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

…SE_next_minor

# Conflicts:
#	doc/user_guide/eels.rst
#	hyperspy/_components/skew_normal.py
#	hyperspy/_components/voigt.py
#	hyperspy/tests/drawing/test_plot_signal.py

.github/workflows/tests.yml

@@ -18,7 +18,6 @@ jobs:
         os: [ubuntu, windows, macos]
         PYTHON_VERSION: [3.8, 3.9]
         PIP_SELECTOR: ['[all, tests]']
-        DEPENDENCIES_DEV: [false]
         include:
           # test oldest supported version of main dependencies on python 3.6
           - os: ubuntu
@@ -39,13 +38,6 @@ jobs:
             PIP_SELECTOR: '[all, tests, coverage]'
             PYTEST_ARGS_COVERAGE: --cov=. --cov-report=xml
             LABEL: -coverage
-          # Run test suite against dependencies development version
-          - os: ubuntu
-            PYTHON_VERSION: 3.8
-            PIP_SELECTOR: '[all, tests]'
-            LABEL: -dependencies_dev
-            DEPENDENCIES_DEV: true
-            DEPENDENCIES: numpy scipy scikit-learn scikit-image
           - os: ubuntu
             PYTHON_VERSION: 3.7
             PIP_SELECTOR: '[all, tests]'
@@ -77,13 +69,6 @@ jobs:
         run: |
           pip install ${{ matrix.DEPENDENCIES }}
 
-      - name: Install dependencies development version
-        if: ${{ matrix.DEPENDENCIES_DEV }}
-        run: |
-          pip install --upgrade --no-deps --pre \
-            -i https://pypi.anaconda.org/scipy-wheels-nightly/simple \
-            ${{ matrix.DEPENDENCIES }}
-
       - name: Run test suite
         run: |
           pytest ${{ env.PYTEST_ARGS }} ${{ matrix.PYTEST_ARGS_COVERAGE }}

doc/user_guide/eels.rst

@@ -75,13 +75,13 @@ more information about the edges.
     +-------+-------------------+-----------+-----------------------------+
 
 The method :py:meth:`~._signals.eels.EELSSpectrum.edges_at_energy` allows
-inspecting different sections of the signal for interactive edge 
-identification (the default). A region can be selected by dragging the mouse 
-across the signal and after clicking the `Update` button, edges with onset 
-energies within the selected energy range will be displayed. By toggling the 
-edge buttons, it will put or remove the corresponding edges on the signal. When 
-the `Complementary edge` box is ticked, edges outside the selected range with 
-the same element of edges within the selected energy range will be shown as well 
+inspecting different sections of the signal for interactive edge
+identification (the default). A region can be selected by dragging the mouse
+across the signal and after clicking the `Update` button, edges with onset
+energies within the selected energy range will be displayed. By toggling the
+edge buttons, it will put or remove the corresponding edges on the signal. When
+the `Complementary edge` box is ticked, edges outside the selected range with
+the same element of edges within the selected energy range will be shown as well
 to aid identification of edges.
 
 .. code-block:: python
@@ -94,7 +94,7 @@ to aid identification of edges.
    :width:   500
 
    Labels of edges can be put or remove by toggling the edge buttons.
-    
+
 
 .. _eels_thickness-label:
 
@@ -260,8 +260,9 @@ We must enable them to accurately fit this spectrum.
     >>> m.enable_fine_structure()
 
 
-We use smart_fit instead of standard fit method because smart_fit is optimized
-to fit EELS core-loss spectra
+We use :py:meth:`~.models.eelsmodel.EELSModel.smart_fit` instead of standard
+fit method because :py:meth:`~.models.eelsmodel.EELSModel.smart_fit` is
+optimized to fit EELS core-loss spectra
 
 .. code-block:: python
 
@@ -277,12 +278,15 @@ image
 
 .. NOTE::
 
-    `m.smart_fit()` and `m.multifit(kind='smart')` are methods specific to the EELS model.
-    The fitting procedure acts in iterative manner along the energy-loss-axis.
-    First it fits only the background up to the first edge. It continues by deactivating all edges except the first one, then performs the fit.
-    Then it only activates the the first two, fits, and repeats this until all edges are fitted simultanously.
+    `m.smart_fit()` and `m.multifit(kind='smart')` are methods specific to the
+    EELS model. The fitting procedure acts in iterative manner along the
+    energy-loss-axis. First it fits only the background up to the first edge.
+    It continues by deactivating all edges except the first one, then performs
+    the fit. Then it only activates the the first two, fits, and repeats this
+    until all edges are fitted simultanously.
 
