Merge 1d6f2ba into 1158b95

.travis.yml

@@ -43,17 +43,16 @@ before_install:
 install:
 
   - if [[ $MINIMAL_ENV == 'False' ]] ; then
-      DEPS="pip numpy scipy matplotlib=2.2.3 ipython h5py sympy scikit-learn dill natsort setuptools scikit-image cython ipyparallel dask traits traitsui numexpr numba";
-    else DEPS="pip ipython numpy scipy matplotlib=2.2.3 h5py sympy scikit-image numexpr";
+      DEPS="pip numpy scipy matplotlib>2.2.3 ipython h5py sympy scikit-learn dill natsort setuptools scikit-image cython ipyparallel dask traits traitsui numexpr numba";
+    else DEPS="pip ipython numpy scipy matplotlib>2.2.3 h5py sympy scikit-image numexpr";
     fi
   - conda create -n testenv --yes python=$PYTHON;
     source activate testenv;
     conda install -y -c conda-forge $DEPS;
   - if [[ $MINIMAL_ENV == 'False' ]] ; then
-      pip install .[all];
-    else pip install .;
+      pip install .[dev] && pip install 'matplotlib>=3.0.0';
+    else pip install "matplotlib>=3.0.0" && pip install .[tests];
     fi
-  - python setup.py build_ext --inplace;
 
 before_script: # configure a headless display to test plot generation
   - if [ "${TRAVIS_OS_NAME}" = "linux" ]; then sh -e /etc/init.d/xvfb start; fi
@@ -64,8 +63,8 @@ before_script: # configure a headless display to test plot generation
 
 script:
   - python -c 'import matplotlib.pyplot as plt; print(plt.get_backend())';
-  - pip install coverage coveralls pytest pytest-cov pytest-mpl;
-    py.test --mpl --cov=hyperspy --pyargs hyperspy;
+  - pip install coverage coveralls pytest-cov;
+    pytest --mpl --cov=hyperspy --pyargs hyperspy;
 
 #after_failure: # run only on failure in case there is a need to check matplotlib image comparison
 # This needs a service to upload the artifacts (and corresponding configuration)

appveyor.yml

@@ -5,7 +5,7 @@ environment:
 
   global:
     TEST_DEPS: "pytest pytest-cov pytest-mpl wheel"
-    DEPS: "numpy scipy matplotlib=2.2.3 ipython h5py sympy scikit-learn dill setuptools natsort scikit-image cython ipyparallel dask numexpr sparse numba"
+    DEPS: "numpy scipy matplotlib ipython h5py sympy scikit-learn dill setuptools natsort scikit-image cython ipyparallel dask numexpr sparse numba pywinpty"
     MPLBACKEND: "agg"
 
 
@@ -47,19 +47,17 @@ install:
 
   # Install the dependencies of the project.
   - ps: Add-AppveyorMessage "Installing conda packages..."
-  - "conda install -yq -c conda-forge %TEST_DEPS%"
-  - "conda install -yq -c conda-forge %DEPS%"
+  - "conda install -yq -c conda-forge %DEPS% %TEST_DEPS%"
 
   - ps: Add-AppveyorMessage "Installing hyperspy..."
-  - "pip install .[all]"
+  - "pip install \"matplotlib>=3.0.0\" & pip install .[dev]"
 
 build: false  # Not a C# project, build stuff at the test step instead.
 
 test_script:
   # Run the project tests
   - ps: Add-AppveyorMessage "Running tests..."
-  - "python setup.py build_ext --inplace"
-  - "py.test --mpl"
+  - "pytest --mpl"
   - "python setup.py clean"
   - ps: Add-AppveyorMessage "Testing completed."
 

doc/README.txt

@@ -1,6 +1,5 @@
 1. To build the documentation you need the following libraries to be installed:
 - sphinx
 - numpydoc
-- sphinxcontrib-napoleon
 - sphinx_rtd_theme
 2. Run the make command in this folder, for example 'make html' to build the whole documentation in html format. See the make command documentation for more details.

doc/dev_guide.rst

@@ -239,18 +239,11 @@ If you need to add or change some plots, follow the workflow below:
     3. Run again the tests and this time they should pass.
     4. Use ``git add`` to put the new file in the git repository.
 
