Merge pull request #1 from ericpre/add_github_actions

Add GitHub actions and templates

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,27 @@
+---
+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 environement:
+ - exSpy version: 0.x.x
+ - 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

@@ -0,0 +1,30 @@
+### Requirements
+* Read the [contributing guidelines](https://github.com/hyperspy/exspy/blob/main/CONTRIBUTING.rst).
+* Fill 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. 
+
+*You can delete this section after you read it.*
+
+### Description of the change
+A few sentences and/or a bulleted list to describe and motivate the change:
+- Change A.
+- Change B.
+- etc.
+
+### Progress of the PR
+- [ ] Change implemented (can be split into several points),
+- [ ] docstring updated (if appropriate),
+- [ ] update user guide (if appropriate),
+- [ ] added tests,
+- [ ] added line to CHANGES.rst,
+- [ ] ready for review.
+
+### Minimal example of the bug fix or the new feature
+```python
+import exspy
+import numpy as np
+s = exspy.signals.EELSSpectrum(np.arange(100).reshape(10,10))
+# Your new feature...
+```
+
+

.github/workflows/black.yml

@@ -0,0 +1,11 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+      - uses: psf/black@stable

.github/workflows/build.yml

@@ -0,0 +1,65 @@
+name: Build
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    name: Build
+    runs-on: ubuntu-latest
+    env:
+      PYTHON_VERSION: '3.11'
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: Display version
+        run: |
+          python --version
+          pip --version
+
+      - name: Install pypa/build
+        run: |
+          pip install build
+
+      - name: Build a binary wheel and a source tarball
+        run: |
+          python -m build
+
+      - name: Display content dist folder
+        run: |
+          ls -l dist/
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./dist/*
+          name: dist
+
+  test:
+    name: Test Packaging
+    needs: build
+    runs-on: ubuntu-latest
+    env:
+      PYTHON_VERSION: '3.11'
+    steps:
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - uses: actions/download-artifact@v3
+
+      - name: Display content working folder
+        run: |
+          ls -R
+
+      - name: Install distribution
+        run: |
+          pip install --pre --find-links dist exspy[tests]
+
+      - name: Test distribution
+        run: |
+          pytest --pyargs exspy

.github/workflows/release.yml

@@ -0,0 +1,85 @@
+name: Release
+
+# 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.
+on:
+  push:
+    # Sequence of patterns matched against refs/tags
+    tags:
+    - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+
+jobs:
+  build_wheels:
+    name: Build wheels
+    runs-on: ubuntu-latest
+    env:
+      CIBW_TEST_COMMAND: "pytest --pyargs exspy"
+      CIBW_TEST_EXTRAS: "tests"
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: ./wheelhouse/*.whl
+          if-no-files-found: error
+
+  make_sdist:
+    name: Make SDist
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Build SDist
+      run: pipx run build --sdist
+
+    - uses: actions/upload-artifact@v3
+      with:
+        path: dist/*.tar.gz
+
+  upload_to_pypi:
+    needs: [build_wheels, make_sdist]
+    runs-on: ubuntu-latest
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+    steps:
+    - name: Download dist
+      uses: actions/download-artifact@v3
+      with:
+        name: artifact
+        path: dist
+
+    - name: Download wheels
+      uses: actions/download-artifact@v3
+      with:
+        name: wheels
+        path: dist
+
+    - name: Display structure of downloaded files
+      run: ls -R
+      working-directory: dist
+
+    - uses: pypa/gh-action-pypi-publish@release/v1
+      if: github.repository_owner == 'hyperspy'
+      # See https://docs.pypi.org/trusted-publishers/using-a-publisher/
+
+  create_release:
+    # TODO: once we are happy with the workflow
+    # setup zenodo to create a DOI automatically
+    needs: upload_to_pypi
+    permissions:
+      contents: write
+    name: Create Release
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+      - name: Create Release
+        id: create_release
+        uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844

.github/workflows/tests.yml

@@ -0,0 +1,52 @@
+name: Tests
+
+on: [push, pull_request]
+
+jobs:
+  run_test_site:
+    name: ${{ matrix.os }}-py${{ matrix.PYTHON_VERSION }}${{ matrix.LABEL }}
+    runs-on: ${{ matrix.os }}-latest
+    timeout-minutes: 30
+    env:
+      MPLBACKEND: agg
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu, windows, macos]
+        PYTHON_VERSION: ['3.9', '3.10']
+        LABEL: ['']
+        include:
+          - os: ubuntu
+            PYTHON_VERSION: '3.8'
+          - os: ubuntu
+            PYTHON_VERSION: '3.11'
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: ${{ matrix.PYTHON_VERSION }}
+
+      - name: Display version
+        run: |
+          python --version
+          pip --version
+
+      - name: Install
+        shell: bash
+        run: |
+          pip install -e .[tests]
+
+      - name: Pip list
+        run: |
+          pip list
+
+      - name: Run test suite
+        run: |
+          pytest --pyargs exspy
+
+      - name: Upload coverage to Codecov
+        if: ${{ always() }}
+        uses: codecov/codecov-action@v3

setup.py

@@ -26,6 +26,12 @@
 # https://setuptools.readthedocs.io/en/latest/setuptools.html#declaring-extras-optional-features-with-their-own-dependencies
 
 extra_feature_requirements = {
+    "gui-jupyter": [
+        "hyperspy_gui_ipywidgets @ git+https://github.com/ericpre/[email protected]",
+    ],
+    "gui-traitsui": [
+        "hyperspy_gui_traitsui @ git+https://github.com/ericpre/[email protected]",
+    ],
     "doc": [
         "numpydoc",
         "pydata-sphinx-theme>=0.13",
@@ -36,6 +42,7 @@
     ],
     "tests": [
         "pytest     >= 5.0",
+        "pytest-mpl",
         "pytest-cov >= 2.8.1",
     ],
     "dev": ["black", "pre-commit >=1.16"],
@@ -58,10 +65,10 @@
     ],
     classifiers=[
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
         "Development Status :: 4 - Beta",
         "Intended Audience :: Science/Research",
         "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
@@ -76,10 +83,19 @@
     package_dir={"exspy": "exspy"},
     extras_require=extra_feature_requirements,
     install_requires=[
-        "hyperspy_gui_ipywidgets @ git+https://github.com/ericpre/[email protected]",
-        "hyperspy_gui_traitsui @ git+https://github.com/ericpre/[email protected]",
+        "dask[array]",
+        "hyperspy @ git+https://github.com/hyperspy/hyperspy@RELEASE_next_major",
+        "matplotlib",
+        "numexpr",
+        "numpy",
+        "pint",
+        "pooch",
+        "prettytable",
+        "requests",
+        "scipy",
+        "traits",
         ],
-    python_requires=">=3.7",
+    python_requires="~=3.8",
     package_data={
         "": ["LICENSE", "README.rst"],
         "exspy": [