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

…SE_next_minor

.github/workflows/tests_extension.yml

@@ -10,7 +10,7 @@ on:
 
 jobs:
   integration_test:
-    if: ${{ contains(github.event.pull_request.labels.*.name, 'run-extension-tests') }}
+    if: ${{ contains(github.event.pull_request.labels.*.name, 'run-extension-tests') || github.event_name == 'workflow_dispatch' }}
     name: Extension_${{ matrix.EXTENSION_VERSION }}
     runs-on: ubuntu-latest
     strategy:
@@ -63,10 +63,17 @@ jobs:
           pip install https://github.com/pyxem/pyxem/archive/master.zip
           pip install https://gitlab.com/atomap/atomap/-/archive/master/atomap-master.zip
 
+      - name: Install xvfb
+        run: |
+          # required for running kikuchipy test suite
+          sudo apt-get install xvfb
+
       - name: Run Kikuchipy Test Suite
         if: ${{ always() }}
         run: |
-          python -m pytest --pyargs kikuchipy
+          # Virtual buffer (xvfb) required for tests using PyVista
+          sudo apt-get install xvfb
+          xvfb-run python -m pytest --pyargs kikuchipy
 
       - name: Run LumiSpy Test Suite
         if: ${{ always() }}

azure-pipelines.yml

@@ -69,6 +69,11 @@ steps:
     conda list
   displayName: Install package
 
+- bash: |
+    source activate $ENV_NAME
+    conda clean --all -y
+  displayName: Clean conda cache
+
 # Note we must use `-n 2` argument for pytest-xdist due to
 # https://github.com/pytest-dev/pytest-xdist/issues/9.
 - bash: |
@@ -88,4 +93,3 @@ steps:
 #     # Set the token generated with github from the developer settings/personal
 #     # access tokens menu in azure pipeline
 #     github_token_name: ''
-

hyperspy/_signals/hologram_image.py

@@ -238,9 +238,6 @@ def estimate_sideband_position(
             max_workers=max_workers,
             ragged=False)
 
-        # Workaround to a map disfunctionality:
-        sb_position.set_signal_type('signal1d')
-
         return sb_position
 
     estimate_sideband_position.__doc__ %= (SHOW_PROGRESSBAR_ARG, PARALLEL_ARG, MAX_WORKERS_ARG)

hyperspy/signal.py

@@ -4994,7 +4994,9 @@ def _map_iterate(
             testing_kwargs = {}
             for ikey, key in enumerate(arg_keys):
                 test_ind = (0,) * len(os_am.navigation_axes)
-                testing_kwargs[key] = np.squeeze(args[ikey][test_ind]).compute()
+                # For discussion on if squeeze is necessary, see
+                # https://github.com/hyperspy/hyperspy/pull/2981
+                testing_kwargs[key] = np.squeeze(args[ikey][test_ind].compute())[()]
             testing_kwargs = {**kwargs, **testing_kwargs}
             test_data = np.array(
                 old_sig.inav[(0,) * len(os_am.navigation_shape)].data.compute()

hyperspy/signal_tools.py

@@ -184,11 +184,11 @@ def _length_changed(self, old, new):
 
     def apply(self):
         if self.new_length is t.Undefined:
-            _logger.warn("Input a new length before pressing apply.")
+            _logger.warning("Input a new length before pressing apply.")
             return
         x0, y0, x1, y1 = self.x0, self.y0, self.x1, self.y1
         if np.isnan(x0) or np.isnan(y0) or np.isnan(x1) or np.isnan(y1):
-            _logger.warn("Line position is not valid")
+            _logger.warning("Line position is not valid")
             return
         self.signal._calibrate(
             x0=x0, y0=y0, x1=x1, y1=y1, new_length=self.new_length, units=self.units
@@ -208,7 +208,7 @@ def __init__(self, signal):
         # Plot the signal (or model) if it is not already plotted
         if signal._plot is None or not signal._plot.is_active:
             signal.plot()
-        
+
         from hyperspy.model import BaseModel
         if isinstance(signal, BaseModel):
             signal = signal.signal
@@ -257,7 +257,7 @@ def span_selector_changed(self, *args, **kwargs):
             return
 
