Merge pull request #13279 from tylerjereddy/treddy_160rc2_backports

MAINT: 1.6.0 rc2 backports
scipy · Dec 22, 2020 · 939ecfc · 939ecfc
2 parents 2e4c610 + 550f87e
commit 939ecfc
Show file tree

Hide file tree

Showing 13 changed files with 227 additions and 109 deletions.
diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
@@ -19,6 +19,7 @@ jobs:
       - uses: actions/checkout@v2
       - name: Configuring Test Environment
         run: |
+          sudo apt-get update
           sudo apt install python3.7-dbg python3.7-dev libatlas-base-dev liblapack-dev gfortran libgmp-dev libmpfr-dev libsuitesparse-dev ccache swig libmpc-dev
           free -m
           python3.7-dbg --version # just to check

diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
@@ -29,65 +29,53 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Setup openblas
+    - name: Setup gfortran
       run: |
-        # this setup is originally taken from the .travis.yml
-
-        # virtualenv needed for the multibuild steps
-        pip install virtualenv
-        brew install libmpc gcc@6 suitesparse swig
-        # The openblas binary used here was built using a gfortran older than 7,
-        # so it needs the older abi libgfortran.
-        export FC=gfortran-6
-        export CC=gcc-6
-        export CXX=g++-6
-        mkdir gcc_aliases
-        pushd gcc_aliases
-        ln -s `which gcc-6` gcc
-        ln -s `which g++-6` g++
-        ln -s `which gfortran-6` gfortran
-        # make gcc aliases in current dir
-        export PATH=$PWD/gcc_aliases:$PATH
-        popd
-        touch config.sh
-        git clone --depth=1 https://github.com/matthew-brett/multibuild.git
+        # this is taken verbatim from the numpy azure pipeline setup.
+        set -xe
+        # same version of gfortran as the open-libs and numpy-wheel builds
+        curl -L https://github.com/MacPython/gfortran-install/raw/master/archives/gfortran-4.9.0-Mavericks.dmg -o gfortran.dmg
+        GFORTRAN_SHA256=$(shasum -a 256 gfortran.dmg)
+        KNOWN_SHA256="d2d5ca5ba8332d63bbe23a07201c4a0a5d7e09ee56f0298a96775f928c3c4b30  gfortran.dmg"
+        if [ "$GFORTRAN_SHA256" != "$KNOWN_SHA256" ]; then
+            echo sha256 mismatch
+            exit 1
+        fi
+        hdiutil attach -mountpoint /Volumes/gfortran gfortran.dmg
+        sudo installer -pkg /Volumes/gfortran/gfortran.pkg -target /
+        otool -L /usr/local/gfortran/lib/libgfortran.3.dylib
+        # Manually symlink gfortran-4.9 to plain gfortran for f2py.
+        # No longer needed after Feb 13 2020 as gfortran is already present
+        # and the attempted link errors. Keep this for future reference.
+        # ln -s /usr/local/bin/gfortran-4.9 /usr/local/bin/gfortran
 
-        # designed for travis, but probably work on github actions
-        source multibuild/common_utils.sh
-        source multibuild/travis_steps.sh
-        before_install
-        export CFLAGS="-arch x86_64"
-        export CXXFLAGS="-arch x86_64"
-        printenv
+    - name: Setup openblas
+      run: |
+        # this is taken verbatim from the numpy azure pipeline setup.
+        set -xe
+        target=$(python tools/openblas_support.py)
+        ls -lR $target
+        # manually link to appropriate system paths
+        cp $target/lib/lib* /usr/local/lib/
+        cp $target/include/* /usr/local/include/
 
-        # Grab openblas
-        OPENBLAS_PATH=$(python tools/openblas_support.py)
-        # Copy it to the working directory
-        mv $OPENBLAS_PATH ./
+        # otool -L /usr/local/lib/libopenblas*
 
