Merge pull request #16901 from tylerjereddy/treddy_191_backports

MAINT: 1.9.1 backports
scipy · Aug 26, 2022 · 987c698 · 987c698
2 parents 31ad726 + 8b97528
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diff --git a/doc/API.rst.txt b/doc/API.rst.txt
@@ -125,6 +125,8 @@ change is made.
 
 * `scipy.optimize`
 
+  - `scipy.optimize.cython_optimize`
+
 * `scipy.signal`
 
   - `scipy.signal.windows`

diff --git a/doc/release/1.9.1-notes.rst b/doc/release/1.9.1-notes.rst
@@ -5,15 +5,44 @@ SciPy 1.9.1 Release Notes
 .. contents::
 
 SciPy 1.9.1 is a bug-fix release with no new features
-compared to 1.9.0.
+compared to 1.9.0. Notably, some important meson build
+fixes are included.
 
 Authors
 =======
 
+* Anirudh Dagar (1)
+* Ralf Gommers (4)
+* Matt Haberland (2)
+* Tyler Reddy (10)
+* Atsushi Sakai (1)
+* Eli Schwartz (1)
+* Warren Weckesser (1)
+
+A total of 7 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 1.9.1
 -----------------------
 
+* `#14517 <https://github.com/scipy/scipy/issues/14517>`__: scipy/linalg/tests/test_decomp.py::TestSchur::test_sort test...
+* `#16765 <https://github.com/scipy/scipy/issues/16765>`__: DOC: \`scipy.stats.skew\` no longer returns 0 on constant input
+* `#16787 <https://github.com/scipy/scipy/issues/16787>`__: BUG: Can't build 1.10 with mingw-w64 toolchain and numpy 1.21.6...
+* `#16813 <https://github.com/scipy/scipy/issues/16813>`__: BUG: scipy.interpolate interp1d extrapolate behaviour change...
+* `#16878 <https://github.com/scipy/scipy/issues/16878>`__: BUG: optimize.milp fails to execute when given exactly 3 constraints
+
 
 Pull requests for 1.9.1
 -----------------------
+
+* `#16736 <https://github.com/scipy/scipy/pull/16736>`__: REL: prep for SciPy 1.9.1
+* `#16749 <https://github.com/scipy/scipy/pull/16749>`__: BLD: install missing \`.pxd\` files, and update TODOs/FIXMEs...
+* `#16750 <https://github.com/scipy/scipy/pull/16750>`__: BLD: make OpenBLAS detection work with CMake
+* `#16760 <https://github.com/scipy/scipy/pull/16760>`__: BLD: use a bit more idiomatic approach to constructing paths...
+* `#16768 <https://github.com/scipy/scipy/pull/16768>`__: DOC: stats.skew/kurtosis: returns NaN when input has only one...
+* `#16794 <https://github.com/scipy/scipy/pull/16794>`__: BLD/REL: on Windows use numpy 1.22.3 as the version to build...
+* `#16822 <https://github.com/scipy/scipy/pull/16822>`__: BUG/TST: linalg: Check the results of 'schur' more carefully.
+* `#16825 <https://github.com/scipy/scipy/pull/16825>`__: BUG: interpolate: fix "previous" and "next" extrapolate logic...
+* `#16862 <https://github.com/scipy/scipy/pull/16862>`__: BUG, DOC: Fix sphinx autosummary generation for \`odr\` and \`czt\`
+* `#16881 <https://github.com/scipy/scipy/pull/16881>`__: MAINT: optimize.milp: fix input validation when three constraints...
diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -261,6 +261,16 @@
 
 autosummary_generate = True
 
+# maps functions with a name same as a class name that is indistinguishable
+# Ex: scipy.signal.czt and scipy.signal.CZT or scipy.odr.odr and scipy.odr.ODR
+# Otherwise, the stubs are overwritten when the name is same for
+# OS (like MacOS) which has a filesystem that ignores the case
+# See https://github.com/sphinx-doc/sphinx/pull/7927
+autosummary_filename_map = {
+    "scipy.odr.odr": "odr-function",
+    "scipy.signal.czt": "czt-function",
+}
+
 
