ci: smoke test with/out optional dependencies, mark more tests #1050
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name: FloPy continuous integration | |
on: | |
push: | |
branches: | |
- master | |
- develop | |
- ci-diagnose* | |
- notebooks | |
pull_request: | |
branches: | |
- master | |
- develop | |
jobs: | |
build: | |
name: Build | |
runs-on: ubuntu-latest | |
defaults: | |
run: | |
shell: bash | |
timeout-minutes: 10 | |
steps: | |
- name: Checkout repo | |
uses: actions/checkout@v3 | |
- name: Setup Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: 3.8 | |
cache: 'pip' | |
cache-dependency-path: pyproject.toml | |
- name: Install Python dependencies | |
run: | | |
pip install --upgrade pip | |
pip install build twine | |
pip install . | |
python -c "import flopy; print(f'{flopy.__version__}')" | |
- name: Build package | |
run: | | |
python -m build | |
- name: Check package | |
run: | | |
twine check --strict dist/* | |
lint: | |
name: Lint | |
runs-on: ubuntu-latest | |
defaults: | |
run: | |
shell: bash | |
timeout-minutes: 10 | |
steps: | |
- name: Checkout repo | |
uses: actions/checkout@v3 | |
- name: Setup Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: 3.8 | |
cache: 'pip' | |
cache-dependency-path: pyproject.toml | |
- name: Install Python dependencies | |
run: | | |
pip install . | |
pip install ".[lint]" | |
- name: Run isort | |
run: | | |
echo "if isort check fails update isort using" | |
echo " pip install isort --upgrade" | |
echo "and run" | |
echo " isort ./flopy" | |
echo "and then commit the changes." | |
isort --check --diff ./flopy | |
- name: Run black | |
run: | | |
echo "if black check fails update black using" | |
echo " pip install black --upgrade" | |
echo "and run" | |
echo " black ./flopy" | |
echo "and then commit the changes." | |
black --check --diff ./flopy | |
- name: Run flake8 | |
run: | | |
flake8 --count --show-source --exit-zero ./flopy | |
- name: Run pylint | |
run: | | |
pylint --jobs=2 --errors-only --exit-zero ./flopy | |
- name: Check CITATION.cff | |
run: | | |
cffconvert --validate | |
cffconvert -f apalike | |
cffconvert -f bibtex | |
smoke: | |
name: Smoke test | |
runs-on: ubuntu-latest | |
defaults: | |
run: | |
shell: bash | |
timeout-minutes: 10 | |
env: | |
PYTHON_VERSION: 3.8 | |
strategy: | |
fail-fast: false | |
matrix: | |
optdeps: | |
- "all optional dependencies" | |
- "no optional dependencies" | |
- "some optional dependencies" | |
steps: | |
- name: Checkout repo | |
uses: actions/checkout@v3 | |
- name: Setup Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ env.PYTHON_VERSION }} | |
cache: 'pip' | |
cache-dependency-path: pyproject.toml | |
- name: Install Python dependencies | |
run: | | |
pip install --upgrade pip | |
pip install . | |
pip install ".[test]" | |
# Install optional dependencies according to matrix.optdeps. | |
# If matrix.optdeps is "some" remove 3 optional dependencies | |
# selected randomly using the current date as the seed. | |
if [[ ! "${{ matrix.optdeps }}" == *"no"* ]]; then | |
pip install ".[optional]" | |
fi | |
if [[ "${{ matrix.optdeps }}" == *"some"* ]]; then | |
deps=$(sed '/optional =/,/]/!d' pyproject.toml | sed -e '1d;$d' -e 's/\"//g' -e 's/,//g' | tr -d ' ' | cut -f 1 -d ';') | |
rmvd=$(echo $deps | tr ' ' '\n' | shuf --random-source <(yes date +%d.%m.%y) | head -n 3) | |
echo "Removing optional dependencies: $rmvd" >> removed_dependencies.txt | |
cat removed_dependencies.txt | |
pip uninstall --yes $rmvd | |
fi | |
- name: Upload removed dependencies log | |
uses: actions/upload-artifact@v3 | |
with: | |
name: smoke-test-removed-dependencies | |
