Tests #1205
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
name: Tests | |
on: [push, pull_request, workflow_dispatch] | |
jobs: | |
run_test_site: | |
name: ${{ matrix.os }}-${{ matrix.os_version }}-py${{ matrix.PYTHON_VERSION }}${{ matrix.LABEL }} | |
runs-on: ${{ matrix.os }}-${{ matrix.os_version }} | |
timeout-minutes: 30 | |
env: | |
MPLBACKEND: agg | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ubuntu, windows, macos] | |
os_version: [latest] | |
PYTHON_VERSION: ['3.9', '3.10'] | |
LABEL: [''] | |
include: | |
# test oldest supported version of main dependencies on python 3.8 | |
- os: ubuntu | |
os_version: latest | |
PYTHON_VERSION: '3.8' | |
# Set pillow and scikit-image version to be compatible with imageio and scipy | |
# matplotlib needs 3.5 to support markers in hyperspy 2.0 (requires `collection.set_offset_transform`) | |
DEPENDENCIES: matplotlib==3.5 numpy==1.20.0 tifffile==2022.7.28 dask[array]==2021.3.1 numba==0.52 imageio==2.16 pillow==8.3.2 scikit-image==0.18.0 python-box==6.0.0 | |
LABEL: '-oldest' | |
# test minimum requirement | |
- os: ubuntu | |
os_version: latest | |
PYTHON_VERSION: '3.9' | |
LABEL: '-minimum' | |
- os: ubuntu | |
os_version: latest | |
PYTHON_VERSION: '3.12' | |
LABEL: '-minimum-without-hyperspy' | |
- os: ubuntu | |
os_version: latest | |
PYTHON_VERSION: '3.11' | |
LABEL: '-hyperspy-dev' | |
- os: ubuntu | |
os_version: latest | |
PYTHON_VERSION: '3.9' | |
LABEL: '-without-hyperspy' | |
- os: ubuntu | |
os_version: latest | |
PYTHON_VERSION: '3.8' | |
- os: ubuntu | |
os_version: latest | |
PYTHON_VERSION: '3.11' | |
- os: macos | |
os_version: '13' | |
PYTHON_VERSION: '3.11' | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 0 | |
- name: get repository name | |
shell: bash | |
run: echo "REPOSITORY_NAME=${GITHUB_REPOSITORY#*/}" >> $GITHUB_ENV | |
- name: Fetch tags upstream | |
if: ${{ github.repository_owner != 'hyperspy' }} | |
# Needs to fetch the tags from upstream to get the | |
# correct version with setuptools_scm | |
run: | | |
git remote add upstream https://github.com/hyperspy/${{ env.REPOSITORY_NAME }}.git | |
git fetch upstream --tags | |
- uses: actions/setup-python@v5 | |
name: Install Python | |
with: | |
python-version: ${{ matrix.PYTHON_VERSION }} | |
- name: Get the number of CPUs | |
id: cpus | |
run: | | |
import os, platform | |
num_cpus = os.cpu_count() | |
print(f"Number of CPU: {num_cpus}") | |
print(f"Architecture: {platform.machine()}") | |
output_file = os.environ["GITHUB_OUTPUT"] | |
with open(output_file, "a", encoding="utf-8") as output_stream: | |
output_stream.write(f"count={num_cpus}\n") | |
shell: python | |
- name: Set Environment Variable | |
shell: bash | |
# Set PIP_SELECTOR environment variable according to matrix.LABEL | |
run: | | |
if [[ -n "${{ matrix.LABEL }}" && "${{ matrix.LABEL }}" == *"minimum"* ]]; then | |
PIP_SELECTOR="[tests]" | |
else | |
PIP_SELECTOR="[all, tests]" | |
fi | |
echo "PIP_SELECTOR=${PIP_SELECTOR}" >> $GITHUB_ENV | |
- name: Display version | |
run: | | |
python --version | |
pip --version | |
- name: Install oldest supported version | |
if: contains(matrix.LABEL, 'oldest') | |
run: | | |
pip install ${{ matrix.DEPENDENCIES }} | |
- name: Install hyperspy and exspy | |
if: ${{ ! contains(matrix.LABEL, 'without-hyperspy') }} | |
run: | | |
pip install hyperspy exspy | |
- name: Install hyperspy and exspy (dev) | |
if: ${{ contains(matrix.LABEL, 'hyperspy-dev') }} | |
run: | | |
pip install git+https://github.com/hyperspy/hyperspy.git | |
pip install git+https://github.com/hyperspy/exspy.git | |
- name: Install pint and python-mrcz dev | |
# for numpy 2.0 support for python >= 3.9 | |
# https://github.com/em-MRCZ/python-mrcz/pull/15 | |
# https://github.com/hgrecco/pint/issues/1974 | |
if: ${{ ! contains(matrix.LABEL, 'oldest') && matrix.PYTHON_VERSION != '3.8' }} | |
run: | | |
pip install git+https://github.com/ericpre/python-mrcz.git@numpy2.0_and_deprecation_fixes | |
pip install git+https://github.com/hgrecco/pint | |
- name: Install | |
shell: bash | |
run: | | |
pip install --upgrade -e .'${{ env.PIP_SELECTOR }}' | |
- name: Uninstall pyUSID | |
# remove when pyUSID supports numpy 2 | |
if: ${{ ! contains(matrix.LABEL, 'oldest') && matrix.PYTHON_VERSION != '3.8' }} | |
run: | | |
pip uninstall -y pyUSID | |
- name: Install numpy 2.0 | |
if: ${{ ! contains(matrix.LABEL, 'oldest') && matrix.PYTHON_VERSION != '3.8' }} | |
run: | | |
pip install numpy==2 | |
- name: Pip list | |
run: | | |
pip list | |
- name: Run test suite | |
run: | | |
pytest --pyargs rsciio --reruns 3 -n ${{ steps.cpus.outputs.count }} --cov=. --cov-report=xml | |
- name: Upload coverage to Codecov | |
if: ${{ always() }} | |
uses: codecov/codecov-action@v4 | |
env: | |
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |