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Update gitignore (#537) #1160

Update gitignore (#537)

Update gitignore (#537) #1160

Workflow file for this run

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", "3.12"] # Check against oldest and newest versions
jax: ["", "_jax"]
exclude: # Skip win + jax
- jax: "_jax"
os: windows-latest
env:
PYVER: ${{ matrix.python-version }}
CI_OS: ${{ matrix.os }}
PACKAGE: "pymbar"
steps:
- name: Checkout the code
uses: actions/checkout@v3
- name: Additional info about the build
shell: bash
run: |
uname -a
df -h
ulimit -a
- name: Setup Conda via Mamba
uses: mamba-org/setup-micromamba@v1
with:
environment-file: devtools/conda-envs/test_env${{ matrix.jax }}.yaml
environment-name: test
condarc: |
channels:
- conda-forge
- defaults
create-args: >-
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"