Merge remote-tracking branch 'upstream/RELEASE_next_patch' into RELEA…

…SE_next_minor

# Conflicts:
#	.github/workflows/release.yml

.github/workflows/release.yml

@@ -18,15 +18,10 @@ jobs:
       upload_url: ${{ steps.create_release.outputs.upload_url }}
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3.3.0
+        uses: actions/checkout@v3
       - name: Create Release
         id: create_release
         uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions
-        with:
-          draft: false
-          prerelease: false
 
   build_wheels:
     name: Wheels on ${{ matrix.os }}/py${{ matrix.python-version }}
@@ -39,7 +34,7 @@ jobs:
         python-version: ['3.7', '3.8', '3.9', '3.10']
 
     steps:
-      - uses: actions/checkout@v3.3.0
+      - uses: actions/checkout@v3
 
       - uses: actions/setup-python@v4
         name: Install Python
@@ -92,16 +87,12 @@ jobs:
     needs: create_release
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3.3.0
+      - uses: actions/checkout@v3
 
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
-
-      - name: install twine
-        run: |
-          python -m pip install twine
+          python-version: '3.10'
 
       - name: Build source distribution
         run: |
@@ -134,13 +125,10 @@ jobs:
 
       - name: Publish wheels to PyPI
         if: github.repository_owner == 'hyperspy'
-        env:
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
           # Github secret set in the hyperspy/hyperspy repository
           # Not available from fork or pull request
           # Secrets are not passed to workflows that are triggered by a pull request from a fork
-          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-        run: |
-          twine upload dist/*-manylinux*.whl --verbose 
-          twine upload dist/*.tar.gz --verbose 
+          password: ${{ secrets.PYPI_API_TOKEN }}
 

hyperspy/signal.py

@@ -4890,14 +4890,14 @@ def map(
             # inspect.
             _logger.warning(error)
 
+        # If the function has an `axes` or `axis` argument
+        # we suppose that it can operate on the full array and we don't
+        # iterate over the coordinates.
         if not ndkwargs and not lazy_output and (self.axes_manager.signal_dimension == 1 and
                              "axis" in fargs):
             kwargs['axis'] = self.axes_manager.signal_axes[-1].index_in_array
 
             result = self._map_all(function, inplace=inplace, **kwargs)
-        # If the function has an axes argument
-        # we suppose that it can operate on the full array and we don't
-        # iterate over the coordinates.
         elif not ndkwargs and not lazy_output and "axes" in fargs and not parallel:
             kwargs['axes'] = tuple([axis.index_in_array for axis in
                                     self.axes_manager.signal_axes])

hyperspy/tests/misc/test_utils.py

@@ -36,7 +36,7 @@
     to_numpy,
     get_array_module
 )
-from hyperspy.exceptions import VisibleDeprecationWarning, LazyCupyConversion
+from hyperspy.exceptions import VisibleDeprecationWarning
 
 try:
     import cupy as cp

hyperspy/tests/signals/test_hologram_image.py

@@ -21,7 +21,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import pytest
-from scipy.interpolate import interp2d
+from scipy.interpolate import RectBivariateSpline
 
 import hyperspy.api as hs
 from hyperspy.decorators import lazifyTestClass
@@ -192,16 +192,16 @@ def test_reconstruct_phase_nonstandard(lazy):
     # interpolate reconstructed phase to compare with the input (reference
     # phase):
     interp_x = np.arange(output_shape[0])
-    phase_interp0 = interp2d(
-        interp_x, interp_x, wave_image2.inav[0].unwrapped_phase().data, kind="cubic",
+    phase_interp0 = RectBivariateSpline(
+        interp_x, interp_x, wave_image2.inav[0].unwrapped_phase().data,
     )
     phase_new0 = phase_interp0(
         np.linspace(0, output_shape[0], img_size),
         np.linspace(0, output_shape[0], img_size),
     )
 
-    phase_interp1 = interp2d(
-        interp_x, interp_x, wave_image2.inav[1].unwrapped_phase().data, kind="cubic",
+    phase_interp1 = RectBivariateSpline(
+        interp_x, interp_x, wave_image2.inav[1].unwrapped_phase().data,
     )
     phase_new1 = phase_interp1(
         np.linspace(0, output_shape[0], img_size),

hyperspy/tests/signals/test_map_method.py

@@ -50,7 +50,9 @@ def test_constant_sigma(self, parallel):
               [14.15585247, 14.7337787, 15.31170493]]]))
 
     @pytest.mark.parametrize('parallel', [True, False])
-    def test_constant_sigma_navdim0(self, parallel):
+    def test_constant_sigma_signal_navdim0(self, parallel):
+        # navigation dimension of signal is 0
+        # sigma is constant
         s = self.im.inav[0]
         s.map(gaussian_filter, sigma=1, parallel=parallel, ragged=self.ragged, inplace= not self.ragged)
         np.testing.assert_allclose(s.data, np.array(
@@ -62,25 +64,32 @@ def test_constant_sigma_navdim0(self, parallel):
     def test_variable_sigma(self, parallel):
         s = self.im
 
-        sigmas = np.array([0, 1])
+        sigmas = hs.signals.BaseSignal(np.array([0, 1])).T
+        s.map(gaussian_filter, sigma=sigmas, parallel=parallel, ragged=self.ragged)
 
-        s.map(gaussian_filter,
-              sigma=sigmas, parallel=parallel, ragged=self.ragged)
-        np.testing.assert_allclose(s.data, np.array(
-            [[[0.42207377, 1., 1.57792623],
-              [3.42207377, 4., 4.57792623],
-              [6.42207377, 7., 7.57792623]],
-
-             [[9.42207377, 10., 10.57792623],
-              [12.42207377, 13., 13.57792623],
-              [15.42207377, 16., 16.57792623]]]))
+        # For inav[0], sigma is 0, data unchanged
+        np.testing.assert_allclose(s.inav[0].data, np.arange(9).reshape((3, 3)))
+        # For inav[1], sigma is 1
+        np.testing.assert_allclose(s.inav[1].data, np.array(
+            [[10.68829507, 11.2662213 , 11.84414753],
+             [12.42207377, 13.        , 13.57792623],
+             [14.15585247, 14.7337787 , 15.31170493]]))
 
     @pytest.mark.parametrize('parallel', [True, False])
     def test_variable_sigma_navdim0(self, parallel):
+        # navigation dimension of signal is 1, length 2
+        # navigation dimension of sigmas is 1, length 1
+        # raise ValueError because of navigation dimension mismatch
         s = self.im
 
-        sigma = 1
-        s.map(gaussian_filter, sigma=sigma, parallel=parallel,
+        sigmas = hs.signals.BaseSignal(np.array([[0], ])).T
+        with pytest.raises(ValueError):
+            s.map(gaussian_filter, sigma=sigmas, parallel=parallel,
+                  ragged=self.ragged)
+
+        # sigmas is a number
+        sigmas = 1
+        s.map(gaussian_filter, sigma=sigmas, parallel=parallel,
               ragged=self.ragged)
         np.testing.assert_allclose(s.data, np.array(
             [[[1.68829507, 2.2662213, 2.84414753],

upcoming_changes/3117.maintenance.rst

@@ -0,0 +1 @@
+Simplify release workflow and replace deprecated ``actions/create-release`` action with ``softprops/action-gh-release``.

upcoming_changes/3124.bugfix.rst

@@ -0,0 +1 @@
+Fix test with scipy1.11 and update deprecated ``scipy.interpolate.interp2d`` in the test suite