         x0, x1 = sorted(self.span_selector.extents)
-        
+
         # typically during initialisation
         if x0 == x1:
             return
@@ -267,7 +267,7 @@ def span_selector_changed(self, *args, **kwargs):
             x0 = self.axis.low_value
         if x1 > self.axis.high_value or x1 < self.axis.low_value:
             x1 = self.axis.high_value
-        
+
         if np.diff(self.axis.value2index(np.array([x0, x1]))) == 0:
             return
 
@@ -1180,7 +1180,7 @@ def update_histogram(self, clear_selector=True):
         if self.auto and self._is_selector_visible and clear_selector:
             # in auto mode, the displayed contrast cover the full range
             # and we need to reset the span selector
-            # no need to clear the line, it will updated 
+            # no need to clear the line, it will updated
             self.span_selector.clear()
 
         self.update_line()

hyperspy/tests/misc/test_date_time_tools.py

@@ -103,7 +103,9 @@ def test_update_date_time_in_metadata():
     assert_deep_almost_equal(md12.General.time, md1.General.time)
     import locale
     if locale.getlocale()[0] in ['en_GB', 'en_US']:
-        assert md12.General.time_zone in ('UTC', 'Coordinated Universal Time')
+        assert md12.General.time_zone in (
+            'UTC', 'Coordinated Universal Time', 'Co-ordinated Universal Time',
+            )
 
     md13 = dtt.update_date_time_in_metadata(iso2, md.deepcopy())
     assert_deep_almost_equal(md13.General.date, md2.General.date)

hyperspy/tests/signals/test_map_method.py

@@ -466,6 +466,7 @@ def test_not_lazy_input_lazy_output_inplace(self):
 
 
 class TestOutputDtype:
+
     @pytest.mark.parametrize("dtype", [np.uint16, np.uint32, np.uint64, np.int32, np.float32])
     def test_output_dtype_specified_not_inplace(self, dtype):
         def a_function_dtype(data):
@@ -496,8 +497,6 @@ def a_function_dtype(data, dtype_to_function):
         s_out.compute()
         assert s_out.data.dtype == dtype
 
-
-class TestOutputDtype:
     @pytest.mark.parametrize("output_signal_size", [(10,), (10, 20), (10, 20, 30)])
     def test_output_signal_size(self, output_signal_size):
         def a_function_signal_size(data, output_signal_size_for_function):
@@ -671,7 +670,6 @@ def test_no_change_1d_signal(self, input_shape):
         chunks = (10,) * len(input_shape)
         dask_array = da.random.random(input_shape, chunks=chunks)
         s = hs.signals.Signal1D(dask_array).as_lazy()
-        output_signal_size = input_shape[-1:]
         arg_pairs, adjust_chunks, new_axis, output_pattern = _get_block_pattern((s.data,), input_shape)
         assert new_axis == {}
         assert adjust_chunks == {}
@@ -832,10 +830,9 @@ def test_lazy_output_true(self):
     def test_iterating_kwargs_none(self):
         s = self.s
         s_out = s._map_iterate(np.sum, iterating_kwargs=None)
-        s_out.compute()
         assert (s_out.data == self.dx * self.dy).all()
 
-    def test_iterating_kwargs_none(self):
+    def test_iterating_kwargs_dict(self):
         def add_sum(image, add):
             out = np.sum(image) + add
             return out

upcoming_changes/2981.bugfix.rst

@@ -0,0 +1 @@
+Fix error which occurs when guessing output size in the :py:meth:`~.signal.BaseSignal.map` function and using dask newer than 2022.7.1 

upcoming_changes/2982.maintenance.rst

@@ -0,0 +1 @@
+Fix extension test suite CI workflow. Enable workflow manual trigger

upcoming_changes/2984.maintenance.rst

@@ -0,0 +1 @@
+Fix deprecation warning and time zone test failing on windows (locale dependent)