-    Other, non-EELSCLEdge components, are never deactivated, and fitted on every iteration.
+    Other, non-EELSCLEdge components, are never deactivated, and fitted on every
+    iteration.
 
 Print the result of the fit
 

hyperspy/_components/error_function.py

@@ -17,7 +17,7 @@
 # along with  HyperSpy.  If not, see <http://www.gnu.org/licenses/>.
 
 from hyperspy._components.expression import Expression
-from distutils.version import LooseVersion
+from packaging.version import Version
 import sympy
 
 
@@ -51,7 +51,7 @@ class Erf(Expression):
 
     def __init__(self, A=1., sigma=1., origin=0., module=["numpy", "scipy"],
                  **kwargs):
-        if LooseVersion(sympy.__version__) < LooseVersion("1.3"):
+        if Version(sympy.__version__) < Version("1.3"):
             raise ImportError("The `ErrorFunction` component requires "
                               "SymPy >= 1.3")
         super().__init__(

hyperspy/_components/skew_normal.py

@@ -16,15 +16,15 @@
 # You should have received a copy of the GNU General Public License
 # along with  HyperSpy.  If not, see <http://www.gnu.org/licenses/>.
 
-import numpy as np
 import dask.array as da
+import numpy as np
+from packaging.version import Version
 import sympy
 
 from hyperspy.component import _get_scaling_factor
 from hyperspy._components.expression import Expression
 from hyperspy.misc.utils import is_binned # remove in v2.0
 
-from distutils.version import LooseVersion
 
 sqrt2pi = np.sqrt(2 * np.pi)
 
@@ -139,7 +139,7 @@ class SkewNormal(Expression):
 
     def __init__(self, x0=0., A=1., scale=1., shape=0.,
                  module=['numpy', 'scipy'], **kwargs):
-        if LooseVersion(sympy.__version__) < LooseVersion("1.3"):
+        if Version(sympy.__version__) < Version("1.3"):
             raise ImportError("The `SkewNormal` component requires "
                               "SymPy >= 1.3")
         # We use `_shape` internally because `shape` is already taken in sympy

hyperspy/_components/voigt.py

@@ -17,14 +17,15 @@
 # along with  HyperSpy.  If not, see <http://www.gnu.org/licenses/>.
 
 import math
-import sympy
 import numpy as np
+from packaging.version import Version
+import sympy
 
 from hyperspy.component import _get_scaling_factor
 from hyperspy._components.expression import Expression
 from hyperspy._components.gaussian import _estimate_gaussian_parameters
 from hyperspy.misc.utils import is_binned # remove in v2.0
-from distutils.version import LooseVersion
+
 
 sqrt2pi = math.sqrt(2 * math.pi)
 sigma2fwhm = 2 * math.sqrt(2 * math.log(2))
@@ -90,7 +91,7 @@ def __init__(self, centre=10., area=1., gamma=0.2, sigma=0.1,
         # Not to break scripts once we remove the legacy Voigt
         if "legacy" in kwargs:
             del kwargs["legacy"]
-        if LooseVersion(sympy.__version__) < LooseVersion("1.3"):
+        if Version(sympy.__version__) < Version("1.3"):
             raise ImportError("The `Voigt` component requires "
                               "SymPy >= 1.3")
         # We use `_gamma` internally to workaround the use of the `gamma`

hyperspy/_signals/lazy.py

@@ -26,8 +26,7 @@
 import dask
 from dask.diagnostics import ProgressBar
 from itertools import product
-from distutils.version import LooseVersion
-
+from packaging.version import Version
 
 from hyperspy.signal import BaseSignal
 from hyperspy.defaults_parser import preferences
@@ -1165,7 +1164,7 @@ def compute_navigator(self, index=None, chunks_number=None,
             # Needs to reverse the chunks list to match dask chunking order
             signal_chunks = list(signal_chunks)[::-1]
             navigation_chunks = ['auto'] * len(self.axes_manager.navigation_shape)
-            if LooseVersion(dask.__version__) >= LooseVersion("2.30.0"):
+            if Version(dask.__version__) >= Version("2.30.0"):
                 kwargs = {'balance':True}
             else:
                 kwargs = {}

hyperspy/axes.py

@@ -2014,19 +2014,18 @@ def _update_attributes(self):
         self.signal_axes = self.signal_axes[::-1]
         self.navigation_axes = self.navigation_axes[::-1]
         self._getitem_tuple = tuple(getitem_tuple)
-        self.signal_dimension = len(self.signal_axes)
+        if len(self.signal_axes) == 1 and self.signal_axes[0].size == 1:
+            self.signal_dimension = 0
+        else:
+            self.signal_dimension = len(self.signal_axes)
         self.navigation_dimension = len(self.navigation_axes)
         if self.navigation_dimension != 0:
             self.navigation_shape = tuple([
                 axis.size for axis in self.navigation_axes])
         else:
             self.navigation_shape = ()
 