-During the execution of plot tests, the figures are created but not deleted
-after execution. It is necessary to delete the figure and this can be done
-by using mpl_cleanup fixture: you juste need to add ``mpl_cleanup``
-as the first argument of the tests.
-
 When the plotting tests are failling, it is possible to download the figure comparison images generated by pytest-mpl in the `artifacts tabs <https://ci.appveyor.com/project/hyperspy/hyperspy/build/1.0.2500/job/2c2qccaktd90po2q/artifacts>`_ of the corresponding build.
 
 
-The plotting tests need matplotlib > 2.0.0, since the matplotlib `style change
-<http://matplotlib.org/style_changes.html>`_ between matplotlib 1.x and 2.x is
-enough to make the test failed. Freetype>=2.8 is also required to pass the 
-plotting tests.
+The plotting tests need matplotlib > 3.0.0, since small changes in the way 
+ matplotlib generates the figure can make the tests fail.
 
 In travis and appveyor, the matplotlib backend is set to ``agg`` by setting
 the ``MPLBACKEND`` environment variable to ``agg``. At the first import of

hyperspy/conftest.py

@@ -28,12 +28,4 @@ def setup_module(mod):
         import dask
         dask.set_options(get=dask.local.get_sync)
 
-
-@pytest.fixture
-def mpl_cleanup():
-    from matplotlib.testing.decorators import _do_cleanup
-
-    original_units_registry = matplotlib.units.registry.copy()
-    original_settings = matplotlib.rcParams.copy()
-    yield
-    _do_cleanup(original_units_registry, original_settings)
+from matplotlib.testing.conftest import mpl_test_settings

hyperspy/io_plugins/msa.py

@@ -219,9 +219,9 @@ def parse_msa_string(string, filename=None):
     # The data parameter needs some extra care
     # It is necessary to change the locale to US english to read the date
     # keyword
-    loc = locale.getlocale(locale.LC_TIME)
     # Setting locale can raise an exception because
     # their name depends on library versions, platform etc.
+    # https://docs.python.org/3.7/library/locale.html
     try:
         if os_name == 'posix':
             locale.setlocale(locale.LC_TIME, ('en_US', 'utf8'))
@@ -232,18 +232,17 @@ def parse_msa_string(string, filename=None):
             mapped.set_item('General.time', time.time().isoformat())
         except BaseException:
             if 'TIME' in parameters and parameters['TIME']:
-                _logger.warning('The time information could not be retrieved')
+                _logger.warning('The time information could not be retrieved.')
         try:
             date = dt.strptime(parameters['DATE'], "%d-%b-%Y")
             mapped.set_item('General.date', date.date().isoformat())
         except BaseException:
             if 'DATE' in parameters and parameters['DATE']:
-                _logger.warning('The date information could not be retrieved')
-    except BaseException:
-        warnings.warn("I couldn't read the date information due to"
-                      "an unexpected error. Please report this error to "
-                      "the developers")
-    locale.setlocale(locale.LC_TIME, loc)  # restore saved locale
+                _logger.warning('The date information could not be retrieved.')
+    except locale.Error:
+        _logger.warning("The date and time could not be retrieved because the "
+                        "english US locale is not installed on the system.")
+    locale.setlocale(locale.LC_TIME, '')  # restore user’s default settings 
 
     axes = [{
         'size': len(y),

hyperspy/tests/drawing/test_mpl_testing_setup.py

@@ -41,7 +41,7 @@ def test_mpl_version():
                    " not working.",
                    strict=True)
 @pytest.mark.mpl_image_compare(baseline_dir='', tolerance=2)
-def test_plotting_test_working(mpl_cleanup):
+def test_plotting_test_working():
     # If this test passes, it means that the plotting tests are not working!
     # In this case, the test will be reported as failed because the xfail is
     # 'strict'.

