Merge pull request #2824 from ericpre/add_extension_CI_on_label

Run extension test suite from PR

.github/workflows/tests_extension.yml

@@ -0,0 +1,85 @@
+name: Integration tests
+
+on:
+  workflow_dispatch:
+    workflow: "*"
+  label:
+    types: [created]
+  pull_request_review:
+    types: [submitted, edited]
+
+jobs:
+  integration_test:
+    if: ${{ github.event.review || github.event.label.name == 'run-extension-tests' }}
+    name: Extension_${{ matrix.EXTENSION_VERSION }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        EXTENSION_VERSION: ['release', 'dev']
+
+    env:
+      MPLBACKEND: agg
+      EXTENSION: kikuchipy lumispy pyxem atomap
+      TEST_DEPS: pytest pytest-xdist pytest-rerunfailures pytest-instafail
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: conda-incubator/setup-miniconda@master
+        with:
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          # use base environment, so that when using pip, this is from the
+          # mambaforge distribution
+          auto-activate-base: true
+          activate-environment: ""
+
+      - name: Conda info
+        run: |
+          conda info
+          conda list
+
+      - name: Install extensions and Test dependencies
+        run: |
+          mamba install hyperspy-base ${{ env.EXTENSION }} ${{ env.TEST_DEPS }}
+
+      - name: Conda list
+        run: |
+          conda list
+
+      - name: Install HyperSpy
+        run: |
+          pip install .
+
+      - name: Install Extension Dev
+        if: contains(matrix.EXTENSION_VERSION, 'dev')
+        run: |
+          pip install https://github.com/lumispy/lumispy/archive/main.zip
+          pip install https://github.com/pyxem/kikuchipy/archive/develop.zip
+          pip install https://github.com/pyxem/pyxem/archive/master.zip
+          pip install https://https://gitlab.com/atomap/atomap/-/archive/master/atomap-master.zip
+
+      - name: Run Kikuchipy Test Suite
+        if: ${{ always() }}
+        run: |
+          python -m pytest --pyargs kikuchipy
+
+      - name: Run LumiSpy Test Suite
+        if: ${{ always() }}
+        run: |
+          python -m pytest --pyargs lumispy
+
+      - name: Run Pyxem Test Suite
+        if: ${{ always() }}
+        run: |
+          python -m pytest --pyargs pyxem
+
+      # atomap test suite doesn't run headless 
+      #- name: Run atomap Test Suite
+      #  if: ${{ always() }}
+      #  run: |
+      #    python -m pytest --pyargs atomap

doc/dev_guide/testing.rst

@@ -179,6 +179,8 @@ The testing matrix is as follows:
   all dependencies are installed from `Anaconda Cloud <https://anaconda.org/>`_
   using the `"conda-forge" <https://anaconda.org/conda-forge>`_ channel.
   See ``azure-pipelines.yml`` in the HyperSpy repository for further details.
+- The testing of **HyperSpy extensions** is described in the 
+  :ref:`integration test suite <integration_test_suite-label>` section.
 
 This testing matrix has been designed to be simple and easy to maintain, whilst
 ensuring that packages from PyPI and Anaconda cloud are not mixed in order to
@@ -220,7 +222,7 @@ tests. The reference images are located in the folder defined by the argument
 
 To run plot tests, you simply need to add the option ``--mpl``:
 
-:: code:: bash
+.. code:: bash
 
     $ pytest --mpl
 

doc/dev_guide/writing_extensions.rst

@@ -26,7 +26,7 @@ data.
 Models can also be provided by external packages, but don't need to
 be registered. Instead, they are returned by the ``create_model`` method of
 the relevant :py:class:`hyperspy.signal.BaseSignal` subclass, see for example,
-the :py:meth:`hyperspy._signals.eds_tem.EDSTEM_mixin.create_model` of the
+the :py:meth:`~._signals.eds_tem.EDSTEMSpectrum.create_model` of the
 :py:class:`~._signals.eds_tem.EDSTEMSpectrum`.
 
 It is good practice to add all packages that extend HyperSpy
@@ -421,3 +421,8 @@ 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.
 
+A similar `Integration test  <https://github.com/hyperspy/hyperspy/actions/workflows/tests_extension.yml>`__
+workflow can run from pull requests (PR) to the
+`hyperspy <https://github.com/hyperspy/hyperspy>`_ repository when the label
+``run-extension-tests`` is added to a PR or when a PR review is edited.
+

upcoming_changes/2824.enhancements.rst

@@ -0,0 +1 @@
+Add Github workflow to run test suite of extension from a pull request.