[pre-commit.ci] auto fixes from pre-commit.com hooks #197
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name: Tests | |
on: | |
pull_request: | |
push: | |
branches-ignore: | |
- 'dependabot/**' | |
- 'pre-commit-ci-update-config' | |
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: '3.9' | |
# Set pillow and scikit-image version to be compatible with imageio and scipy | |
# align matplotlib dependency with hyperspy | |
DEPENDENCIES: matplotlib==3.6 numpy==1.20.0 tifffile==2022.7.28 dask[array]==2021.5.1 distributed==2021.5.1 numba==0.53 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: '3.10' | |
LABEL: '-minimum' | |
- os: ubuntu | |
os_version: latest | |
PYTHON_VERSION: '3.12' | |
LABEL: '-hyperspy-dev' | |
- os: ubuntu | |
os_version: latest | |
PYTHON_VERSION: '3.10' | |
LABEL: '-without-hyperspy' | |
- os: ubuntu | |
os_version: latest | |
PYTHON_VERSION: '3.9' | |
- os: ubuntu | |
os_version: latest | |
PYTHON_VERSION: '3.12' | |
- os: ubuntu | |
os_version: latest | |
PYTHON_VERSION: '3.13' | |
# can remove minimum dependencies when numba supports 3.13 | |
LABEL: '-minimum' | |
- os: macos | |
os_version: latest | |
PYTHON_VERSION: '3.13' | |
# can remove minimum dependencies when numba supports 3.13 | |
LABEL: '-minimum' | |
- os: windows | |
os_version: latest | |
PYTHON_VERSION: '3.13' | |
# can remove minimum dependencies when numba supports 3.13 | |
LABEL: '-minimum' | |
- os: macos | |
os_version: '13' | |
PYTHON_VERSION: '3.12' | |
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: ${{ matrix.PYTHON_VERSION }} | |
cache: 'pip' | |
- name: Get the number of CPUs | |
id: cpus | |
run: | | |
import os, platform | |
num_cpus = os.cpu_count() | |
print(f"Number of CPU: {num_cpus}") | |
print(f"Architecture: {platform.machine()}") | |
output_file = os.environ["GITHUB_OUTPUT"] | |
with open(output_file, "a", encoding="utf-8") as output_stream: | |
output_stream.write(f"count={num_cpus}\n") | |
shell: python | |
- name: Set Environment Variable | |
shell: bash | |
# Set PIP_SELECTOR environment variable according to matrix.LABEL | |
run: | | |
if [[ -n "${{ 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 traits dev for python 3.13 | |
if: ${{ matrix.PYTHON_VERSION == '3.13' }} | |
run: | | |
# traits release with python 3.13 pending | |
pip install git+https://github.com/enthought/traits.git | |
- name: Install hyperspy and exspy | |
if: ${{ ! contains(matrix.LABEL, 'without-hyperspy') && matrix.PYTHON_VERSION != '3.13'}} | |
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 hyperspy (python 3.13) and exspy (dev) | |
if: ${{ matrix.PYTHON_VERSION == '3.13' }} | |
run: | | |
# speed up installing scikit-image using pre-release with python 3.13 wheels | |
pip install scikit-image --pre | |
pip install git+https://github.com/ericpre/hyperspy.git@python313 | |
pip install git+https://github.com/hyperspy/exspy.git | |
- name: Install python-mrcz dev | |
# for numpy 2.0 support for python >= 3.9 | |
# https://github.com/em-MRCZ/python-mrcz/pull/15 | |
if: ${{ ! contains(matrix.LABEL, 'oldest') && ! contains(matrix.LABEL, 'minimum') }} | |
run: | | |
pip install git+https://github.com/ericpre/[email protected]_and_deprecation_fixes | |
- name: Install | |
shell: bash | |
run: | | |
pip install --upgrade -e .'${{ 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 oldest supported version | |
if: contains(matrix.LABEL, 'oldest') | |
run: | | |
pip install ${{ matrix.DEPENDENCIES }} | |
- 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@v5 | |
env: | |
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |