Adds Docker build and GHA test of container #58
Workflow file for this run
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# Workflow to build nii2dcm, run unit tests and then execute command line interface (CLI) end-to-end | |
name: Build & Test nii2dcm | |
on: | |
pull_request: | |
jobs: | |
venv-build-and-test: | |
name: venv + E2E | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ ubuntu-latest ] | |
python-version: [ '3.9' ] | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Install Python packages | |
run: | | |
python -m pip install --upgrade pip | |
pip install setuptools wheel | |
pip install flake8 pytest pytest-cov | |
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
- name: Display installed pip packages | |
run: | | |
pip list | |
- name: Setup flake8 annotations | |
uses: rbialon/flake8-annotations@v1 | |
- name: Lint with flake8 | |
run: | | |
# stop the build if there are Python syntax errors or undefined names | |
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
- name: Build nii2dcm | |
run: | | |
pip install . | |
- name: Test nii2dcm install | |
run: | | |
nii2dcm -h | |
nii2dcm -v | |
- name: Run unit tests | |
run: | | |
pytest tests/ | |
- name: Test DicomMRISVR creation | |
run: | | |
# run nii2dcm | |
mkdir output | |
nii2dcm tests/data/DicomMRISVR/t2-svr-atlas-35wk.nii.gz ./output -d SVR | |
ls ./output | |
# assert DICOM files exist | |
[ -f "./output/IM_0001.dcm" ] && echo "Output DICOM file exists" || exit 1 | |
- name: Build pytest coverage file | |
run: | | |
pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=nii2dcm tests/ | tee pytest-coverage.txt ; echo $? | |
- name: Pytest coverage comment | |
id: coverageComment | |
uses: MishaKav/pytest-coverage-comment@main | |
with: | |
pytest-coverage-path: ./pytest-coverage.txt | |
junitxml-path: ./pytest.xml | |
default-branch: unit-tests | |
- name: Update Coverage Badge | |
uses: schneegans/[email protected] | |
with: | |
auth: ${{ secrets.PYTEST_COVERAGE_COMMENT }} | |
gistID: 57ef8057d04f67dbe6e64df410b83079 | |
filename: nii2dcm-pytest-coverage-comment.json | |
label: Coverage Report | |
message: ${{ steps.coverageComment.outputs.coverage }} | |
color: ${{ steps.coverageComment.outputs.color }} | |
namedLogo: python | |
container-build-and-test: | |
name: Container | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ ubuntu-latest ] | |
python-version: [ '3.9' ] | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- name: Build container | |
run: | | |
docker build -t nii2dcm --progress=plain --no-cache . | |
docker ps | |
- name: Test nii2dcm container | |
run: | | |
docker run nii2dcm -h | |
echo "nii2dcm version:" | |
docker run nii2dcm -v |