CI #783
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name: CI | |
on: | |
push: | |
branches: | |
- 'master' | |
- 'pymbar4' | |
- 'gha' | |
pull_request: | |
branches: | |
- 'master' | |
- 'pymbar4' | |
- 'gha' | |
schedule: | |
# Nightly Tests | |
- cron: '0 0 * * *' | |
jobs: | |
test: | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [macOS-latest, ubuntu-latest, windows-latest] | |
python-version: [3.8, 3.11] # Check against oldest and newest versions | |
jax: ["", "_jax"] | |
exclude: # Skip win + jax | |
- jax: "_jax" | |
os: windows-latest | |
env: | |
PYVER: ${{ matrix.python-version }} | |
CI_OS: ${{ matrix.os }} | |
PACKAGE: "pymbar" | |
steps: | |
- name: Checkout the code | |
uses: actions/checkout@v3 | |
- name: Additional info about the build | |
shell: bash | |
run: | | |
uname -a | |
df -h | |
ulimit -a | |
- name: Setup Conda via Mamba | |
uses: mamba-org/provision-with-micromamba@main | |
with: | |
environment-file: devtools/conda-envs/test_env${{ matrix.jax }}.yaml | |
environment-name: test | |
channels: conda-forge,defaults | |
extra-specs: | | |
python=${{ matrix.python-version }} | |
- name: Install package | |
shell: bash -l {0} | |
run: | | |
python -m pip install . --no-deps | |
micromamba list | |
- name: Run tests (pytest) | |
shell: bash -l {0} | |
run: | | |
pytest -v --cov=$PACKAGE --cov-report=xml --color=yes --doctest-modules $PACKAGE/ | |
- name: Run examples | |
shell: bash -l {0} | |
run: | | |
### constant-force-optical-trap | |
cd examples/constant-force-optical-trap | |
python extract-data.py | |
python force-bias-optical-trap.py | |
### harmonic-oscillators | |
cd ../harmonic-oscillators | |
python harmonic-oscillators.py | |
python harmonic-oscillators-distributions.py | |
cd ../heat-capacity | |
python heat-capacity.py -b 2 | |
### parallel-tempering-2dfes | |
cd ../parallel-tempering-2dfes | |
python parallel-tempering-2dfes.py | |
### umbrella-sampling-fes | |
cd ../umbrella-sampling-fes | |
python umbrella-sampling.py | |
python umbrella-sampling-advanced-fes.py | |
- name: CodeCov | |
uses: codecov/codecov-action@v1 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
file: ./coverage.xml | |
flags: unittests | |
yml: ./.codecov.yml | |
lint-format: | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
python-version: [3.8] | |
env: | |
PACKAGE: "pymbar" | |
steps: | |
- name: Checkout the code | |
uses: actions/checkout@v1 | |
- name: Setup Conda via Mamba | |
uses: mamba-org/provision-with-micromamba@main | |
with: | |
environment-file: devtools/conda-envs/test_env.yaml | |
environment-name: test | |
channels: conda-forge,defaults | |
extra-specs: | | |
python=${{ matrix.python-version }} | |
- name: Install linter and formatter | |
shell: bash -l {0} | |
run: | | |
micromamba install pylint black | |
- name: Run pylint | |
shell: bash -l {0} | |
run: | | |
pylint $PACKAGE/ | |
# Black has a default --exclude which reads .gitignore. | |
# Black's --exclude and --extend-exclude are single specified RegEx patterns and overwrite if multi-marked. | |
- name: Run black check | |
shell: bash -l {0} | |
if: always() | |
run: | | |
black --check -l 99 $PACKAGE/ examples/ --extend-exclude "$PACKAGE/_version.py" |