Merge branch 'master' into 0.13.x

.github/workflows/build.yml

@@ -22,9 +22,11 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Display versions
         run: python -V; pip -V
-      - name: Install depedencies and package
+      - name: Install dependencies and package
         shell: bash
         run: pip install -U -e .'[tests]'
+      - name: Run docstring tests
+        run: pytest --doctest-modules --ignore=pyxem/tests pyxem
       - name: Run tests
         run: pytest --cov=pyxem --runslow --pyargs pyxem
       - name: Generate line coverage

CHANGELOG.md

@@ -4,7 +4,6 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-
 ## 2021-04-14 - version 0.13.2
 ### Added
  - Code now support python 3.9 

pytest.ini

@@ -0,0 +1,2 @@
+[pytest]
+addopts = --ignore=pyxem/detectors/generic_flat_detector.py --ignore=pyxem/detectors/medipix_256x256.py --ignore=pyxem/detectors/medipix_515x515.py --ignore pyxem/signals/common_diffraction.py --ignore=pyxem/signals/diffraction2d.py --ignore=pyxem/signals/indexation_results.py --ignore=pyxem/utils/marker_tools.py

pyxem/conftest.py

@@ -0,0 +1,45 @@
+# -*- coding: utf-8 -*-
+# Copyright 2016-2021 The pyXem developers
+#
+# This file is part of pyXem.
+#
+# pyXem is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# pyXem is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with pyXem.  If not, see <http://www.gnu.org/licenses/>.
+
+import os
+from tempfile import TemporaryDirectory
+import pytest
+import numpy
+import matplotlib.pyplot as plt
+import hyperspy.api as hs
+import pyxem as pxm
+
+
+@pytest.fixture(autouse=True)
+def doctest_setup_teardown(request):
+    plt.ioff()
+    tmp_dir = TemporaryDirectory()
+    hs.preferences.General.show_progressbar = False
+    org_dir = os.getcwd()
+    os.chdir(tmp_dir.name)
+    yield
+    os.chdir(org_dir)
+    tmp_dir.cleanup()
+    plt.close("all")
+
+
+@pytest.fixture(autouse=True)
+def add_np_am(doctest_namespace):
+    doctest_namespace["np"] = numpy
+    doctest_namespace["hs"] = hs
+    doctest_namespace["pxm"] = pxm

pyxem/dummy_data/make_diffraction_test_data.py

@@ -90,7 +90,7 @@ def _get_elliptical_ring(xx, yy, x, y, semi_len0, semi_len1, rotation, lw_r=1):
     Examples
     --------
     >>> from hyperspy.signals import Signal2D
-    >>> from pyxem.dummy_data importmake_diffraction_test_data as mdtd
+    >>> from pyxem.dummy_data import make_diffraction_test_data as mdtd
     >>> s = Signal2D(np.zeros((110, 130)))
     >>> s.axes_manager[0].offset, s.axes_manager[1].offset = -50, -80
     >>> xx, yy = np.meshgrid(

pyxem/utils/dask_tools.py

@@ -106,9 +106,9 @@ def _get_chunking(signal, chunk_shape=None, chunk_bytes=None):
     Examples
     --------
     >>> import dask.array as da
-    >>> import pyxem as pxm
+    >>> from hyperspy.signals import Signal2D
     >>> import pyxem.utils.dask_tools as dt
-    >>> s = pxm.LazySignal2D(da.zeros((32, 32, 256, 256), chunks=(16, 16, 256, 256)))
+    >>> s = Signal2D(da.zeros((32, 32, 256, 256), chunks=(16, 16, 256, 256))).as_lazy()
     >>> chunks = dt._get_chunking(s)
 
     Limiting to 60 MiB per chunk
@@ -272,7 +272,8 @@ def _process_dask_array(
     ...     return image * value
     >>> dask_array = da.ones((4, 6, 10, 15), chunks=(2, 2, 2, 2))
     >>> iter_array = da.random.randint(0, 99, (4, 6), chunks=(2, 2))
-    >>> output_dask_array = _process_dask_array(dask_array, test_function2)
+    >>> output_dask_array = _process_dask_array(
+    ...     dask_array, test_function2, iter_array)
     >>> output_array = output_dask_array.compute()
 
     Getting output which is different shape than the input. For example

pyxem/utils/pixelated_stem_tools.py

@@ -385,7 +385,7 @@ def _get_angle_sector_mask(
     --------
     >>> import numpy as np
     >>> import pyxem.utils.pixelated_stem_tools as pst
-    >>> s = ps.PixelatedSTEM(np.arange(100).reshape(10, 10))
+    >>> s = pxm.signals.Diffraction2D(np.arange(100).reshape(10, 10))
     >>> s.axes_manager.signal_axes[0].offset = -5
     >>> s.axes_manager.signal_axes[1].offset = -5
     >>> mask = pst._get_angle_sector_mask(s, 0.5*np.pi, np.pi)

pyxem/utils/radial_utils.py

@@ -655,7 +655,7 @@ def fit_single_ellipse_to_signal(
 
     Examples
     --------
-    >>> import pyxem.dummy_data import make_diffraction_test_data as mdtd
+    >>> from pyxem.dummy_data import make_diffraction_test_data as mdtd
     >>> s = pxm.signals.Diffraction2D(np.zeros((200, 220)))
     >>> s.axes_manager[0].offset, s.axes_manager[1].offset = -100, -110
     >>> xx, yy = np.meshgrid(s.axes_manager[0].axis, s.axes_manager[1].axis)
@@ -715,13 +715,13 @@ def fit_ellipses_to_signal(
 
     Examples
     --------
-    >>> import pyxem.dummy_data import make_diffraction_test_data as mdtd
-    >>> s = ps.PixelatedSTEM(np.zeros((200, 220)))
+    >>> from pyxem.dummy_data import make_diffraction_test_data as mdtd
+    >>> s = pxm.signals.Diffraction2D(np.zeros((200, 220)))
     >>> s.axes_manager[0].offset, s.axes_manager[1].offset = -100, -110
     >>> xx, yy = np.meshgrid(s.axes_manager[0].axis, s.axes_manager[1].axis)
     >>> ellipse_ring = mdtd._get_elliptical_ring(xx, yy, 0, 0, 50, 70, 0.8)
     >>> s.data += ellipse_ring
-    >>> from pyxem..utils.radial_tools import fit_ellipses_to_signal
+    >>> from pyxem.utils.radial_utils import fit_ellipses_to_signal
     >>> output = fit_ellipses_to_signal(
     ...     s, [(40, 80)], angleN=30, show_progressbar=False)