-        # Modify the openblas dylib so it can be used in its current location
-        # Also make it use the current install location for libgfortran, libquadmath, and libgcc_s.
-        pushd openblas/lib
-        install_name_tool -id $PWD/libopenblasp-r*.dylib libopenblas.dylib
-        install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib /usr/local/Cellar/gcc@6/6.5.0_5/lib/gcc/6/libgfortran.3.dylib libopenblas.dylib
-        install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib /usr/local/Cellar/gcc@6/6.5.0_5/lib/gcc/6/libquadmath.0.dylib libopenblas.dylib
-        install_name_tool -change /usr/local/gfortran/lib/libgcc_s.1.dylib /usr/local/Cellar/gcc@6/6.5.0_5/lib/gcc/6/libgcc_s.1.dylib libopenblas.dylib
-        popd
         echo "[openblas]" > site.cfg
         echo "libraries = openblas" >> site.cfg
-        echo "library_dirs = $PWD/openblas/lib" >> site.cfg
-        echo "include_dirs = $PWD/openblas/include" >> site.cfg
-        echo "runtime_library_dirs = $PWD/openblas/lib" >> site.cfg
-        # remove a spurious gcc/gfortran toolchain install
-        rm -rf /usr/local/Cellar/gcc/9.2.0_2
-        #
-        export PATH="$PATH:$PWD/openblas"
+        echo "library_dirs = /usr/local/lib" >> site.cfg
+        echo "include_dirs = /usr/local/include" >> site.cfg
+        echo "runtime_library_dirs = /usr/local/lib" >> site.cfg
+
+    - name: A few other packages
+      run: |
+        brew install libmpc suitesparse swig
+
     - name: Install packages
       run: |
         pip install ${{ matrix.numpy-version }}
         pip install setuptools wheel cython pytest pytest-xdist pybind11 pytest-xdist mpmath gmpy2
 
     - name: Test SciPy
       run: |
-        export DYLD_LIBRARY_PATH=/usr/local/Cellar/gcc@6/6.5.0_5/lib/gcc/6/:$DYLD_LIBRARY_PATH
         python -u runtests.py
diff --git a/doc/release/1.6.0-notes.rst b/doc/release/1.6.0-notes.rst
@@ -402,6 +402,7 @@ Authors
 * Sambit Panda
 * Dima Pasechnik
 * Tirth Patel +
+* Matti Picus
 * Paweł Redzyński +
 * Vladimir Philipenko +
 * Philipp Thölke +
@@ -449,7 +450,7 @@ Authors
 * ZhihuiChen0903 +
 * Jacob Zhong +
 
-A total of 121 people contributed to this release.
+A total of 122 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.
 
@@ -589,6 +590,8 @@ Issues closed for 1.6.0
 * `#13182 <https://github.com/scipy/scipy/issues/13182>`__: Key appears twice in \`test_optimize.test_show_options\`
 * `#13191 <https://github.com/scipy/scipy/issues/13191>`__: \`scipy.linalg.lapack.dgesjv\` overwrites original arrays if...
 * `#13207 <https://github.com/scipy/scipy/issues/13207>`__: TST: Erratic test failure in test_cossin_separate
+* `#13221 <https://github.com/scipy/scipy/issues/13221>`__: BUG: pavement.py glitch
+* `#13248 <https://github.com/scipy/scipy/issues/13248>`__: ndimage: improper cval handling for complex-valued inputs
 
 Pull requests for 1.6.0
 -----------------------
@@ -927,6 +930,13 @@ Pull requests for 1.6.0
 * `#13190 <https://github.com/scipy/scipy/pull/13190>`__: BUG: optimize: fix a duplicate key bug for \`test_show_options\`
 * `#13192 <https://github.com/scipy/scipy/pull/13192>`__: BUG:linalg: Add overwrite option to gejsv wrapper
 * `#13194 <https://github.com/scipy/scipy/pull/13194>`__: BUG: slsqp should be able to use rel_step
+* `#13199 <https://github.com/scipy/scipy/pull/13199>`__: [skip travis] DOC: 1.6.0 release notes
 * `#13203 <https://github.com/scipy/scipy/pull/13203>`__: fix typos
 * `#13209 <https://github.com/scipy/scipy/pull/13209>`__: TST:linalg: set the seed for cossin test
 * `#13212 <https://github.com/scipy/scipy/pull/13212>`__: [DOC] Backtick and directive consistency.
+* `#13217 <https://github.com/scipy/scipy/pull/13217>`__: REL: add necessary setuptools and numpy version pins in pyproject.toml...
+* `#13226 <https://github.com/scipy/scipy/pull/13226>`__: BUG: pavement.py file handle fixes
+* `#13249 <https://github.com/scipy/scipy/pull/13249>`__: Handle cval correctly for ndimage functions with complex-valued...
+* `#13253 <https://github.com/scipy/scipy/pull/13253>`__: BUG,MAINT: Ensure all Pool objects are closed
+* `#13260 <https://github.com/scipy/scipy/pull/13260>`__: CI: fix macOS testing
+* `#13269 <https://github.com/scipy/scipy/pull/13269>`__: CI: github actions: In the linux dbg tests, update apt before...
diff --git a/pavement.py b/pavement.py
@@ -209,7 +209,7 @@ def compute_md5(idirs):
     for fn in sorted(released):
         with open(fn, 'rb') as f:
             m = md5(f.read())
-        checksums.append('%s  %s' % (m.hexdigest(), os.path.basename(f)))
+        checksums.append('%s  %s' % (m.hexdigest(), os.path.basename(fn)))
 