 # -----------------------------------------------------------------------------
 # Autodoc

diff --git a/environment.yml b/environment.yml
@@ -45,4 +45,4 @@ dependencies:
   - rich-click
   - click
   - doit>=0.36.0
-  - pydevtool==0.2.0
+  - pydevtool
diff --git a/meson.build b/meson.build
@@ -10,7 +10,7 @@ project(
   default_options: [
     'buildtype=debugoptimized',
     'c_std=c99',
-    'cpp_std=c++14',  # TODO: use c++11 if 14 is not available
+    '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',

diff --git a/pyproject.toml b/pyproject.toml
@@ -37,24 +37,32 @@ requires = [
     # loongarch64 requires numpy>=1.22.0
     "numpy==1.22.0; platform_machine=='loongarch64'",
 
+    # On Windows we need to avoid 1.21.6, 1.22.0 and 1.22.1 because they were
+    # built with vc142. 1.22.3 is the first version that has 32-bit Windows
+    # wheels *and* was built with vc141. So use that:
+    "numpy==1.22.3; python_version=='3.10' and platform_system=='Windows' and platform_python_implementation != 'PyPy'",
+
     # default numpy requirements
     "numpy==1.18.5; python_version=='3.8' and (platform_machine!='arm64' or platform_system!='Darwin') and platform_machine!='aarch64' and platform_machine!='loongarch64' and platform_python_implementation != 'PyPy'",
     "numpy==1.19.3; python_version=='3.9' and (platform_machine!='arm64' or platform_system!='Darwin') and platform_machine!='loongarch64' and platform_python_implementation != 'PyPy'",
     # Note that 1.21.3 was the first version with a complete set of 3.10 wheels,
-    # however macOS was broken and it's safe to build against 1.21.6 on all platforms
+    # however macOS was broken and it's safe C API/ABI-wise to build against 1.21.6
     # (see oldest-supported-numpy issues gh-28 and gh-45)
-    "numpy==1.21.6; python_version=='3.10' and platform_machine!='loongarch64' and platform_python_implementation != 'PyPy'",
+    "numpy==1.21.6; python_version=='3.10' and (platform_machine!='win32' and platform_machine!='loongarch64') and platform_python_implementation != 'PyPy'",
+    "numpy==1.23.2; python_version=='3.11' and platform_python_implementation != 'PyPy'",
 
     # 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>='3.11'",
+    "numpy; python_version>='3.12'",
     "numpy; python_version>='3.8' and platform_python_implementation=='PyPy'",
 ]
 
 [project]
 name = "SciPy"
+# TODO: add `license-files` once PEP 639 is accepted (see meson-python#88)
+#       at that point, no longer include them in `py3.install_sources()`
 license = {file = "LICENSE.txt"}
 description = "Fundamental algorithms for scientific computing in Python"
 maintainers = [

diff --git a/scipy/_lib/_uarray/meson.build b/scipy/_lib/_uarray/meson.build
@@ -1,8 +1,3 @@
-# TODO: add_data_files('license')
-
-# TODO: this used -std=c++14 if available, add c++11 otherwise
-#       can we now rely on c++14 unconditionally?
-
 py3.extension_module('_uarray',
   ['_uarray_dispatch.cxx', 'vectorcall.cxx'],
   cpp_args: ['-Wno-terminate', '-Wno-unused-function'],
@@ -15,6 +10,7 @@ py3.extension_module('_uarray',
 python_sources = [
   '__init__.py',
   '_backend.py',
+  'LICENSE'
 ]
 
 py3.install_sources(

diff --git a/scipy/fft/_pocketfft/meson.build b/scipy/fft/_pocketfft/meson.build
@@ -16,7 +16,6 @@ else
   pocketfft_threads += ['-DPOCKETFFT_NO_MULTITHREADING']
 endif
 
-#TODO: add the equivalent of set_cxx_flags_hook
 py3.extension_module('pypocketfft',
   'pypocketfft.cxx',
   cpp_args: pocketfft_threads,
@@ -32,6 +31,7 @@ python_sources = [
   '__init__.py',
   'basic.py',
   'helper.py',
+  'LICENSE.md',
   'realtransforms.py'
 ]
 

diff --git a/scipy/integrate/meson.build b/scipy/integrate/meson.build
@@ -190,8 +190,6 @@ py3.extension_module('_test_multivariate',
   subdir: 'scipy/integrate'
 )
 
