Merge pull request hyperspy#3288 from ericpre/RELEASE_next_patch

Merge fast forward into release next patch after 2.0 release

.github/dependabot.yml

@@ -0,0 +1,12 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
+    target-branch: "RELEASE_next_patch"

.github/workflows/doc.yml

@@ -0,0 +1,13 @@
+name: Documentation
+
+on: [push, pull_request]
+
+jobs:
+  Build:
+    # Use the "reusable workflow" from the hyperspy organisation
+    uses: hyperspy/.github/.github/workflows/doc.yml@main
+    with:
+      # install with speed extra to avoid warnings
+      pip_extra_doc: 'doc,speed'
+      # graphviz is required to build mermaid graph
+      install_package_ubuntu: graphviz

.github/workflows/package_and_test.yml

@@ -0,0 +1,9 @@
+name: Package & Test
+
+on: [push, pull_request]
+
+jobs:
+  package_and_test:
+    name: Package and Test
+    # Use the "reusable workflow" from the hyperspy organisation
+    uses: hyperspy/.github/.github/workflows/package_and_test.yml@main

.github/workflows/release.yml

@@ -1,4 +1,9 @@
 name: Release
+# Reusable workflow are not supported with trusted publisher
+# https://github.com/pypa/gh-action-pypi-publish/issues/166
+# copy and paste
+# https://github.com/hyperspy/.github/blob/main/.github/workflows/release_pure_python.yml
+
 # This workflow builds the wheels "on tag".
 # If run from the hyperspy/hyperspy repository, the wheels will be uploaded to pypi ;
 # otherwise, the wheels will be available as a github artifact.
@@ -9,139 +14,42 @@ on:
     - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
 
 jobs:
-  create_release:
+  package_and_test:
+    name: Package and Test
+    # Use the "reusable workflow" from the hyperspy organisation
+    uses: hyperspy/.github/.github/workflows/package_and_test.yml@main
+
+  upload_to_pypi:
+    needs: [package_and_test]
+    runs-on: ubuntu-latest
+    name: Upload to pypi
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+    steps:
+    - name: Download dist
+      uses: actions/download-artifact@v4
+
+    - name: Display downloaded files
+      run: |
+        ls -shR
+      working-directory: dist
+
+    - uses: pypa/gh-action-pypi-publish@release/v1
+      if: ${{ startsWith(github.ref, 'refs/tags/') && github.repository_owner == 'hyperspy' }}
+      # See https://docs.pypi.org/trusted-publishers/using-a-publisher/
+
+  create_github_release:
+    # If zenodo is setup to create a DOI automatically on a GitHub release,
+    # this step will trigger the mining of the DOI
+    needs: upload_to_pypi
     permissions:
       contents: write
-    name: Create Release
+    name: Create GitHub Release
     runs-on: ubuntu-latest
-    outputs: 
-      upload_url: ${{ steps.create_release.outputs.upload_url }}
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
       - name: Create Release
-        id: create_release
+        if: ${{ startsWith(github.ref, 'refs/tags/') && github.repository_owner == 'hyperspy' }}
         uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844
-
-  build_wheels:
-    name: Wheels on ${{ matrix.os }}/py${{ matrix.python-version }}
-    needs: create_release
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [windows-latest, macos-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-python@v4
-        name: Install Python
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: What OS and Python version
-        run: |
-          uname -a
-          python --version
-          which python
-
-      - name: install build and twine
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install build twine
-
-      - name: Build wheels
-        run: |
-          python -m build
-
-      - name: Display content dist folder
-        run: |
-          ls dist/
-
-      - name: Install and test distribution
-        env:
-          MPLBACKEND: agg
-        run: |
-          pip install --pre --find-links dist hyperspy[tests]==1.7.6
-          pytest --pyargs hyperspy -k "not test_navigation_shape_signal2D"
-
-      - uses: actions/upload-artifact@v3
-        with:
-          path: ./dist/*.whl
-
-      - name: Publish wheels to PyPI
-        if: github.repository_owner == 'hyperspy'
-        env:
-          # Github secret set in the hyperspy/hyperspy repository
-          # Not available from fork or pull request
-          # Secrets are not passed to workflows that are triggered by a pull request from a fork
-          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-        run: |
-          twine upload dist/*.whl --verbose
-
-  build_wheels_linux:
-    name: Wheels on ubuntu-latest
-    needs: create_release
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.10'
-
-      - name: Build source distribution
-        run: |
-          pip install build
-          python -m build --sdist
-
-      - name: Build manylinux Python wheels
-        uses: RalfG/python-wheels-manylinux-build@ff8504699f7a33a08d3ff85b3c6d4e8f0e70462b
-        with:
-          python-versions: 'cp37-cp37m cp38-cp38 cp39-cp39 cp310-cp310 cp311-cp311'
-          build-requirements: 'cython'
-
-      - name: Display content dist folder
-        run: |
-          ls dist/
-
-      - name: Install and test distribution
-        env:
-          MPLBACKEND: agg
-        run: |
-          pip install --pre --find-links dist hyperspy[tests]==1.7.6
-          pytest --pyargs hyperspy -k "not test_navigation_shape_signal2D"
-
-      - uses: actions/upload-artifact@v3
-        if: always()
-        with:
-          path: |
-            ./dist/*-manylinux*.whl
-            ./sdist/*.tar.gz
-
-      - name: Publish wheels to PyPI
-        if: github.repository_owner == 'hyperspy'
-        env:
-          # Github secret set in the hyperspy/hyperspy repository
-          # Not available from fork or pull request
-          # Secrets are not passed to workflows that are triggered by a pull request from a fork
-          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-        run: |
-          twine upload dist/*-manylinux*.whl --verbose 
-          twine upload dist/*.tar.gz --verbose 
-
-      # Don't use the pypa publish action for now as we need to filter the `linux` wheels
-      # With hyperspy 2.0, it will be noarch and the release workflow will refactor
-      # - name: Publish wheels to PyPI
-      #   if: github.repository_owner == 'hyperspy'
-      #   uses: pypa/gh-action-pypi-publish@release/v1
-      #   with:
-      #     # Github secret set in the hyperspy/hyperspy repository
-      #     # Not available from fork or pull request
-      #     # Secrets are not passed to workflows that are triggered by a pull request from a fork
-      #     password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/tests.yml

