, -np.inf, where=bounds.lb > -np.inf)
+        modified_ub = np.nextafter(bounds.ub, np.inf, where=bounds.ub < np.inf)
+        modified_lb = np.where(np.isfinite(bounds.lb), modified_lb, bounds.lb)
+        modified_ub = np.where(np.isfinite(bounds.ub), modified_ub, bounds.ub)
+        bounds = Bounds(modified_lb, modified_ub, keep_feasible=bounds.keep_feasible)
         finite_diff_bounds = strict_bounds(bounds.lb, bounds.ub,
                                            bounds.keep_feasible, n_vars)
     else:

diff --git a/scipy/optimize/_zeros_py.py b/scipy/optimize/_zeros_py.py
@@ -290,7 +290,10 @@ class of similar problems can be solved together.
                              full_output)
 
     # Convert to float (don't use float(x0); this works also for complex x0)
-    x0 = np.asarray(x0)[()]
+    # Use np.asarray because we want x0 to be a numpy object, not a Python
+    # object. e.g. np.complex(1+1j) > 0 is possible, but (1 + 1j) > 0 raises
+    # a TypeError
+    x0 = np.asarray(x0)[()] * 1.0
     p0 = x0
     funcalls = 0
     if fprime is not None:

diff --git a/scipy/optimize/tests/test_least_squares.py b/scipy/optimize/tests/test_least_squares.py
@@ -822,3 +822,31 @@ def chi2(x):
     # if we choose an initial condition that is close to the solution
     # we shouldn't return an answer that is further away from the solution
     assert_allclose(res.x, answer, atol=initial_guess-answer)
+
+
+def test_gh_19103():
+    # Checks that least_squares trf method selects a strictly feasible point,
+    # and thus succeeds instead of failing,
+    # when the initial guess is reported exactly at a boundary point.
+    # This is a reduced example from gh191303
+
+    ydata = np.array([0.] * 66 + [
+        1., 0., 0., 0., 0., 0., 1., 1., 0., 0., 1.,
+        1., 1., 1., 0., 0., 0., 1., 0., 0., 2., 1.,
+        0., 3., 1., 6., 5., 0., 0., 2., 8., 4., 4.,
+        6., 9., 7., 2., 7., 8., 2., 13., 9., 8., 11.,
+        10., 13., 14., 19., 11., 15., 18., 26., 19., 32., 29.,
+        28., 36., 32., 35., 36., 43., 52., 32., 58., 56., 52.,
+        67., 53., 72., 88., 77., 95., 94., 84., 86., 101., 107.,
+        108., 118., 96., 115., 138., 137.,
+    ])
+    xdata = np.arange(0, ydata.size) * 0.1
+
+    def exponential_wrapped(params):
+        A, B, x0 = params
+        return A * np.exp(B * (xdata - x0)) - ydata
+
+    x0 = [0.01, 1., 5.]
+    bounds = ((0.01, 0, 0), (np.inf, 10, 20.9))
+    res = least_squares(exponential_wrapped, x0, method='trf', bounds=bounds)
+    assert res.success