-# FIXME: something is wrong with the signature file, subroutines are not used
-# _test_odeint_banded
 _test_odeint_banded_module = custom_target('_test_odeint_banded_module',
   output: ['_test_odeint_bandedmodule.c', '_test_odeint_banded-f2pywrappers.f'],
   input: 'tests/banded5x5.pyf',

diff --git a/scipy/interpolate/_interpolate.py b/scipy/interpolate/_interpolate.py
@@ -519,7 +519,8 @@ def __init__(self, x, y, kind='linear', axis=-1,
                 self._call = self.__class__._call_previousnext
                 if _do_extrapolate(fill_value):
                     self._check_and_update_bounds_error_for_extrapolation()
-                    fill_value = (np.nan, self.y.max(axis=axis))
+                    # assume y is sorted by x ascending order here.
+                    fill_value = (np.nan, np.take(self.y, -1, axis))
             elif kind == 'next':
                 self._side = 'right'
                 self._ind = 1
@@ -528,7 +529,8 @@ def __init__(self, x, y, kind='linear', axis=-1,
                 self._call = self.__class__._call_previousnext
                 if _do_extrapolate(fill_value):
                     self._check_and_update_bounds_error_for_extrapolation()
-                    fill_value = (self.y.min(axis=axis), np.nan)
+                    # assume y is sorted by x ascending order here.
+                    fill_value = (np.take(self.y, 0, axis), np.nan)
             else:
                 # Check if we can delegate to numpy.interp (2x-10x faster).
                 np_types = (np.float_, np.int_)

diff --git a/scipy/interpolate/tests/test_interpolate.py b/scipy/interpolate/tests/test_interpolate.py
@@ -122,6 +122,28 @@ def setup_method(self):
         self.y235 = np.arange(30.).reshape((2, 3, 5))
         self.y325 = np.arange(30.).reshape((3, 2, 5))
 
+        # Edge updated test matrix 1
+        # array([[ 30,   1,   2,   3,   4,   5,   6,   7,   8, -30],
+        #        [ 30,  11,  12,  13,  14,  15,  16,  17,  18, -30]])
+        self.y210_edge_updated = np.arange(20.).reshape((2, 10))
+        self.y210_edge_updated[:, 0] = 30
+        self.y210_edge_updated[:, -1] = -30
+
+        # Edge updated test matrix 2
+        # array([[ 30,  30],
+        #       [  2,   3],
+        #       [  4,   5],
+        #       [  6,   7],
+        #       [  8,   9],
+        #       [ 10,  11],
+        #       [ 12,  13],
+        #       [ 14,  15],
+        #       [ 16,  17],
+        #       [-30, -30]])
+        self.y102_edge_updated = np.arange(20.).reshape((10, 2))
+        self.y102_edge_updated[0, :] = 30
+        self.y102_edge_updated[-1, :] = -30
+
         self.fill_value = -100.0
 
     def test_validation(self):
@@ -386,6 +408,36 @@ def test_previous(self):
                     bounds_error=True)
         assert_raises(ValueError, interp1d, self.x10, self.y10, **opts)
 
+        # Tests for gh-16813
+        interpolator1D = interp1d([0, 1, 2],
+                                  [0, 1, -1], kind="previous",
+                                  fill_value='extrapolate',
+                                  assume_sorted=True)
+        assert_allclose(interpolator1D([-2, -1, 0, 1, 2, 3, 5]),
+                        [np.nan, np.nan, 0, 1, -1, -1, -1])
+
+        interpolator1D = interp1d([2, 0, 1],  # x is not ascending
+                                  [-1, 0, 1], kind="previous",
+                                  fill_value='extrapolate',
+                                  assume_sorted=False)
+        assert_allclose(interpolator1D([-2, -1, 0, 1, 2, 3, 5]),
+                        [np.nan, np.nan, 0, 1, -1, -1, -1])
+
+        interpolator2D = interp1d(self.x10, self.y210_edge_updated,
+                                  kind="previous",
+                                  fill_value='extrapolate')
+        assert_allclose(interpolator2D([-1, -2, 5, 8, 12, 25]),
+                        [[np.nan, np.nan, 5, 8, -30, -30],
+                         [np.nan, np.nan, 15, 18, -30, -30]])
+
+        interpolator2DAxis0 = interp1d(self.x10, self.y102_edge_updated,
+                                       kind="previous",
+                                       axis=0, fill_value='extrapolate')
+        assert_allclose(interpolator2DAxis0([-2, 5, 12]),
+                        [[np.nan, np.nan],
+                         [10, 11],
+                         [-30, -30]])
+
     def test_next(self):
         # Check the actual implementation of next interpolation.
         interp10 = interp1d(self.x10, self.y10, kind='next')
@@ -425,6 +477,36 @@ def test_next(self):
                     bounds_error=True)
         assert_raises(ValueError, interp1d, self.x10, self.y10, **opts)
 