     return checksums
 
@@ -221,7 +221,7 @@ def compute_sha256(idirs):
     for fn in sorted(released):
         with open(fn, 'rb') as f:
             m = sha256(f.read())
-        checksums.append('%s  %s' % (m.hexdigest(), os.path.basename(f)))
+        checksums.append('%s  %s' % (m.hexdigest(), os.path.basename(fn)))
 
     return checksums
 

diff --git a/scipy/_lib/tests/test__util.py b/scipy/_lib/tests/test__util.py
@@ -124,8 +124,7 @@ def test_mapwrapper_parallel():
     assert_(excinfo.type is ValueError)
 
     # can also set a PoolWrapper up with a map-like callable instance
-    try:
-        p = Pool(2)
+    with Pool(2) as p:
         q = MapWrapper(p.map)
 
         assert_(q._own_pool is False)
@@ -135,8 +134,6 @@ def test_mapwrapper_parallel():
         # because it didn't create it
         out = p.map(np.sin, in_arg)
         assert_equal(list(out), out_arg)
-    finally:
-        p.close()
 
 
 # get our custom ones and a few from the "import *" cases

diff --git a/scipy/integrate/_quad_vec.py b/scipy/integrate/_quad_vec.py
@@ -267,7 +267,6 @@ def quad_vec(f, a, b, epsabs=1e-200, epsrel=1e-8, norm='2', cache_size=100e6, li
     else:
         norm_func = norm_funcs[norm]
 
-    mapwrapper = MapWrapper(workers)
 
     parallel_count = 128
     min_intervals = 2
@@ -341,7 +340,7 @@ def quad_vec(f, a, b, epsabs=1e-200, epsrel=1e-8, norm='2', cache_size=100e6, li
     }
 
     # Process intervals
-    with mapwrapper:
+    with MapWrapper(workers) as mapwrapper:
         ier = NOT_CONVERGED
 
         while intervals and len(intervals) < limit:

diff --git a/scipy/ndimage/filters.py b/scipy/ndimage/filters.py
@@ -51,23 +51,32 @@ def _invalid_origin(origin, lenw):
     return (origin < -(lenw // 2)) or (origin > (lenw - 1) // 2)
 
