Merge pull request #2663 from ericpre/add_python3.9

Add python3.9

.github/workflows/release.yml

@@ -36,7 +36,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [windows-latest, macos-latest]
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.6, 3.7, 3.8, 3.9]
 
     steps:
       - uses: actions/checkout@v2
@@ -52,11 +52,6 @@ jobs:
           python --version
           which python
 
-      - name: Install Visual C++ for Python 2.7
-        if: runner.os == 'Windows'
-        run: |
-          choco install vcpython27 -f -y
-
       - name: install pep517 and twine
         run: |
           python -m pip install --upgrade pip
@@ -109,8 +104,9 @@ jobs:
           python -m pip install twine
 
       - name: Build manylinux Python wheels
-        uses: RalfG/python-wheels-manylinux-build@v0.3.2-manylinux2010_x86_64
+        uses: RalfG/python-wheels-manylinux-build@v0.3.3
         with:
+          python-versions: 'cp36-cp36m cp37-cp37m cp38-cp38 cp39-cp39'
           build-requirements: 'cython'
 
       - name: Build source distribution

.github/workflows/tests.yml

@@ -9,7 +9,7 @@ jobs:
     timeout-minutes: 30
     env:
       MPLBACKEND: agg
-      PIP_ARGS: --upgrade --use-feature=2020-resolver -e
+      PIP_ARGS: --upgrade -e
       PYTEST_ARGS: --pyargs hyperspy --reruns 3 -n 2 --instafail
       PYTEST_ARGS_COVERAGE: 
     strategy:
@@ -18,13 +18,13 @@ jobs:
         os: [ubuntu, windows, macos]
         PYTHON_VERSION: [3.7, 3.8]
         PIP_SELECTOR: ['[all, tests]']
-        UPSTREAM_DEV: [false]
+        DEPENDENCIES_DEV: [false]
         include:
           # test oldest supported version of main dependencies on python 3.6 
           - os: ubuntu
             PYTHON_VERSION: 3.6
             OLDEST_SUPPORTED_VERSION: true
-            DEPENDENCIES: matplotlib==2.2.3 numpy==1.16.0 scipy==1.1 imagecodecs==2019.12.3 dask==2.0.0
+            DEPENDENCIES: matplotlib==2.2.3 numpy==1.17.1 scipy==1.1 imagecodecs==2019.12.3 dask==2.1.0
             PIP_SELECTOR: '[all, tests]'
             LABEL: -oldest
           # test minimum requirement
@@ -38,13 +38,16 @@ jobs:
             PIP_SELECTOR: '[all, tests, coverage]'
             PYTEST_ARGS_COVERAGE: --cov=. --cov-report=xml
             LABEL: -coverage
-          # Run test suite against upstream development version
+          # Run test suite against dependencies development version
           - os: ubuntu
             PYTHON_VERSION: 3.8
             PIP_SELECTOR: '[all, tests]'
-            LABEL: -upstream_dev
-            UPSTREAM_DEV: true
+            LABEL: -dependencies_dev
+            DEPENDENCIES_DEV: true
             DEPENDENCIES: numpy scipy scikit-learn scikit-image
+          - os: ubuntu
+            PYTHON_VERSION: 3.9
+            PIP_SELECTOR: '[all, tests]'
         exclude:
           # redundant build (same as coverage) 
           - os: ubuntu
@@ -74,7 +77,7 @@ jobs:
           pip install ${{ matrix.DEPENDENCIES }}
 
       - name: Install dependencies development version
-        if: ${{ matrix.UPSTREAM_DEV }}
+        if: ${{ matrix.DEPENDENCIES_DEV }}
         run: |
           pip install --upgrade --no-deps --pre \
             -i https://pypi.anaconda.org/scipy-wheels-nightly/simple \

CHANGES.rst

@@ -34,6 +34,8 @@ RELEASE_next_patch (Unreleased)
 * Plot scalebar when the axis scales have different sign, fixes `#2557 <https://github.com/hyperspy/hyperspy/issues/2557>`_ (`#2657 <https://github.com/hyperspy/hyperspy/pull/2657>`_)
 * Fix align1D returning zeros shifts (`#2675 <https://github.com/hyperspy/hyperspy/pull/2675>`_)
 * Fix finding dataset path for EMD NCEM file containing more than one dataset in a  group `#2673 <https://github.com/hyperspy/hyperspy/pull/2673>`_
+* Add support for python 3.9, fix deprecation warning with matplotlib 3.4.0 and bump minimum requirement to numpy 1.17.1 and dask 2.1.0. (`#2663 <https://github.com/hyperspy/hyperspy/pull/2663>`_)
+* Add integration test suite documentation in the developer guide. (`#2663 <https://github.com/hyperspy/hyperspy/pull/2663>`_)
 