hyperspy/tests/drawing/test_plot_markers.py

@@ -137,7 +137,7 @@ def test_add_marker_not_plot(self):
         m = markers.point(x=5, y=5)
         s.add_marker(m, plot_marker=False)
 
-    def test_add_marker_signal1d_navigation_dim(self, mpl_cleanup):
+    def test_add_marker_signal1d_navigation_dim(self):
         s = Signal1D(np.zeros((3, 50, 50)))
         m0 = markers.point(5, 5)
         m1 = markers.point((5, 10), (10, 15))
@@ -147,7 +147,7 @@ def test_add_marker_signal1d_navigation_dim(self, mpl_cleanup):
             s.add_marker(m1)
         s.add_marker(m2)
 
-    def test_add_marker_signal2d_navigation_dim(self, mpl_cleanup):
+    def test_add_marker_signal2d_navigation_dim(self):
         s = Signal2D(np.zeros((3, 50, 50)))
         m0 = markers.point(5, 5)
         m1 = markers.point((5, 10), (10, 15))
@@ -157,7 +157,7 @@ def test_add_marker_signal2d_navigation_dim(self, mpl_cleanup):
             s.add_marker(m1)
         s.add_marker(m2)
 
-    def test_add_markers_as_list(self, mpl_cleanup):
+    def test_add_markers_as_list(self):
         s = Signal1D(np.arange(10))
         marker_list = []
         for i in range(12):
@@ -167,7 +167,7 @@ def test_add_markers_as_list(self, mpl_cleanup):
 
 class Test_permanent_markers:
 
-    def test_add_permanent_marker(self, mpl_cleanup):
+    def test_add_permanent_marker(self):
         s = Signal1D(np.arange(10))
         m = markers.point(x=5, y=5)
         s.add_marker(m, permanent=True)
@@ -179,7 +179,7 @@ def test_add_permanent_marker_not_plot(self):
         s.add_marker(m, permanent=True, plot_marker=False)
         assert list(s.metadata.Markers)[0][1] == m
 
-    def test_remove_permanent_marker_name(self, mpl_cleanup):
+    def test_remove_permanent_marker_name(self):
         s = Signal1D(np.arange(10))
         m = markers.point(x=5, y=5)
         m.name = 'test'
@@ -188,7 +188,7 @@ def test_remove_permanent_marker_name(self, mpl_cleanup):
         del s.metadata.Markers.test
         assert len(list(s.metadata.Markers)) == 0
 
-    def test_permanent_marker_names(self, mpl_cleanup):
+    def test_permanent_marker_names(self):
         s = Signal1D(np.arange(10))
         m0 = markers.point(x=5, y=5)
         m1 = markers.point(x=5, y=5)
@@ -201,22 +201,22 @@ def test_permanent_marker_names(self, mpl_cleanup):
         assert s.metadata.Markers.test1 == m1
         assert m1.name == 'test1'
 
-    def test_add_permanent_marker_twice(self, mpl_cleanup):
+    def test_add_permanent_marker_twice(self):
         s = Signal1D(np.arange(10))
         m = markers.point(x=5, y=5)
         s.add_marker(m, permanent=True)
         with pytest.raises(ValueError):
             s.add_marker(m, permanent=True)
 
-    def test_add_permanent_marker_twice_different_signal(self, mpl_cleanup):
+    def test_add_permanent_marker_twice_different_signal(self):
         s0 = Signal1D(np.arange(10))
         s1 = Signal1D(np.arange(10))
         m = markers.point(x=5, y=5)
         s0.add_marker(m, permanent=True)
         with pytest.raises(ValueError):
             s1.add_marker(m, permanent=True)
 
-    def test_add_several_permanent_markers(self, mpl_cleanup):
+    def test_add_several_permanent_markers(self):
         s = Signal1D(np.arange(10))
         m_point = markers.point(x=5, y=5)
         m_line = markers.line_segment(x1=5, x2=10, y1=5, y2=10)
@@ -238,15 +238,15 @@ def test_add_several_permanent_markers(self, mpl_cleanup):
         with pytest.raises(ValueError):
             s.add_marker(m_rect, permanent=True)
 
