ANY -> OPTIONAL for sessions and runs #118
Workflow file for this run
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--- | |
on: | |
push: | |
branches: | |
- main | |
- maint/* | |
tags: | |
- '*' | |
pull_request: | |
branches: | |
- main | |
- maint/* | |
defaults: | |
run: | |
shell: bash | |
concurrency: | |
group: ${{ github.workflow }}-${{ github.ref }} | |
cancel-in-progress: true | |
permissions: | |
contents: read | |
jobs: | |
check_skip_flags: | |
name: Check skip flags | |
runs-on: ubuntu-latest | |
outputs: | |
head-commit-message: ${{ steps.get_head_commit_message.outputs.headCommitMsg }} | |
steps: | |
- name: Get repo | |
uses: actions/checkout@v3 | |
with: | |
ref: ${{ github.event.pull_request.head.sha }} | |
- name: Print head git commit message | |
id: get_head_commit_message | |
run: echo "headCommitMsg=$(git show -s --format=%s)" >> $GITHUB_OUTPUT | |
download-test-data: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- uses: actions/cache@v3 | |
id: cache | |
env: | |
cache-name: ds000017 | |
with: | |
path: /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data | |
key: ${{ env.cache-name }} | |
- if: ${{ steps.cache.outputs.cache-hit != 'true' }} | |
name: Download fmriprep derivative of ds000017 | |
id: download | |
run: | | |
mkdir -p /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data | |
cd /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data | |
wget --retry-connrefused \ | |
--waitretry=5 \ | |
--read-timeout=20 \ | |
--timeout=15 \ | |
-t 0 \ | |
-q \ | |
-O ds000017.tar.gz \ | |
"https://zenodo.org/record/8091903/files/ds000017-fmriprep22.0.1-downsampled-nosurface.tar.gz?download=1" | |
tar -xzf ds000017.tar.gz | |
rm ds000017.tar.gz | |
build: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: 3 | |
- run: pip install --upgrade build twine | |
- name: Build sdist and wheel | |
run: python -m build | |
- run: twine check dist/* | |
- name: Upload sdist and wheel artifacts | |
uses: actions/upload-artifact@v3 | |
with: | |
name: dist | |
path: dist/ | |
- name: Build git archive | |
run: mkdir archive && git archive -v -o archive/archive.tgz HEAD | |
- name: Upload git archive artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: archive | |
path: archive/ | |
test-package: | |
runs-on: ubuntu-latest | |
needs: [build] | |
strategy: | |
matrix: | |
package: [wheel, sdist, archive] | |
steps: | |
- name: Download sdist and wheel artifacts | |
if: matrix.package != 'archive' | |
uses: actions/download-artifact@v3 | |
with: | |
name: dist | |
path: dist/ | |
- name: Download git archive artifact | |
if: matrix.package == 'archive' | |
uses: actions/download-artifact@v3 | |
with: | |
name: archive | |
path: archive/ | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: 3 | |
- name: Display Python version | |
run: python -c "import sys; print(sys.version)" | |
- name: Update pip | |
run: pip install --upgrade pip | |
- name: Install wheel | |
if: matrix.package == 'wheel' | |
run: pip install dist/*.whl | |
- name: Install sdist | |
if: matrix.package == 'sdist' | |
run: pip install dist/*.tar.gz | |
- name: Install archive | |
if: matrix.package == 'archive' | |
run: pip install archive/archive.tgz | |
test-coverage: | |
runs-on: ubuntu-latest | |
needs: [build, download-test-data, check_skip_flags] | |
strategy: | |
matrix: | |
python-version: ['3.8', '3.9', '3.10', '3.11'] | |
steps: | |
- uses: actions/checkout@v2 | |
name: Set up Python ${{ matrix.python-version }} | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Restore cached data ds000017 | |
id: cache | |
uses: actions/cache/restore@v3 | |
with: | |
path: /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data | |
key: ds000017 | |
- name: Install build dependencies | |
run: python -m pip install --upgrade pip | |
- name: Install task package | |
run: pip install -e .[test] | |
- name: Test with pytest - ignore smoke test. | |
if: ${{ !contains(needs.check_skip_flags.outputs.head-commit-message, 'full_test') }} | |
run: | | |
pytest -m "not smoke" --cov=giga_connectome --cov-report=xml --doctest-modules -v --pyargs giga_connectome | |
- name: Full test - run all the test to generate accurate coverage report. | |
if: ${{ contains(needs.check_skip_flags.outputs.head-commit-message, 'full_test') }} || ${{ github.event.pull_request.merged }} | |
run: pytest --cov=giga_connectome --cov-report=xml --doctest-modules -v --pyargs giga_connectome | |
- uses: codecov/codecov-action@v3 | |
if: ${{ always() }} | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
docker: | |
# build and test docker image | |
if: ${{ contains(needs.check_skip_flags.outputs.head-commit-message, 'full_test') }} | |
runs-on: ubuntu-latest | |
needs: [download-test-data, check_skip_flags] | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Build the Docker image | |
run: | | |
user_name="bids" | |
docker build . --file Dockerfile --tag ${user_name}/giga_connectome | |
mkdir -p "${HOME}/docker" | |
docker save "${user_name}/giga_connectome" > "${HOME}/docker/image.tar" | |
- name: Restore cached data ds000017 | |
id: cache | |
uses: actions/cache/restore@v3 | |
with: | |
path: /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data | |
key: ds000017 | |
- name: Test the Docker image | |
run: | | |
docker load -i ${HOME}/docker/image.tar | |
docker run --rm --read-only \ | |
-v /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data:/test_data \ | |
-v ./outputs:/outputs \ | |
-v ./outputs/working_dir:/work \ | |
bids/giga_connectome \ | |
/test_data/ds000017-fmriprep22.0.1-downsampled-nosurface \ | |
/outputs \ | |
participant \ | |
-w /work \ | |
--participant_label 1 \ | |
--reindex-bids | |
- name: Upload output artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: connectome | |
path: ./outputs/ | |
- name: Upload docker image artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: docker-image | |
path: ${HOME}/docker/image.tar | |
# publish: | |
# runs-on: ubuntu-latest | |
# needs: [test-package, test-coverage] | |
# if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/') | |
# steps: | |
# - uses: actions/download-artifact@v3 | |
# with: | |
# name: dist | |
# path: dist/ | |
# - uses: pypa/gh-action-pypi-publish@release/v1 | |
# with: | |
# user: __token__ | |
# password: ${{ secrets.PYPI_API_TOKEN }} |