 
 Changelog

doc/dev_guide/intro.rst

@@ -24,12 +24,11 @@ Getting started
 Probably you would not be interested in contributing to HyperSpy, if you were 
 not already a user, but, just in case: the best way to start understanding how
 HyperSpy works and to build a broad overview of the code as it stands is to
-use it -- so what are you waiting for? `Install HyperSpy
-<http://hyperspy.org/hyperspy-doc/current/user_guide/install.html>`_.
+use it -- so what are you waiting for? :ref:`Install HyperSpy <install-label>`!
 
-The `HyperSpy User-Guide <http://www.hyperspy.org/hyperspy-doc/current/index
-.html>`_ also provides a good overview of all the parts of the code that
-are currently implemented as well as much information about how everything
+The HyperSpy :ref:`User Guide <user_guide-label>` also provides a good overview
+of all the parts of the code that are currently implemented as well as much 
+information about how everything
 works -- so read it well.
 
 

doc/dev_guide/writing_extensions.rst

@@ -33,7 +33,11 @@ It is good practice to add all packages that extend HyperSpy
 `to the list of known extensions
 <https://github.com/hyperspy/hyperspy-extensions-list>`_ regardless of their
 maturity level. In this way, we can avoid duplication of efforts and issues
-arising from naming conflicts.
+arising from naming conflicts. This repository also runs an `integration test
+suite <https://github.com/hyperspy/hyperspy-extensions-list/actions>`__ daily,
+which runs the test suite of all extensions to check the status of
+the ecosystem. See the :ref:`corresponding section <integration_test_suite-label>`
+for more details.
 
 At this point, it is worth noting that HyperSpy's main strength is its amazing
 community of users and developers. We trust that the developers of packages
@@ -331,7 +335,7 @@ Registering toolkeys
 ^^^^^^^^^^^^^^^^^^^^
 To register a new toolkey:
 
-1. Declare a new toolkey, *e. g.* by adding the :py:func:`hyperspy.ui_registry.add_gui_method`
+1. Declare a new toolkey, *e. g.* by adding the :py:func:`~.ui_registry.add_gui_method`
    decorator to the function you want to assign a widget to.
 2. Register a new toolkey that you have declared in your package by adding it to
    the ``hyperspy_extension.yaml`` file, as in the following example:
@@ -367,3 +371,53 @@ resides.
             function: get_mycomponent_widget
             # The module where the function resides.
             module: my_package.widgets
+
+
+.. _integration_test_suite-label:
+
+Integration test suite
+----------------------
+
+The `integration test suite <https://github.com/hyperspy/hyperspy-extensions-list/actions>`__
+runs the test suite of hyperspy and hyperspy extension on a daily basis against both the
+release and development versions. The build matrix is as follows:
+
+.. list-table:: Build matrix of the integration test suite
+   :widths: 25 25 25
+   :header-rows: 1
+
+   * - HyperSpy
+     - Extension
+     - Dependencies
+   * - Release
+     - Release
+     - Release
+   * - Release
+     - Development
+     - Release
+   * - RELEASE_next_patch
+     - Release
+     - Release
+   * - RELEASE_next_patch
+     - Development
+     - Release
+   * - RELEASE_next_minor
+     - Release
+     - Release
+   * - RELEASE_next_minor
+     - Development
+     - Release
+   * - RELEASE_next_minor
+     - Development
+     - Development
+   * - RELEASE_next_minor
+     - Development
+     - Pre-release
+
+The development packages of the dependencies are provided by the
+`scipy-wheels-nightly <https://pypi.anaconda.org/scipy-wheels-nightly/simple>`_
+repository, which provides ``scipy``, ``numpy``, ``scikit-learn`` and ``scikit-image``
+at the time of writing.
+The pre-release packages are obtained from `pypi <https://pypi.org>`_ and these
+will be used for any dependency which provides a pre-release package on pypi.
+

doc/index.rst

@@ -3,6 +3,7 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
+.. _user_guide-label:
 