path: ./removed_dependencies.txt | |
- name: Install Modflow executables | |
uses: modflowpy/install-modflow-action@v1 | |
- name: Smoke test (${{ matrix.optdeps }}) | |
working-directory: autotest | |
run: pytest -v -n=auto --smoke --cov=flopy --cov-report=xml --durations=0 --keep-failed=.failed | |
env: | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
- name: Upload failed test outputs | |
uses: actions/upload-artifact@v3 | |
if: failure() | |
with: | |
name: failed-smoke-${{ runner.os }}-${{ env.PYTHON_VERSION }} | |
path: ./autotest/.failed/** | |
# - name: Upload coverage | |
# if: github.repository_owner == 'modflowpy' && (github.event_name == 'push' || github.event_name == 'pull_request') | |
# uses: codecov/codecov-action@v3 | |
# with: | |
# files: ./autotest/coverage.xml | |
test: | |
name: Test | |
needs: smoke | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ ubuntu-latest, macos-latest, windows-latest ] | |
python-version: [ 3.8, 3.9, "3.10", "3.11" ] | |
exclude: | |
# avoid shutil.copytree infinite recursion bug | |
# https://github.com/python/cpython/pull/17098 | |
- python-version: '3.8.0' | |
defaults: | |
run: | |
shell: bash | |
timeout-minutes: 45 | |
steps: | |
- name: Checkout repo | |
uses: actions/checkout@v3 | |
- name: Setup Python | |
if: runner.os != 'Windows' | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
cache: 'pip' | |
cache-dependency-path: pyproject.toml | |
- name: Install Python dependencies | |
if: runner.os != 'Windows' | |
run: | | |
pip install --upgrade pip | |
pip install . | |
pip install ".[test, optional]" | |
- name: Setup Micromamba | |
if: runner.os == 'Windows' | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: etc/environment.yml | |
cache-environment: true | |
cache-downloads: true | |
create-args: >- | |
python=${{ matrix.python-version }} | |
init-shell: >- | |
bash | |
powershell | |
- name: Install Python dependencies | |
shell: bash -l {0} | |
if: runner.os == 'Windows' | |
run: | | |
pip install xmipy | |
pip install . | |
- name: Install Modflow-related executables | |
uses: modflowpy/install-modflow-action@v1 | |
- name: Install Modflow dev build executables | |
uses: modflowpy/install-modflow-action@v1 | |
with: | |
repo: modflow6-nightly-build | |
- name: Update FloPy packages | |
if: runner.os != 'Windows' | |
run: python -c 'import flopy; flopy.mf6.utils.generate_classes(ref="develop", backup=False)' | |
- name: Update FloPy packages | |
if: runner.os == 'Windows' | |
shell: bash -l {0} | |
run: python -c 'import flopy; flopy.mf6.utils.generate_classes(ref="develop", backup=False)' | |
- name: Run tests | |
if: runner.os != 'Windows' | |
working-directory: ./autotest | |
run: | | |
pytest -v -m="not example and not regression" -n=auto --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile | |
coverage report | |
env: | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
- name: Run tests | |
if: runner.os == 'Windows' | |
shell: bash -l {0} | |
working-directory: ./autotest | |
run: | | |
pytest -v -m="not example and not regression" -n=auto --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile | |
coverage report | |
env: | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
- name: Upload failed test outputs | |
uses: actions/upload-artifact@v3 | |
if: failure() | |
with: | |
name: failed-${{ matrix.os }}-${{ matrix.python-version }} | |
path: | | |
./autotest/.failed/** | |
- name: Upload coverage | |
if: github.repository_owner == 'modflowpy' && (github.event_name == 'push' || github.event_name == 'pull_request') | |
uses: codecov/codecov-action@v3 | |
with: | |
files: ./autotest/coverage.xml |