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": [