 Welcome to HyperSpy's documentation!
 ====================================

hyperspy/_signals/eds.py

@@ -443,7 +443,8 @@ def add_lines(self,
                     "%s is not a valid symbol of an element." % element)
         xray_not_here = self._get_xray_lines_in_spectral_range(xray_lines)[1]
         for xray in xray_not_here:
-            warnings.warn("%s is not in the data energy range." % xray)
+            warnings.warn(f"{xray} is not in the data energy range.",
+                          UserWarning)
         if "Sample.elements" in self.metadata:
             extra_elements = (set(self.metadata.Sample.elements) -
                               elements)

hyperspy/drawing/_markers/vertical_line.py

@@ -60,7 +60,6 @@ def __repr__(self):
             self.name,
             self.get_data_position('x1'),
             self.marker_properties['color'],
-            self.get_data_position('size'),
         )
         return(string)
 

hyperspy/drawing/utils.py

@@ -160,7 +160,7 @@ def create_figure(window_title=None,
             window_title = window_title.replace(c, '')
         window_title = window_title.replace('\n', ' ')
         window_title = window_title.replace(':', ' -')
-        fig.canvas.set_window_title(window_title)
+        fig.canvas.manager.set_window_title(window_title)
     if disable_xyscale_keys and hasattr(fig.canvas, 'toolbar'):
         # hack the `key_press_handler` to disable the `k`, `l`, `L` shortcuts
         manager = fig.canvas.manager
@@ -671,11 +671,12 @@ def __check_single_colorbar(cbar):
     if cmap is None:
         cmap = [preferences.Plot.cmap_signal]
     elif cmap == 'mpl_colors':
-        for n_color, c in enumerate(mpl.rcParams['axes.prop_cycle']):
-            make_cmap(colors=['#000000', c['color']],
-                      name='mpl{}'.format(n_color))
-        cmap = ['mpl{}'.format(i) for i in
-                range(len(mpl.rcParams['axes.prop_cycle']))]
+        cycle = mpl.rcParams['axes.prop_cycle']
+        for n_color, c in enumerate(cycle):
+            name = f'mpl{n_color}'
+            if name not in plt.colormaps():
+                make_cmap(colors=['#000000', c['color']], name=name)
+        cmap = [f'mpl{i}' for i in range(len(cycle))]
         __check_single_colorbar(colorbar)
     # cmap is list, tuple, or something else iterable (but not string):
     elif hasattr(cmap, '__iter__') and not isinstance(cmap, str):

hyperspy/misc/label_position.py

@@ -47,9 +47,9 @@ def __init__(self, signal):
 
     def _set_active_figure_properties(self):
         # set the properties which depend on the figure
-        self.signal_figure = self.signal._plot.signal_plot.figure
-        self.figsize = self.signal_figure.get_size_inches()
-        self.smin, self.smax = self.signal_figure.get_axes()[0].get_ylim()
+        self.figure = self.signal._plot.signal_plot.figure
+        self.figsize = self.figure.get_size_inches()
+        self.smin, self.smax = self.signal._plot.signal_plot.ax.get_ylim()
 
         self.sig_index = self._get_current_signal_index()
         self.text_width, self.text_height = self._estimate_textbox_dimension()
@@ -67,19 +67,26 @@ def _check_signal_figure_changed(self):
         # check if the spectrum is changed
         # reset its properties if changed
         current_sig_index = self._get_current_signal_index()
-        current_figsize = self.signal_figure.get_size_inches()
+        current_figsize = self.figure.get_size_inches()
         if (current_sig_index != self.sig_index) or \
             not np.isclose(current_figsize, self.figsize).all():
             return True
         else:
             return False
 
-    def _get_bbox_from_textbox_patch(self, fig, textbox):
+    def _get_bbox_from_text_artist(self, text):
+        """
+        Parameters
+        ----------
+        text : matplotlib.text.Text instance
+
+        """
         # get the bbox object of the textbox
-        ax = fig.axes[0]
-        r = fig.canvas.get_renderer()
+        ax = text.axes
+        fig = text.figure
+        r = text.figure.canvas.get_renderer()
         fig.draw(r)
-        extent = textbox.get_bbox_patch().get_window_extent()
+        extent = text.get_bbox_patch().get_window_extent()
         bbox_patch = extent.transformed(ax.transData.inverted())
 
         return bbox_patch
@@ -95,8 +102,7 @@ def _estimate_textbox_dimension(self, dummy_text='My_g8'):
                                **dummy_style)
         self.signal.add_marker(tx)
 
-        fig = tx.marker.get_figure()
-        dummybb = self._get_bbox_from_textbox_patch(fig, tx.marker)
+        dummybb = self._get_bbox_from_text_artist(tx.marker)
         tx.close()
 
         text_width = dummybb.width