-        if self.signal_dimension != 0:
-            self.signal_shape = tuple([
-                axis.size for axis in self.signal_axes])
-        else:
-            self.signal_shape = ()
+        self.signal_shape = tuple([axis.size for axis in self.signal_axes])
         self.navigation_size = (np.cumprod(self.navigation_shape)[-1]
                                 if self.navigation_shape else 0)
         self.signal_size = (np.cumprod(self.signal_shape)[-1]

hyperspy/component.py

@@ -22,7 +22,7 @@
 from traits.trait_numeric import Array
 import sympy
 from sympy.utilities.lambdify import lambdify
-from distutils.version import LooseVersion
+from packaging.version import Version
 from pathlib import Path
 
 import hyperspy
@@ -1206,7 +1206,7 @@ def _load_dictionary(self, dic):
 
         if dic['_id_name'] == self._id_name:
             if (self._id_name == "Polynomial" and
-                    LooseVersion(hyperspy.__version__) >= LooseVersion("2.0")):
+                    Version(hyperspy.__version__) >= Version("2.0")):
                 # in HyperSpy 2.0 the polynomial definition changed
                 from hyperspy._components.polynomial import convert_to_polynomial
                 dic = convert_to_polynomial(dic)

hyperspy/drawing/image.py

@@ -17,7 +17,7 @@
 # along with HyperSpy. If not, see <http://www.gnu.org/licenses/>.
 
 import math
-from distutils.version import LooseVersion
+from packaging.version import Version
 
 import numpy as np
 import matplotlib
@@ -520,7 +520,7 @@ def format_coord(x, y):
                 sym_log_kwargs = {'linthresh':self.linthresh,
                                   'linscale':self.linscale,
                                   'vmin':vmin, 'vmax':vmax}
-                if LooseVersion(matplotlib.__version__) >= LooseVersion("3.2"):
+                if Version(matplotlib.__version__) >= Version("3.2"):
                     sym_log_kwargs['base'] = 10
                 norm = SymLogNorm(**sym_log_kwargs)
             elif inspect.isclass(norm) and issubclass(norm, Normalize):

hyperspy/drawing/utils.py

@@ -18,7 +18,7 @@
 
 import copy
 import itertools
-from distutils.version import LooseVersion
+from packaging.version import Version
 import textwrap
 import traits.api as t
 import matplotlib.pyplot as plt
@@ -1645,7 +1645,7 @@ def plot_histograms(signal_list,
 
 def picker_kwargs(value, kwargs={}):
     # picker is deprecated in favor of pickradius
-    if LooseVersion(mpl.__version__) >= LooseVersion("3.3.0"):
+    if Version(mpl.__version__) >= Version("3.3.0"):
         kwargs.update({'pickradius': value, 'picker':True})
     else:
         kwargs['picker'] = value

hyperspy/external/progressbar.py

@@ -16,10 +16,10 @@
 # You should have received a copy of the GNU General Public License
 # along with  HyperSpy.  If not, see <http://www.gnu.org/licenses/>.
 
-from distutils.version import LooseVersion
+from packaging.version import Version
 from tqdm import __version__ as tqdm_version
 
-if LooseVersion(tqdm_version) >= LooseVersion("4.36.0"):
+if Version(tqdm_version) >= Version("4.36.0"):
     # API change for 5.0 https://github.com/tqdm/tqdm/pull/800
     from tqdm import tqdm
     from tqdm.notebook import tqdm as tqdm_notebook

hyperspy/io_plugins/hspy.py

@@ -16,7 +16,7 @@
 # You should have received a copy of the GNU General Public License
 # along with  HyperSpy.  If not, see <http://www.gnu.org/licenses/>.
 