-    def test_add_markers_as_list(self, mpl_cleanup):
+    def test_add_markers_as_list(self):
         s = Signal1D(np.arange(10))
         marker_list = []
         for i in range(10):
             marker_list.append(markers.point(1, 2))
         s.add_marker(marker_list, permanent=True)
         assert len(s.metadata.Markers) == 10
 
-    def test_add_markers_as_list_add_same_twice(self, mpl_cleanup):
+    def test_add_markers_as_list_add_same_twice(self):
         s = Signal1D(np.arange(10))
         marker_list = []
         for i in range(10):
@@ -255,7 +255,7 @@ def test_add_markers_as_list_add_same_twice(self, mpl_cleanup):
         with pytest.raises(ValueError):
             s.add_marker(marker_list, permanent=True)
 
-    def test_add_markers_as_list_add_different_twice(self, mpl_cleanup):
+    def test_add_markers_as_list_add_different_twice(self):
         s = Signal1D(np.arange(10))
         marker_list0 = []
         for i in range(10):
@@ -268,13 +268,13 @@ def test_add_markers_as_list_add_different_twice(self, mpl_cleanup):
         s.add_marker(marker_list1, permanent=True)
         assert len(s.metadata.Markers) == 20
 
-    def test_add_permanent_marker_signal2d(self, mpl_cleanup):
+    def test_add_permanent_marker_signal2d(self):
         s = Signal2D(np.arange(100).reshape(10, 10))
         m = markers.point(x=5, y=5)
         s.add_marker(m, permanent=True)
         assert list(s.metadata.Markers)[0][1] == m
 
-    def test_deepcopy_permanent_marker(self, mpl_cleanup):
+    def test_deepcopy_permanent_marker(self):
         x, y, color, name = 2, 9, 'blue', 'test_point'
         s = Signal2D(np.arange(100).reshape(10, 10))
         m = markers.point(x=x, y=y, color=color)
@@ -372,7 +372,7 @@ def _test_plot_rectange_markers():
 
 @pytest.mark.mpl_image_compare(
     baseline_dir=baseline_dir, tolerance=default_tol, style=style_pytest_mpl)
-def test_plot_rectange_markers(mpl_cleanup):
+def test_plot_rectange_markers():
     im = _test_plot_rectange_markers()
     return im._plot.signal_plot.figure
 
@@ -397,7 +397,7 @@ def _test_plot_point_markers():
 
 @pytest.mark.mpl_image_compare(
     baseline_dir=baseline_dir, tolerance=default_tol, style=style_pytest_mpl)
-def test_plot_point_markers(mpl_cleanup):
+def test_plot_point_markers():
     s = _test_plot_point_markers()
     return s._plot.signal_plot.figure
 
@@ -421,14 +421,14 @@ def _test_plot_text_markers():
 
 @pytest.mark.mpl_image_compare(
     baseline_dir=baseline_dir, tolerance=default_tol, style=style_pytest_mpl)
-def test_plot_text_markers_nav(mpl_cleanup):
+def test_plot_text_markers_nav():
     s = _test_plot_text_markers()
     return s._plot.navigator_plot.figure
 
 
 @pytest.mark.mpl_image_compare(
     baseline_dir=baseline_dir, tolerance=default_tol, style=style_pytest_mpl)
-def test_plot_text_markers_sig(mpl_cleanup):
+def test_plot_text_markers_sig():
     s = _test_plot_text_markers()
     return s._plot.signal_plot.figure
 
@@ -455,7 +455,7 @@ def _test_plot_line_markers():
 
 @pytest.mark.mpl_image_compare(
     baseline_dir=baseline_dir, tolerance=default_tol, style=style_pytest_mpl)
-def test_plot_line_markers(mpl_cleanup):
+def test_plot_line_markers():
     im = _test_plot_line_markers()
     return im._plot.signal_plot.figure