 
-def _complex_via_real_components(func, input, weights, output, **kwargs):
+def _complex_via_real_components(func, input, weights, output, cval, **kwargs):
     """Complex convolution via a linear combination of real convolutions."""
     complex_input = input.dtype.kind == 'c'
     complex_weights = weights.dtype.kind == 'c'
     if complex_input and complex_weights:
         # real component of the output
-        func(input.real, weights.real, output=output.real, **kwargs)
-        output.real -= func(input.imag, weights.imag, output=None, **kwargs)
+        func(input.real, weights.real, output=output.real,
+             cval=numpy.real(cval), **kwargs)
+        output.real -= func(input.imag, weights.imag, output=None,
+                            cval=numpy.imag(cval), **kwargs)
         # imaginary component of the output
-        func(input.real, weights.imag, output=output.imag, **kwargs)
-        output.imag += func(input.imag, weights.real, output=None, **kwargs)
+        func(input.real, weights.imag, output=output.imag,
+             cval=numpy.real(cval), **kwargs)
+        output.imag += func(input.imag, weights.real, output=None,
+                            cval=numpy.imag(cval), **kwargs)
     elif complex_input:
-        func(input.real, weights, output=output.real, **kwargs)
-        func(input.imag, weights, output=output.imag, **kwargs)
+        func(input.real, weights, output=output.real, cval=numpy.real(cval),
+             **kwargs)
+        func(input.imag, weights, output=output.imag, cval=numpy.imag(cval),
+             **kwargs)
     else:
-        func(input, weights.real, output=output.real, **kwargs)
-        func(input, weights.imag, output=output.imag, **kwargs)
+        if numpy.iscomplexobj(cval):
+            raise ValueError("Cannot provide a complex-valued cval when the "
+                             "input is real.")
+        func(input, weights.real, output=output.real, cval=cval, **kwargs)
+        func(input, weights.imag, output=output.imag, cval=cval, **kwargs)
     return output
 
 
@@ -104,10 +113,10 @@ def correlate1d(input, weights, axis=-1, output=None, mode="reflect",
         if complex_weights:
             weights = weights.conj()
             weights = weights.astype(numpy.complex128, copy=False)
-        kwargs = dict(axis=axis, mode=mode, cval=cval, origin=origin)
+        kwargs = dict(axis=axis, mode=mode, origin=origin)
         output = _ni_support._get_output(output, input, complex_output=True)
         return _complex_via_real_components(correlate1d, input, weights,
-                                            output, **kwargs)
+                                            output, cval, **kwargs)
 
     output = _ni_support._get_output(output, input)
     weights = numpy.asarray(weights, dtype=numpy.float64)
@@ -638,12 +647,12 @@ def _correlate_or_convolve(input, weights, output, mode, cval, origin,
             # As for numpy.correlate, conjugate weights rather than input.
             weights = weights.conj()
         kwargs = dict(
-            mode=mode, cval=cval, origin=origin, convolution=convolution
+            mode=mode, origin=origin, convolution=convolution
         )
         output = _ni_support._get_output(output, input, complex_output=True)
 
         return _complex_via_real_components(_correlate_or_convolve, input,
-                                            weights, output, **kwargs)
+                                            weights, output, cval, **kwargs)
 
     origins = _ni_support._normalize_sequence(origin, input.ndim)
     weights = numpy.asarray(weights, dtype=numpy.float64)
@@ -889,9 +898,9 @@ def uniform_filter1d(input, size, axis=-1, output=None,
                                    origin)
     else:
         _nd_image.uniform_filter1d(input.real, size, axis, output.real, mode,
-                                   cval, origin)
+                                   numpy.real(cval), origin)
         _nd_image.uniform_filter1d(input.imag, size, axis, output.imag, mode,
-                                   cval, origin)
+                                   numpy.imag(cval), origin)
     return output
 
 

diff --git a/scipy/ndimage/interpolation.py b/scipy/ndimage/interpolation.py
@@ -329,12 +329,14 @@ def geometric_transform(input, mapping, output_shape=None,
     output = _ni_support._get_output(output, input, shape=output_shape,
                                      complex_output=complex_output)
     if complex_output:
-        kwargs = dict(order=order, mode=mode, cval=cval, prefilter=prefilter,
+        kwargs = dict(order=order, mode=mode, prefilter=prefilter,
                       output_shape=output_shape,
                       extra_arguments=extra_arguments,
                       extra_keywords=extra_keywords)
-        geometric_transform(input.real, mapping, output=output.real, **kwargs)
-        geometric_transform(input.imag, mapping, output=output.imag, **kwargs)
+        geometric_transform(input.real, mapping, output=output.real,
+                            cval=numpy.real(cval), **kwargs)
+        geometric_transform(input.imag, mapping, output=output.imag,
+                            cval=numpy.imag(cval), **kwargs)
         return output
 