-from distutils.version import LooseVersion
+from packaging.version import Version
 import warnings
 import logging
 import datetime
@@ -101,7 +101,7 @@
 not_valid_format = 'The file is not a valid HyperSpy hdf5 file'
 
 current_file_version = None  # Format version of the file being read
-default_version = LooseVersion(version)
+default_version = Version(version)
 
 
 def get_hspy_format_version(f):
@@ -119,7 +119,7 @@ def get_hspy_format_version(f):
         version = "2.0"
     else:
         raise IOError(not_valid_format)
-    return LooseVersion(version)
+    return Version(version)
 
 
 def file_reader(filename, backing_store=False,
@@ -212,7 +212,7 @@ def file_reader(filename, backing_store=False,
 def hdfgroup2signaldict(group, lazy=False):
     global current_file_version
     global default_version
-    if current_file_version < LooseVersion("1.2"):
+    if current_file_version < Version("1.2"):
         metadata = "mapped_parameters"
         original_metadata = "original_parameters"
     else:
@@ -281,7 +281,7 @@ def hdfgroup2signaldict(group, lazy=False):
         if '__unnamed__' == exp['metadata']['General']['title']:
             exp['metadata']["General"]['title'] = ''
 
-    if current_file_version < LooseVersion("1.1"):
+    if current_file_version < Version("1.1"):
         # Load the decomposition results written with the old name,
         # mva_results
         if 'mva_results' in group.keys():
@@ -305,7 +305,7 @@ def hdfgroup2signaldict(group, lazy=False):
                 exp['metadata']['name']
             del exp['metadata']['name']
 
-    if current_file_version < LooseVersion("1.2"):
+    if current_file_version < Version("1.2"):
         if '_internal_parameters' in exp['metadata']:
             exp['metadata']['_HyperSpy'] = \
                 exp['metadata']['_internal_parameters']
@@ -391,7 +391,7 @@ def hdfgroup2signaldict(group, lazy=False):
                 exp["metadata"]["Signal"][key] = exp["metadata"][key]
                 del exp["metadata"][key]
 
-    if current_file_version < LooseVersion("3.0"):
+    if current_file_version < Version("3.0"):
         if "Acquisition_instrument" in exp["metadata"]:
             # Move tilt_stage to Stage.tilt_alpha
             # Move exposure time to Detector.Camera.exposure_time
@@ -722,7 +722,7 @@ def write_signal(signal, group, **kwds):
     "Writes a hyperspy signal to a hdf5 group"
 
     group.attrs.update(get_object_package_info(signal))
-    if default_version < LooseVersion("1.2"):
+    if default_version < Version("1.2"):
         metadata = "mapped_parameters"
         original_metadata = "original_parameters"
     else:
@@ -742,7 +742,7 @@ def write_signal(signal, group, **kwds):
     overwrite_dataset(group, signal.data, 'data',
                       signal_axes=signal.axes_manager.signal_indices_in_array,
                       **kwds)
-    if default_version < LooseVersion("1.2"):
+    if default_version < Version("1.2"):
         metadata_dict["_internal_parameters"] = \
             metadata_dict.pop("_HyperSpy")
     # Remove chunks from the kwds since it wouldn't have the same rank as the

hyperspy/io_plugins/mrcz.py

@@ -16,7 +16,7 @@
 # You should have received a copy of the GNU General Public License
 # along with  HyperSpy.  If not, see <http://www.gnu.org/licenses/>.
 
-from distutils.version import LooseVersion
+from packaging.version import Version
 import mrcz as _mrcz
 import logging
 
@@ -46,7 +46,7 @@
 
 # API changes in mrcz 0.5
 def _parse_metadata(metadata):
-    if LooseVersion(_mrcz.__version__) < LooseVersion("0.5"):
+    if Version(_mrcz.__version__) < Version("0.5"):
         return metadata[0]
     else:
         return metadata

hyperspy/io_plugins/tiff.py

@@ -25,7 +25,7 @@
 import tifffile
 import traits.api as t
 import numpy as np
-from distutils.version import LooseVersion
+from packaging.version import Version
 
 from hyperspy.misc import rgb_tools
 from hyperspy.misc.date_time_tools import get_date_time_from_metadata
@@ -170,7 +170,7 @@ def _read_serie(tiff, serie, filename, force_read_resolution=False,
                           'formats': [dtype] * lastshape})
         shape = shape[:-1]
 
-    if LooseVersion(tifffile.__version__) >= LooseVersion("2020.2.16"):
+    if Version(tifffile.__version__) >= Version("2020.2.16"):
         op = {tag.name: tag.value for tag in page.tags}
     else:
         op = {key: tag.value for key, tag in page.tags.items()}