@@ -15,37 +15,42 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu, windows, macos]
-        PYTHON_VERSION: ['3.8', '3.9']
+        PYTHON_VERSION: ['3.9', '3.10', ]
         PIP_SELECTOR: ['[all, tests, coverage]']
         include:
-          # test oldest supported version of main dependencies on python 3.7
+          # test oldest supported version of main dependencies on python 3.8
           - os: ubuntu
-            PYTHON_VERSION: '3.7'
+            PYTHON_VERSION: '3.8'
             PIP_SELECTOR: '[all, tests, coverage]'
             OLDEST_SUPPORTED_VERSION: true
-            DEPENDENCIES: matplotlib==3.1.3 numpy==1.19.0 scipy==1.4 imagecodecs==2020.1.31 tifffile==2020.2.16 dask==2.11.0 distributed==2.11.0 scikit-image==0.15 numba==0.52 scikit-learn==1.0.1
+            DEPENDENCIES: dask[array]==2021.3.1 matplotlib==3.1.3 numba==0.52 numpy==1.20.0 scipy==1.5 scikit-image==0.18 scikit-learn==1.0.1
             LABEL: -oldest
           # test minimum requirement
           - os: ubuntu
-            PYTHON_VERSION: '3.8'
+            PYTHON_VERSION: '3.12'
             PIP_SELECTOR: '[tests, coverage]'
             LABEL: -minimum
-          # Run coverage
-          - os: ubuntu
-            PYTHON_VERSION: '3.7'
-            PIP_SELECTOR: '[all, tests, coverage]'
+            # Run coverage
           - os: ubuntu
             PYTHON_VERSION: '3.8'
             PIP_SELECTOR: '[all, tests, coverage]'
-          - os: ubuntu
-            PYTHON_VERSION: '3.10'
-            PIP_SELECTOR: '[all, tests, coverage]'
           - os: ubuntu
             PYTHON_VERSION: '3.11'
             PIP_SELECTOR: '[all, tests, coverage]'
 
     steps:
       - uses: actions/checkout@v4
+        with: 
+          fetch-depth: 0
+          fetch-tags: true
+
+      - name: Fetch tags upstream
+        if: ${{ github.repository_owner != 'hyperspy' }}
+        # Needs to fetch the tags from upstream to get the
+        # correct version with setuptools_scm
+        run: |
+          git remote add upstream https://github.com/hyperspy/hyperspy.git
+          git fetch upstream --tags
 
       - uses: actions/setup-python@v4
         name: Install Python
@@ -57,17 +62,10 @@ jobs:
           python --version
           pip --version
 
-      - name: Install numba rc
-        if: contains(matrix.PYTHON_VERSION, '3.11')
-        # Require for python 3.11 support, remove when numba 0.57 is release
-        shell: bash
-        run: |
-          pip install numba --pre
-
       - name: Install oldest supported version
         if: ${{ matrix.OLDEST_SUPPORTED_VERSION }}
         run: |
-          pip install ${{ matrix.DEPENDENCIES }}
+          pip install ${{ matrix.DEPENDENCIES }} -v
 
       - name: Install
         shell: bash
@@ -82,6 +80,10 @@ jobs:
         run: |
           pytest ${{ env.PYTEST_ARGS }} --cov=. --cov-report=xml
 
+      - name: Run doctest (Docstring)
+        run: |
+          pytest ${{ env.PYTEST_ARGS }} --doctest-modules --ignore=hyperspy/tests
+
       - name: Upload coverage to Codecov
         if: ${{ always() }}
         uses: codecov/codecov-action@v3