Skip to content

fix #216: angle parameters are not being read from topology file #274

fix #216: angle parameters are not being read from topology file

fix #216: angle parameters are not being read from topology file #274

Workflow file for this run

name: CI
on:
# run every month on day 14 and 28 at 4:44 UTC
schedule:
- cron: "44 4 14,28 * *"
push:
branches:
- "main"
pull_request:
branches:
- "main"
concurrency:
group: "${{ github.ref }}-${{ github.head_ref }}"
cancel-in-progress: true
defaults:
run:
shell: bash -l {0}
jobs:
test:
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest, macOS-latest]
python-version: ["2.7", "3.6", "3.7", "3.8", "3.9", "3.10", "3.11"]
gromacs-version: ["2021.1"]
# Test other GROMACS versions selectively on a recent Python.
# On macOS only test one GROMACS version and two Python versions
# to keep the testing matrix manageable.
exclude:
- os: macOS-latest
python-version: "3.6"
- os: macOS-latest
python-version: "3.7"
- os: macOS-latest
python-version: "3.8"
- os: macOS-latest
python-version: "3.9"
- os: macOS-latest
python-version: "3.10"
include:
- os: ubuntu-latest
python-version: "2.7"
gromacs-version: "4.6.5"
- os: ubuntu-latest
python-version: "3.11"
gromacs-version: "4.6.5"
- os: ubuntu-latest
python-version: "3.11"
gromacs-version: "2018.6"
- os: ubuntu-latest
python-version: "3.11"
gromacs-version: "2019.1"
- os: ubuntu-latest
python-version: "3.11"
gromacs-version: "2020.6"
- os: ubuntu-latest
python-version: "3.11"
gromacs-version: "2022.4"
- os: ubuntu-latest
python-version: "3.11"
gromacs-version: "2023.1"
env:
MPLBACKEND: agg
steps:
- uses: actions/checkout@v3
- name: micromamba environment and package installation (Python ${{ matrix.python-version }})
uses: mamba-org/setup-micromamba@v1
with:
environment-file: ci/conda-envs/test_env.yaml
condarc: |
channels:
- conda-forge
- bioconda
channel_priority: flexible
cache-downloads: true
cache-environment: true
create-args: >-
python=${{ matrix.python-version }}.*=*_cpython
- name: Python version information ${{ matrix.python-version }}
run: |
python -c "import sys; print(sys.version)"
- name: micromamba environment information
run: |
micromamba info
micromamba list
- name: Install pytest and plugins
run: |
micromamba install pytest pytest-pep8 pytest-cov codecov
- name: Install GROMACS (${{ matrix.gromacs-version }})
# UGLY HACK/FIX (probably to issues with bioconda packages)
# - For 3.9, micromamba insists on using pypy 3.9 (and --py-pin does not help).
# - For 2.7 macOS, numkit would get uninstalled.
# We can't freeze because then it's not possible to install older GROMACS versions from bioconda.
run: |
micromamba install 'gromacs==${{ matrix.gromacs-version }}' pocl numkit python=${{ matrix.python-version }}.*=*_cpython
- name: Install package (with no dependencies)
run: |
python -m pip install --no-deps .
- name: Run tests
run: |
pytest -v --disable-pytest-warnings --durations=20 --low-performance --cov=gromacs --cov-report=xml --color=yes ./tests
- name: Codecov
uses: codecov/codecov-action@v3
with:
token: ${{ secrets.CODECOV_TOKEN }}
name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
file: ./coverage.xml
fail_ci_if_error: false