Added a py.typed for type checkers

.git-blame-ignore-revs

@@ -0,0 +1,4 @@
+# Run ruff format
+922f3594ab343a49cbab22073fa79f073932e13d
+8f05320b5419a482ac485f352f352ac4504d08f0
+614ccb9895f8e2aaa9a722712944b9eafa227c8c

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,26 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: 'type: bug'
+
+---
+
+#### Describe the bug
+A clear and concise description of what the bug is.
+
+#### To Reproduce
+Steps to reproduce the behavior:
+```
+Minimum working example of code
+```
+
+#### Expected behavior
+A clear and concise description of what you expected to happen.
+
+#### Python environment:
+ - HyperSpy version: 1.x.x
+ - Python version: 3.x
+
+#### Additional context
+Add any other context about the problem here. If necessary, add screenshots to help explain your problem.

.github/ISSUE_TEMPLATE/custom.md

@@ -0,0 +1,8 @@
+---
+name: Custom issue template
+about: Describe this issue template's purpose here.
+title: ''
+labels: ''
+---
+
+

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,17 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: 'type: feature request'
+assignees: ''
+
+---
+
+#### Describe the functionality you would like to see.
+A clear and concise description of what you would like to do.
+
+#### Describe the context
+Do you want to extend existing functionalities, what types of signals should it apply to, etc.
+
+#### Additional information
+Add any other context or screenshots about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,5 +1,5 @@
 ### Requirements
-* Read the [developer guide](https://hyperspy.org/hyperspy-doc/current/dev_guide/index.html).
+* Read the [developer guide](https://hyperspy.org/hyperspy-doc/current/dev_guide/intro.html).
 * Base your pull request on the [correct branch](https://hyperspy.org/hyperspy-doc/current/dev_guide/git.html#semantic-versioning-and-hyperspy-main-branches).
 * Filling out the template; it helps the review process and it is useful to summarise the PR.
 * This template can be updated during the progression of the PR to summarise its status. 

.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 +1,44 @@
+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
+      # optipng is required to optimize thumbnail
+      install_package_ubuntu: graphviz optipng
+
+  Push_dev:
+    needs: Build
+    # Push only on the "RELEASE_next_minor" and update the "dev" documentation
+    if: ${{ github.repository_owner == 'hyperspy' && github.ref_name == 'RELEASE_next_minor' }}
+    permissions:
+      # needs write permission to push the docs to gh-pages
+      contents: write
+    # Use the "reusable workflow" from the hyperspy organisation
+    uses: hyperspy/.github/.github/workflows/push_doc.yml@main
+    with:
+      repository: 'hyperspy/hyperspy-doc'
+      output_path: 'dev'
+    secrets:
+      access_token: ${{ secrets.PAT_DOCUMENTATION }}
+
+  Push_tag:
+    needs: Build
+    # Push only on tag and update the "current" documentation
+    if: ${{ github.repository_owner == 'hyperspy' && startsWith(github.ref, 'refs/tags/') }}
+    permissions:
+      # needs write permission to push the docs to gh-pages
+      contents: write
+    # Use the "reusable workflow" from the hyperspy organisation
+    uses: hyperspy/.github/.github/workflows/push_doc.yml@main
+    with:
+      repository: 'hyperspy/hyperspy-doc'
+      output_path: 'current'
+    secrets:
+      access_token: ${{ secrets.PAT_DOCUMENTATION }}

.github/workflows/nightly-merge.yml

@@ -12,10 +12,10 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Nightly Merge
-      uses: robotology/gh-action-nightly-merge@v1.3.2
+      uses: robotology/gh-action-nightly-merge@81570ba03dd370f582bd3f52d47672d29191829f
       with:
         stable_branch: 'RELEASE_next_patch'
         development_branch: 'RELEASE_next_minor'

.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.
@@ -9,140 +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@v2
+        uses: actions/checkout@v4
       - name: Create Release
-        id: create_release
-        uses: actions/create-release@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions
-        with:
-          tag_name: ${{ github.ref }}
-          release_name: Release ${{ github.ref }}
-          draft: false
-          prerelease: false
-
-  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: [3.6, 3.7, 3.8, 3.9]
-
-    steps:
-      - uses: actions/checkout@v2
-
-      - uses: actions/setup-python@v2
-        name: Install Python
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: What OS and Python version
-        run: |
-          uname -a
-          python --version
-          which python
-
-      - name: install pep517 and twine
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install pep517 twine
-
-      - name: Build wheels
-        run: |
-          python -m pep517.build --binary --out-dir dist/ .
-
-      - 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]
-          pytest --pyargs hyperspy
-
-      - uses: actions/upload-artifact@v2
-        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@v2
-
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-
-      - name: install twine
-        run: |
-          python -m pip install twine
-
-      - name: Build manylinux Python wheels
-        uses: RalfG/[email protected]
-        with:
-          python-versions: 'cp36-cp36m cp37-cp37m cp38-cp38 cp39-cp39'
-          build-requirements: 'cython'
-
-      - name: Build source distribution
-        run: |
-          pip install pep517
-          python -m pep517.build --source --out-dir sdist/ .
-
-      - name: Display content dist folder
-        run: |
-          ls dist/
-          ls sdist/
-
-      - name: Install and test distribution
-        env:
-          MPLBACKEND: agg
-        run: |
-          pip install --pre --find-links dist hyperspy[tests]
-          pytest --pyargs hyperspy
-
-      - uses: actions/upload-artifact@v2
-        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 sdist/*.tar.gz --verbose 
-
+        if: ${{ startsWith(github.ref, 'refs/tags/') && github.repository_owner == 'hyperspy' }}
+        uses: softprops/action-gh-release@c062e08bd532815e2082a85e87e3ef29c3e6d191