tests #395
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name: tests | |
on: | |
push: | |
branches: | |
- "main" | |
tags: | |
- "*" | |
pull_request: | |
schedule: | |
# Runs at 6:10am UTC on Monday | |
- cron: '10 6 * * 1' | |
workflow_dispatch: | |
env: | |
REGISTRY: ghcr.io | |
IMAGE_NAME: ${{ github.repository }} | |
jobs: | |
linting: | |
name: Linting | |
runs-on: ubuntu-latest | |
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: ${{ matrix.os }} py${{ matrix.python-version }} | |
runs-on: ${{ matrix.os }} | |
env: | |
KERAS_BACKEND: torch | |
strategy: | |
fail-fast: false | |
matrix: | |
# Run tests on ubuntu across all supported versions | |
python-version: ["3.10", "3.11", "3.12"] | |
os: [ubuntu-latest] | |
# Include a Windows test and new Mac runs | |
include: | |
- os: macos-latest | |
python-version: "3.12" | |
- os: windows-latest | |
python-version: "3.12" | |
steps: | |
# Cache atlases | |
- 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: atlases-models | |
fail-on-cache-miss: true | |
enableCrossOsArchive: true | |
# install additional Macos dependencies | |
- name: install HDF5 libraries (needed on M1 Macs only) | |
if: matrix.os == 'macos-latest' | |
run: | | |
brew install hdf5 | |
# Cache cellfinder workflow data | |
- name: Cache data for cellfinder workflow tests | |
uses: actions/cache@v3 | |
with: | |
path: "~/.brainglobe-tests" | |
key: cellfinder-test-data | |
fail-on-cache-miss: true | |
enableCrossOsArchive: true | |
# Run tests | |
- uses: neuroinformatics-unit/actions/test@v2 | |
with: | |
python-version: ${{ matrix.python-version }} | |
secret-codecov-token: ${{ secrets.CODECOV_TOKEN }} | |
- name: Notify slack on scheduled failure | |
if: failure() && github.event_name == 'schedule' | |
uses: ravsamhq/notify-slack-action@v2 | |
with: | |
status: ${{ job.status }} # required | |
notify_when: 'failure' | |
env: | |
SLACK_WEBHOOK_URL: ${{ secrets.SLACK_NOTIFYBOT_WEBHOOK_URL }} # required | |
benchmarks: | |
name: Check benchmarks | |
runs-on: ubuntu-latest | |
# Set shell in login mode as global setting for the job | |
defaults: | |
run: | |
shell: bash -l {0} | |
strategy: | |
matrix: | |
python-version: ["3.12"] | |
steps: | |
- name: Checkout brainglobe-workflows repository | |
uses: actions/checkout@v4 | |
- name: Create and activate conda environment # we need conda for asv management of environments | |
uses: conda-incubator/[email protected] # see https://github.com/conda-incubator/setup-miniconda/issues/261 | |
with: | |
miniconda-version: py310_24.1.2-0 # we need conda<24.3, see https://github.com/airspeed-velocity/asv/pull/1397 | |
python-version: ${{ matrix.python-version }} | |
activate-environment: asv-only | |
- name: Install asv | |
run: | | |
pip install --upgrade pip | |
pip install asv | |
- name: Run asv check with pip dependencies | |
working-directory: ${{ github.workspace }}/benchmarks | |
run: | | |
# check benchmarks with pip dependencies | |
asv check -v --config $GITHUB_WORKSPACE/benchmarks/asv.pip.conf.json | |
- name: Run asv check with latest-github dependencies | |
working-directory: ${{ github.workspace }}/benchmarks | |
run: | | |
# check benchmarks with latest-github dependencies | |
asv check -v --config $GITHUB_WORKSPACE/benchmarks/asv.latest-github.conf.json | |
build_sdist_wheels: | |
name: Build source distribution | |
needs: [test] | |
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_wheels] | |
runs-on: ubuntu-latest | |
if: github.event_name == 'push' && github.ref_type == 'tag' | |
steps: | |
- uses: neuroinformatics-unit/actions/upload_pypi@v2 | |
with: | |
secret-pypi-key: ${{ secrets.TWINE_API_KEY }} |