+        # Tests for gh-16813
+        interpolator1D = interp1d([0, 1, 2],
+                                  [0, 1, -1], kind="next",
+                                  fill_value='extrapolate',
+                                  assume_sorted=True)
+        assert_allclose(interpolator1D([-2, -1, 0, 1, 2, 3, 5]),
+                        [0, 0, 0, 1, -1, np.nan, np.nan])
+
+        interpolator1D = interp1d([2, 0, 1],  # x is not ascending
+                                  [-1, 0, 1], kind="next",
+                                  fill_value='extrapolate',
+                                  assume_sorted=False)
+        assert_allclose(interpolator1D([-2, -1, 0, 1, 2, 3, 5]),
+                        [0, 0, 0, 1, -1, np.nan, np.nan])
+
+        interpolator2D = interp1d(self.x10, self.y210_edge_updated,
+                                  kind="next",
+                                  fill_value='extrapolate')
+        assert_allclose(interpolator2D([-1, -2, 5, 8, 12, 25]),
+                        [[30, 30, 5, 8, np.nan, np.nan],
+                         [30, 30, 15, 18, np.nan, np.nan]])
+
+        interpolator2DAxis0 = interp1d(self.x10, self.y102_edge_updated,
+                                       kind="next",
+                                       axis=0, fill_value='extrapolate')
+        assert_allclose(interpolator2DAxis0([-2, 5, 12]),
+                        [[30, 30],
+                         [10, 11],
+                         [np.nan, np.nan]])
+
     def test_zero(self):
         # Check the actual implementation of zero-order spline interpolation.
         interp10 = interp1d(self.x10, self.y10, kind='zero')

diff --git a/scipy/linalg/meson.build b/scipy/linalg/meson.build
@@ -25,10 +25,10 @@ cython_linalg = custom_target('cython_linalg',
   ],
   input: '_generate_pyx.py',
   command: [py3, '@INPUT@', '-o', '@OUTDIR@'],
-  # FIXME - we only want to install the .pxd files! See comments for
-  #         `pxd_files` further down.
+  # TODO - we only want to install the .pxd files! See comments for
+  #        `pxd_files` further down.
   install: true,
-  install_dir: py3.get_install_dir() + 'scipy/linalg'
+  install_dir: py3.get_install_dir() / 'scipy/linalg'
 )
 
 # pyx -> c, pyx -> cpp generators, depending on __init__.py here.
@@ -166,7 +166,6 @@ py3.extension_module('_interpolative',
     '-Wno-tabs', '-Wno-conversion', '-Wno-argument-mismatch',
     '-Wno-unused-dummy-argument', '-Wno-maybe-uninitialized'
   ],
-  # TODO: add -fallow-argument-mismatch for gfortran >= 10, see gh-11842
   include_directories: [inc_np, inc_f2py],
   dependencies: [py3_dep, lapack],
   install: true,
@@ -332,7 +331,7 @@ py3.install_sources(
 #       https://mesonbuild.com/Installing.html says is for build targets to
 #       use:
 #         `custom_target(..., install: true, install_dir: ...)
-#         # should use `py3.get_install_dir() + 'scipy/linalg'` ?
+#         # should use `py3.get_install_dir() / 'scipy/linalg'` ?
 #       see https://github.com/mesonbuild/meson/issues/3206
 #
 #       For the below code to work, the script generating the files should use
@@ -350,7 +349,7 @@ py3.install_sources(
 #  output : ['cython_blas2.pxd', 'cython_lapack2.pxd'],
 #  command : ['cp', '@INPUT0@', '@OUTPUT0@', '&&', 'cp', '@INPUT1@', '@OUTPUT1@'],
 #  install : true,
-#  install_dir: py3.get_install_dir() + 'scipy/linalg'
+#  install_dir: py3.get_install_dir() / 'scipy/linalg'
 #)
 
 subdir('tests')