temporarily depend on numpy<2 (#448) #656
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name: Test (and Deploy to PyPI on tag) | |
on: | |
# Only run on pushes to main, or when version tags are pushed | |
push: | |
branches: | |
- "main" | |
tags: | |
- "v**" | |
# Run on all pull-requests | |
pull_request: | |
# Allow workflow dispatch from GitHub | |
workflow_dispatch: | |
concurrency: | |
# Cancel this workflow if it is running, | |
# and then changes are applied on top of the HEAD of the branch, | |
# triggering another run of the workflow | |
group: ${{ github.workflow }}-${{ github.ref }} | |
cancel-in-progress: true | |
jobs: | |
linting: | |
runs-on: ubuntu-latest | |
name: Check Linting | |
steps: | |
- uses: neuroinformatics-unit/actions/lint@v2 | |
manifest: | |
name: Check Manifest | |
runs-on: ubuntu-latest | |
steps: | |
- uses: neuroinformatics-unit/actions/check_manifest@v2 | |
test: | |
needs: [linting, manifest] | |
name: Run package tests | |
timeout-minutes: 60 | |
runs-on: ${{ matrix.os }} | |
env: | |
KERAS_BACKEND: torch | |
CELLFINDER_TEST_DEVICE: cpu | |
strategy: | |
matrix: | |
# Run all supported Python versions on linux | |
os: [ubuntu-latest] | |
python-version: ["3.10", "3.11", "3.12"] | |
# Include one windows and two macOS (intel based and arm based) runs | |
include: | |
- os: macos-13 | |
python-version: "3.12" | |
- os: macos-latest | |
python-version: "3.12" | |
- os: windows-latest | |
python-version: "3.12" | |
steps: | |
- name: Cache brainglobe directory | |
uses: actions/cache@v3 | |
with: | |
path: | # ensure we don't cache any interrupted atlas download and extraction, if e.g. we cancel the workflow manually | |
~/.brainglobe | |
!~/.brainglobe/atlas.tar.gz | |
key: brainglobe | |
# Setup pyqt libraries | |
- name: Setup qtpy libraries | |
uses: tlambert03/setup-qt-libs@v1 | |
# Setup VTK with headless display | |
- uses: pyvista/setup-headless-display-action@v2 | |
# Run all tests | |
- uses: neuroinformatics-unit/actions/test@v2 | |
with: | |
python-version: ${{ matrix.python-version }} | |
secret-codecov-token: ${{ secrets.CODECOV_TOKEN }} | |
use-xvfb: true | |
test_numba_disabled: | |
needs: [linting, manifest] | |
name: Run tests with numba disabled | |
timeout-minutes: 60 | |
runs-on: ubuntu-latest | |
env: | |
NUMBA_DISABLE_JIT: "1" | |
steps: | |
- name: Cache brainglobe directory | |
uses: actions/cache@v3 | |
with: | |
path: | # ensure we don't cache any interrupted atlas download and extraction, if e.g. we cancel the workflow manually | |
~/.brainglobe | |
!~/.brainglobe/atlas.tar.gz | |
key: brainglobe | |
# Setup pyqt libraries | |
- name: Setup qtpy libraries | |
uses: tlambert03/setup-qt-libs@v1 | |
# Setup VTK with headless display | |
- uses: pyvista/setup-headless-display-action@v2 | |
# Run test suite with numba disabled | |
- uses: neuroinformatics-unit/actions/test@v2 | |
with: | |
python-version: "3.12" | |
secret-codecov-token: ${{ secrets.CODECOV_TOKEN }} | |
codecov-flags: "numba" | |
# Run brainglobe-workflows brainmapper-CLI tests to check for | |
# breakages | |
test_brainmapper_cli: | |
needs: [linting, manifest] | |
name: Run brainmapper tests to check for breakages | |
timeout-minutes: 60 | |
runs-on: ubuntu-latest | |
env: | |
KERAS_BACKEND: torch | |
CELLFINDER_TEST_DEVICE: cpu | |
steps: | |
- name: Cache brainglobe directory | |
uses: actions/cache@v3 | |
with: | |
path: | # ensure we don't cache any interrupted atlas download and extraction, if e.g. we cancel the workflow manually | |
~/.brainglobe | |
!~/.brainglobe/atlas.tar.gz | |
key: brainglobe | |
- name: Checkout brainglobe-workflows | |
uses: actions/checkout@v3 | |
with: | |
repository: 'brainglobe/brainglobe-workflows' | |
- name: Set up Python 3.12 | |
uses: actions/setup-python@v3 | |
with: | |
python-version: "3.12" | |
- name: Install test dependencies | |
run: | | |
python -m pip install --upgrade pip wheel | |
# Install cellfinder from the latest SHA on this branch | |
python -m pip install "cellfinder @ git+$GITHUB_SERVER_URL/$GITHUB_REPOSITORY@$GITHUB_SHA" | |
# Install checked out copy of brainglobe-workflows | |
python -m pip install .[dev] | |
- name: Run brainmapper tests in brainglobe-workflows | |
run: | | |
python -m pytest --color=yes -v tests/brainmapper | |
build_sdist_wheel: | |
name: Build source distribution and wheel | |
needs: [test, test_numba_disabled] | |
if: github.event_name == 'push' && github.ref_type == 'tag' | |
runs-on: ubuntu-latest | |
steps: | |
- uses: neuroinformatics-unit/actions/build_sdist_wheels@v2 | |
upload_all: | |
name: Publish build distributions | |
needs: [build_sdist_wheel] | |
if: github.event_name == 'push' && github.ref_type == 'tag' | |
runs-on: ubuntu-latest | |
steps: | |
- uses: neuroinformatics-unit/actions/upload_pypi@v2 | |
with: | |
secret-pypi-key: ${{ secrets.TWINE_API_KEY }} |