     if prefilter and order > 1:
@@ -437,9 +439,11 @@ def map_coordinates(input, coordinates, output=None, order=3,
     output = _ni_support._get_output(output, input, shape=output_shape,
                                      complex_output=complex_output)
     if complex_output:
-        kwargs = dict(order=order, mode=mode, cval=cval, prefilter=prefilter)
-        map_coordinates(input.real, coordinates, output=output.real, **kwargs)
-        map_coordinates(input.imag, coordinates, output=output.imag, **kwargs)
+        kwargs = dict(order=order, mode=mode, prefilter=prefilter)
+        map_coordinates(input.real, coordinates, output=output.real,
+                        cval=numpy.real(cval), **kwargs)
+        map_coordinates(input.imag, coordinates, output=output.imag,
+                        cval=numpy.imag(cval), **kwargs)
         return output
     if prefilter and order > 1:
         padded, npad = _prepad_for_spline_filter(input, mode, cval)
@@ -551,9 +555,11 @@ def affine_transform(input, matrix, offset=0.0, output_shape=None,
                                      complex_output=complex_output)
     if complex_output:
         kwargs = dict(offset=offset, output_shape=output_shape, order=order,
-                      mode=mode, cval=cval, prefilter=prefilter)
-        affine_transform(input.real, matrix, output=output.real, **kwargs)
-        affine_transform(input.imag, matrix, output=output.imag, **kwargs)
+                      mode=mode, prefilter=prefilter)
+        affine_transform(input.real, matrix, output=output.real,
+                         cval=numpy.real(cval), **kwargs)
+        affine_transform(input.imag, matrix, output=output.imag,
+                         cval=numpy.imag(cval), **kwargs)
         return output
     if prefilter and order > 1:
         padded, npad = _prepad_for_spline_filter(input, mode, cval)
@@ -655,9 +661,11 @@ def shift(input, shift, output=None, order=3, mode='constant', cval=0.0,
         # import under different name to avoid confusion with shift parameter
         from scipy.ndimage.interpolation import shift as _shift
 
-        kwargs = dict(order=order, mode=mode, cval=cval, prefilter=prefilter)
-        _shift(input.real, shift, output=output.real, **kwargs)
-        _shift(input.imag, shift, output=output.imag, **kwargs)
+        kwargs = dict(order=order, mode=mode, prefilter=prefilter)
+        _shift(input.real, shift, output=output.real, cval=numpy.real(cval),
+               **kwargs)
+        _shift(input.imag, shift, output=output.imag, cval=numpy.imag(cval),
+               **kwargs)
         return output
     if prefilter and order > 1:
         padded, npad = _prepad_for_spline_filter(input, mode, cval)
@@ -763,9 +771,11 @@ def zoom(input, zoom, output=None, order=3, mode='constant', cval=0.0,
         # import under different name to avoid confusion with zoom parameter
         from scipy.ndimage.interpolation import zoom as _zoom
 
-        kwargs = dict(order=order, mode=mode, cval=cval, prefilter=prefilter)
-        _zoom(input.real, zoom, output=output.real, **kwargs)
-        _zoom(input.imag, zoom, output=output.imag, **kwargs)
+        kwargs = dict(order=order, mode=mode, prefilter=prefilter)
+        _zoom(input.real, zoom, output=output.real, cval=numpy.real(cval),
+              **kwargs)
+        _zoom(input.imag, zoom, output=output.imag, cval=numpy.imag(cval),
+              **kwargs)
         return output
     if prefilter and order > 1:
         padded, npad = _prepad_for_spline_filter(input, mode, cval)

diff --git a/scipy/ndimage/src/ni_support.c b/scipy/ndimage/src/ni_support.c
@@ -310,6 +310,7 @@ int NI_ExtendLine(double *buffer, npy_intp line_length,
             break;
         /* kkkkkkkk|abcd]kkkkkkkk */
         case NI_EXTEND_CONSTANT:
+        case NI_EXTEND_GRID_CONSTANT:
             val = extend_value;
             dst = buffer;
             while (size_before--) {
@@ -670,6 +671,7 @@ int NI_InitFilterOffsets(PyArrayObject *array, npy_bool *footprint,
                         }
                         break;
                     case NI_EXTEND_CONSTANT:
+                    case NI_EXTEND_GRID_CONSTANT:
                         if (cc < 0 || cc >= len)
                             cc = *border_flag_value;
                         break;